[1] "ofn"        "-oTSTAD-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/STAD-TP/22507291/STAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/STAD-TP/22533932/transformed.cor.cli.txt"

nPatients in clinical file=443, in cluster file=441, common to both=441
[1]  88 441
[1] "AMP PEAK  1(1P36.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                            66                            375 
  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                            66                            375 
[1] "AMP PEAK  2(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          160                           281 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          160                           281 
[1] "AMP PEAK  3(1Q42.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                          150                           291 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                          150                           291 
[1] "AMP PEAK  4(3Q26.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                          164                           277 
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                          164                           277 
[1] "AMP PEAK  5(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                           130                            311 
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                           130                            311 
[1] "AMP PEAK  6(5P13.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE 
                          126                           315 
  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE 
                          126                           315 
[1] "AMP PEAK  7(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE 
                          124                           317 
  AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE 
                          124                           317 
[1] "AMP PEAK  8(6Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE 
                         88                         353 
  AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE 
                         88                         353 
[1] "AMP PEAK  9(6Q21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE 
                         82                         359 
  AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE 
                         82                         359 
[1] "AMP PEAK 10(7P22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                          229                           212 
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                          229                           212 
[1] "AMP PEAK 11(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                          214                           227 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                          214                           227 
[1] "AMP PEAK 12(7Q21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                          204                           237 
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                          204                           237 
[1] "AMP PEAK 13(7Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE 
                          202                           239 
  AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE 
                          202                           239 
[1] "AMP PEAK 14(8P23.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE 
                          177                           264 
  AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE 
                          177                           264 
[1] "AMP PEAK 15(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                           309                            132 
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                           309                            132 
[1] "AMP PEAK 16(9P24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE 
                           65                           376 
  AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE 
                           65                           376 
[1] "AMP PEAK 17(9P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE 
                           91                           350 
  AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE 
                           91                           350 
[1] "AMP PEAK 18(9Q34.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE 
                          122                           319 
  AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE 
                          122                           319 
[1] "AMP PEAK 19(10P11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE 
                            119                             322 
  AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE 
                            119                             322 
[1] "AMP PEAK 20(10Q22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE 
                            86                            355 
  AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE 
                            86                            355 
[1] "AMP PEAK 21(10Q26.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE 
                             88                             353 
  AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE 
                             88                             353 
[1] "AMP PEAK 22(11P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE 
                          88                          353 
  AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE 
                          88                          353 
[1] "AMP PEAK 23(11P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE 
                            92                            349 
  AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE 
                            92                            349 
[1] "AMP PEAK 24(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE 
                           115                            326 
  AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE 
                           115                            326 
[1] "AMP PEAK 25(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE 
                           128                            313 
  AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE 
                           128                            313 
[1] "AMP PEAK 26(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE 
                         109                          332 
  AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE 
                         109                          332 
[1] "AMP PEAK 27(13Q12.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE 
                           170                            271 
  AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE 
                           170                            271 
[1] "AMP PEAK 28(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE 
                           181                            260 
  AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE 
                           181                            260 
[1] "AMP PEAK 29(14Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(14Q21.3) MUTATED AMP PEAK 29(14Q21.3) WILD-TYPE 
                            54                            387 
  AMP PEAK 29(14Q21.3) MUTATED AMP PEAK 29(14Q21.3) WILD-TYPE 
                            54                            387 
[1] "AMP PEAK 30(15Q26.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 30(15Q26.1) MUTATED AMP PEAK 30(15Q26.1) WILD-TYPE 
                           113                            328 
  AMP PEAK 30(15Q26.1) MUTATED AMP PEAK 30(15Q26.1) WILD-TYPE 
                           113                            328 
[1] "AMP PEAK 31(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 31(17Q12) MUTATED AMP PEAK 31(17Q12) WILD-TYPE 
                         147                          294 
  AMP PEAK 31(17Q12) MUTATED AMP PEAK 31(17Q12) WILD-TYPE 
                         147                          294 
[1] "AMP PEAK 32(18Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 32(18Q11.2) MUTATED AMP PEAK 32(18Q11.2) WILD-TYPE 
                           140                            301 
  AMP PEAK 32(18Q11.2) MUTATED AMP PEAK 32(18Q11.2) WILD-TYPE 
                           140                            301 
[1] "AMP PEAK 33(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE 
                         130                          311 
  AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE 
                         130                          311 
[1] "AMP PEAK 34(19Q13.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE 
                            111                             330 
  AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE 
                            111                             330 
[1] "AMP PEAK 35(20Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE 
                           293                            148 
  AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE 
                           293                            148 
[1] "AMP PEAK 36(XQ27.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE 
                           83                           358 
  AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE 
                           83                           358 
[1] "DEL PEAK  1(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           135                            306 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           135                            306 
[1] "DEL PEAK  2(1P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           93                           348 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           93                           348 
[1] "DEL PEAK  3(1Q44) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         25                         416 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         25                         416 
[1] "DEL PEAK  4(2Q32.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q32.1) MUTATED DEL PEAK  4(2Q32.1) WILD-TYPE 
                           64                           377 
  DEL PEAK  4(2Q32.1) MUTATED DEL PEAK  4(2Q32.1) WILD-TYPE 
                           64                           377 
[1] "DEL PEAK  5(2Q33.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                           49                           392 
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                           49                           392 
[1] "DEL PEAK  6(2Q37.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE 
                           72                           369 
  DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE 
                           72                           369 
[1] "DEL PEAK  7(3P26.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE 
                          143                           298 
  DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE 
                          143                           298 
[1] "DEL PEAK  8(3P21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3P21.1) MUTATED DEL PEAK  8(3P21.1) WILD-TYPE 
                          153                           288 
  DEL PEAK  8(3P21.1) MUTATED DEL PEAK  8(3P21.1) WILD-TYPE 
                          153                           288 
[1] "DEL PEAK  9(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                          157                           284 
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                          157                           284 
[1] "DEL PEAK 10(3Q26.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                            49                            392 
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                            49                            392 
[1] "DEL PEAK 11(4P16.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE 
                          169                           272 
  DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE 
                          169                           272 
[1] "DEL PEAK 12(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                          193                           248 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                          193                           248 
[1] "DEL PEAK 13(4Q35.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(4Q35.1) MUTATED DEL PEAK 13(4Q35.1) WILD-TYPE 
                          204                           237 
  DEL PEAK 13(4Q35.1) MUTATED DEL PEAK 13(4Q35.1) WILD-TYPE 
                          204                           237 
[1] "DEL PEAK 14(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                          170                           271 
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                          170                           271 
[1] "DEL PEAK 15(5Q23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE 
                          158                           283 
  DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE 
                          158                           283 
[1] "DEL PEAK 16(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                          115                           326 
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                          115                           326 
[1] "DEL PEAK 17(6Q14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE 
                           89                           352 
  DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE 
                           89                           352 
[1] "DEL PEAK 18(6Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE 
                           78                           363 
  DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE 
                           78                           363 
[1] "DEL PEAK 19(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                        102                         339 
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                        102                         339 
[1] "DEL PEAK 20(7Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                           71                           370 
  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                           71                           370 
[1] "DEL PEAK 21(7Q36.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                           98                           343 
  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                           98                           343 
[1] "DEL PEAK 22(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                          122                           319 
  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                          122                           319 
[1] "DEL PEAK 23(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                        195                         246 
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                        195                         246 
[1] "DEL PEAK 24(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                          193                           248 
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                          193                           248 
[1] "DEL PEAK 25(9Q21.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                           113                            328 
  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                           113                            328 
[1] "DEL PEAK 26(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE 
                            77                            364 
  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE 
                            77                            364 
[1] "DEL PEAK 27(10Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE 
                            79                            362 
  DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE 
                            79                            362 
[1] "DEL PEAK 28(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                            116                             325 
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                            116                             325 
[1] "DEL PEAK 29(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                            97                            344 
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                            97                            344 
[1] "DEL PEAK 30(11Q23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE 
                            99                            342 
  DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE 
                            99                            342 
[1] "DEL PEAK 31(12P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE 
                            77                            364 
  DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE 
                            77                            364 
[1] "DEL PEAK 32(12Q12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE 
                          59                          382 
  DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE 
                          59                          382 
[1] "DEL PEAK 33(13Q12.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                             63                             378 
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                             63                             378 
[1] "DEL PEAK 34(14Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                           136                            305 
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                           136                            305 
[1] "DEL PEAK 35(14Q32.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                            133                             308 
  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                            133                             308 
[1] "DEL PEAK 36(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                           120                            321 
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                           120                            321 
[1] "DEL PEAK 37(15Q15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE 
                           122                            319 
  DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE 
                           122                            319 
[1] "DEL PEAK 38(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                            98                            343 
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                            98                            343 
[1] "DEL PEAK 39(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                           182                            259 
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                           182                            259 
[1] "DEL PEAK 40(17P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(17P12) MUTATED DEL PEAK 40(17P12) WILD-TYPE 
                         181                          260 
  DEL PEAK 40(17P12) MUTATED DEL PEAK 40(17P12) WILD-TYPE 
                         181                          260 
[1] "DEL PEAK 41(17Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(17Q24.3) MUTATED DEL PEAK 41(17Q24.3) WILD-TYPE 
                            76                            365 
  DEL PEAK 41(17Q24.3) MUTATED DEL PEAK 41(17Q24.3) WILD-TYPE 
                            76                            365 
[1] "DEL PEAK 42(18Q12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(18Q12.2) MUTATED DEL PEAK 42(18Q12.2) WILD-TYPE 
                           181                            260 
  DEL PEAK 42(18Q12.2) MUTATED DEL PEAK 42(18Q12.2) WILD-TYPE 
                           181                            260 
[1] "DEL PEAK 43(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(18Q21.2) MUTATED DEL PEAK 43(18Q21.2) WILD-TYPE 
                           204                            237 
  DEL PEAK 43(18Q21.2) MUTATED DEL PEAK 43(18Q21.2) WILD-TYPE 
                           204                            237 
[1] "DEL PEAK 44(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                           162                            279 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                           162                            279 
[1] "DEL PEAK 45(19Q13.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(19Q13.11) MUTATED DEL PEAK 45(19Q13.11) WILD-TYPE 
                             75                             366 
  DEL PEAK 45(19Q13.11) MUTATED DEL PEAK 45(19Q13.11) WILD-TYPE 
                             75                             366 
[1] "DEL PEAK 46(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE 
                            39                            402 
  DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE 
                            39                            402 
[1] "DEL PEAK 47(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE 
                           182                            259 
  DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE 
                           182                            259 
[1] "DEL PEAK 48(21Q22.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 48(21Q22.13) MUTATED DEL PEAK 48(21Q22.13) WILD-TYPE 
                            196                             245 
  DEL PEAK 48(21Q22.13) MUTATED DEL PEAK 48(21Q22.13) WILD-TYPE 
                            196                             245 
[1] "DEL PEAK 49(22Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 49(22Q13.31) MUTATED DEL PEAK 49(22Q13.31) WILD-TYPE 
                            161                             280 
  DEL PEAK 49(22Q13.31) MUTATED DEL PEAK 49(22Q13.31) WILD-TYPE 
                            161                             280 
[1] "DEL PEAK 50(XP22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                           85                           356 
  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                           85                           356 
[1] "DEL PEAK 51(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                           76                           365 
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                           76                           365 
[1] "DEL PEAK 52(XQ21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 52(XQ21.33) MUTATED DEL PEAK 52(XQ21.33) WILD-TYPE 
                            57                            384 
  DEL PEAK 52(XQ21.33) MUTATED DEL PEAK 52(XQ21.33) WILD-TYPE 
                            57                            384 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "HISTOLOGICAL_TYPE"                   
[14] "RESIDUAL_TUMOR"                      
[15] "NUMBER_OF_LYMPH_NODES"               
[16] "RACE"                                
[17] "ETHNICITY"                           

Input Data has 17 rows and 441 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=54,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=152,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=225,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=33,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 441 columns, 1 survival variables, and 12 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"        "PATHOLOGIC_STAGE"      "PATHOLOGY_T_STAGE"    
 [4] "PATHOLOGY_N_STAGE"     "PATHOLOGY_M_STAGE"     "GENDER"               
 [7] "RADIATION_THERAPY"     "HISTOLOGICAL_TYPE"     "RESIDUAL_TUMOR"       
[10] "NUMBER_OF_LYMPH_NODES" "RACE"                  "ETHNICITY"            
YEARS_TO_BIRTH, nv=54, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=11, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
 23  93 196 119 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 23  93 196 119 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
 23  93 196 119 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 23  93 196 119 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
130 119  86  88 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
130 119  86  88 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
130 119  86  88 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
130 119  86  88 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=7, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=33, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1P36.22) MUTATION ANALYSIS
D1V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  1(1P36.22) MUTATED    37  24
  AMP PEAK  1(1P36.22) WILD-TYPE 209 145
  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                            61                            354 
  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                            24                            145 
$`AMP PEAK  1(1P36.22) MUTATED`
TCGA-CG-4444 TCGA-CG-4475 TCGA-3M-AB46 TCGA-BR-4183 TCGA-BR-7197 TCGA-BR-7901 
       47.05        22.98        58.03         6.61         9.21         3.45 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8484 TCGA-BR-8588 TCGA-BR-A4CQ TCGA-BR-A4J1 
       29.42         2.66        25.18        12.79        34.98         0.72 
TCGA-BR-A4J8 TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4443 
       13.51        13.02        13.35        12.43        12.20        29.98 
TCGA-CG-4449 TCGA-CG-5718 TCGA-CG-5732 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6528 
       19.07        36.00        69.04        18.54        10.26        15.22 
TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-FP-7829 TCGA-HF-A5NB TCGA-HJ-7597 
       16.44        11.24        22.29        19.53        30.51        26.47 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       11.77         8.98         6.58        33.40        36.36         3.45 
TCGA-IN-A6RI TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IP-7968 TCGA-MX-A666 
       18.38         6.44         6.74        11.70         2.53        14.04 
TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-VQ-A8DU 
        9.24         8.61        16.67        37.91       115.69         5.46 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PX 
       18.48        43.36        22.19        17.85         1.87        64.57 
TCGA-VQ-A91U TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA6A 
        1.71         4.54        66.81        42.54        18.41        38.93 
TCGA-VQ-AA6D 
       17.13 

$`AMP PEAK  1(1P36.22) WILD-TYPE`
TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       21.99        79.07        16.24         0.23        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       27.35        26.93        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 
       30.90        31.20        44.94        21.90        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       19.96         2.20        15.58         7.40         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 
        7.36        25.05         3.72         5.39         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        1.48        27.55        28.57        12.89         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 
       13.15        13.18        11.21        12.10        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.30        11.31        11.61         6.58        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4462 
        8.05        54.08         4.01        14.01        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        12.00        30.97         6.97 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 
       15.02        28.96        65.10         4.01        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 
       18.61        17.85        13.35        17.19        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX 
        5.92        36.43        13.78        14.76        26.43        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.44        20.32        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       11.38         3.48        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       63.06        52.21         1.51         5.92        24.39        18.15 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       25.81        21.37        29.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ 
       21.17        14.07        15.68        18.81         3.39        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V 
       13.35        19.53        12.59         6.51        10.62        15.75 
TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         5.56        63.62        37.64        36.95         3.72 
TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       19.73        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 
        4.60        11.05         5.13       122.30        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
       71.38        57.44         8.94        35.61        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E3 
        5.79         0.92        48.79        13.25        13.02        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PO 
       46.26        16.31         2.50        12.79         2.70         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       23.41        15.65        13.35        29.59        14.33        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       39.45        11.70        21.83        61.22        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       32.88        42.64        60.85         9.50         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O 
        9.04         2.01        55.43         6.58         5.72        21.04 
TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F 
        2.66        11.24        43.66        28.41        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        27.55        12.43        17.26         0.79 

  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                          0.72                           0.00 
  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                        115.69                         122.30 
  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                        16.670                         14.565 
[1] "0.7 - 115.7 (16.7)" "0.0 - 122.3 (14.6)"
[1] "hr=" "1.1"
D1V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  1(1P36.22) MUTATED         1        4        6        7         4
  AMP PEAK  1(1P36.22) WILD-TYPE       1       12       35       25        36
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  1(1P36.22) MUTATED           7         0         12         11
  AMP PEAK  1(1P36.22) WILD-TYPE        49         3         69         52
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK  1(1P36.22) MUTATED            5        4
  AMP PEAK  1(1P36.22) WILD-TYPE         34       40
D1V3, multiclass
            clus
vv           AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                              4                             12
  STAGE IB                              6                             35
  STAGE II                              7                             25
  STAGE IIA                             4                             36
  STAGE IIB                             7                             49
  STAGE III                             0                              3
  STAGE IIIA                           12                             69
  STAGE IIIB                           11                             52
  STAGE IIIC                            5                             34
  STAGE IV                              4                             40
[1] 11  2
[1] TRUE
[1] "dimension of 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(1P36.22) MUTATED     6  16  31  12
  AMP PEAK  1(1P36.22) WILD-TYPE  17  77 165 107
D1V4, multiclass
    clus
vv   AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  T1                            6                             17
  T2                           16                             77
  T3                           31                            165
  T4                           12                            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"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK  1(1P36.22) MUTATED    17  18  14  15
  AMP PEAK  1(1P36.22) WILD-TYPE 113 101  72  73
D1V5, multiclass
    clus
vv   AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  N0                           17                            113
  N1                           18                            101
  N2                           14                             72
  N3                           15                             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.22) MUTATED    59   2
  AMP PEAK  1(1P36.22) WILD-TYPE 330  28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.22) MUTATED     59    2
  AMP PEAK  1(1P36.22) WILD-TYPE  330   28
   clus
vv  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  0                           59                            330
  1                            2                             28
[1] 2 2
[1] FALSE
D1V7, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.22) MUTATED    13  53
  AMP PEAK  1(1P36.22) WILD-TYPE 145 230
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.22) MUTATED     13   53
  AMP PEAK  1(1P36.22) WILD-TYPE  145  230
        clus
vv       AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  FEMALE                           13                            145
  MALE                             53                            230
[1] 2 2
[1] FALSE
D1V8, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.22) MUTATED    41  18
  AMP PEAK  1(1P36.22) WILD-TYPE 281  58
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.22) MUTATED     41   18
  AMP PEAK  1(1P36.22) WILD-TYPE  281   58
     clus
vv    AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  NO                            41                            281
  YES                           18                             58
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK  1(1P36.22) MUTATED                                          2
  AMP PEAK  1(1P36.22) WILD-TYPE                                       11
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK  1(1P36.22) MUTATED                                       9
  AMP PEAK  1(1P36.22) WILD-TYPE                                    63
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  1(1P36.22) MUTATED                                                       24
  AMP PEAK  1(1P36.22) WILD-TYPE                                                    139
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK  1(1P36.22) MUTATED                                                   3
  AMP PEAK  1(1P36.22) WILD-TYPE                                                18
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  1(1P36.22) MUTATED                                                                  16
  AMP PEAK  1(1P36.22) WILD-TYPE                                                                66
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK  1(1P36.22) MUTATED                                                    1
  AMP PEAK  1(1P36.22) WILD-TYPE                                                  7
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK  1(1P36.22) MUTATED                                                 10
  AMP PEAK  1(1P36.22) WILD-TYPE                                               69
D1V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK  1(1P36.22) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        9
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      24
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           16
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            10
                                                                   clus
vv                                                                  AMP PEAK  1(1P36.22) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         63
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       139
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              69
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  1(1P36.22) MUTATED    51   2   2   3
  AMP PEAK  1(1P36.22) WILD-TYPE 298  16  17  22
D1V10, multiclass
    clus
vv   AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  R0                           51                            298
  R1                            2                             16
  R2                            2                             17
  RX                            3                             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"
D1V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  1(1P36.22) MUTATED      12                         1
  AMP PEAK  1(1P36.22) WILD-TYPE    76                        11
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK  1(1P36.22) MUTATED                                           1
  AMP PEAK  1(1P36.22) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK  1(1P36.22) MUTATED      42
  AMP PEAK  1(1P36.22) WILD-TYPE   236
D1V12, multiclass
                                           clus
vv                                          AMP PEAK  1(1P36.22) MUTATED
  ASIAN                                                               12
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               42
                                           clus
vv                                          AMP PEAK  1(1P36.22) WILD-TYPE
  ASIAN                                                                 76
  BLACK OR AFRICAN AMERICAN                                             11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V13, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.22) MUTATED     1  43
  AMP PEAK  1(1P36.22) WILD-TYPE   4 273
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.22) MUTATED      1   43
  AMP PEAK  1(1P36.22) WILD-TYPE    4  273
                        clus
vv                       AMP PEAK  1(1P36.22) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           43
                        clus
vv                       AMP PEAK  1(1P36.22) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            273
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(1Q21.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  2(1Q21.3) MUTATED    90  58
  AMP PEAK  2(1Q21.3) WILD-TYPE 156 111
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          148                           267 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           58                           111 
$`AMP PEAK  2(1Q21.3) MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-VQ-A94U TCGA-3M-AB46 
       47.05        21.99        22.98        16.24        26.93        58.03 
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-6456 
       11.01         9.44         6.61         4.08         9.67        17.29 
TCGA-BR-6458 TCGA-BR-6705 TCGA-BR-7197 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 
       19.33        25.61         9.21        18.15        28.73         3.45 
TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8369 
       11.44        29.42         2.66         2.20         6.18        14.04 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       14.79         7.36         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8680 TCGA-BR-8687 TCGA-BR-A4J1 TCGA-BR-A4J5 
        1.12        12.79        31.96         8.22         0.72        28.34 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5800 
       13.51        20.65        20.42         1.15        21.44        13.15 
TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.10        12.76        12.53        12.33        12.30        12.39 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C 
       15.39        12.82         6.31        12.30        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4466 TCGA-CG-4469 
        6.58        12.20         7.99        54.08        18.97         7.07 
TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5730 TCGA-D7-5579 TCGA-D7-6519 
       12.00        36.00        12.03         4.01        20.91        20.55 
TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 
       18.54        17.19        10.26        15.22        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-A4YT TCGA-D7-A4YU 
       11.31        12.33        24.72        19.50        14.27        16.44 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 
       11.24        11.31        22.29        15.65         0.62         7.99 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       72.23         3.48        14.07        13.58         0.56         5.52 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        30.51        26.47         5.92        24.39 
TCGA-HU-8245 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
       18.15         3.25        22.75        25.81        11.77         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 
        6.51         6.58        12.95        23.80        33.40         3.45 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU TCGA-KB-A6F7 
       18.38        13.35         6.44         6.74        11.70        63.62 
TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV 
       14.04        18.21         6.08         8.61        16.67       122.30 
TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
      115.69         8.94        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PX 
       18.48        43.36        21.73         2.70        17.85        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U 
       14.33        73.41        39.45        18.74        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A91Y TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-A94T 
       42.64         9.73         4.54        66.81        42.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6K 
       18.41        43.66        38.93        12.43 

$`AMP PEAK  2(1Q21.3) WILD-TYPE`
TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-B7-5816 
       79.07         0.23        20.15         9.86        27.35        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       11.70        19.56         9.47         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       18.35        30.90         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        6.61        34.68        15.95        13.87        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        32.78        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 
       36.16        35.24        35.84        33.63        39.78        15.32 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        29.56        33.21        37.25        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 
       29.59         9.60        32.25         8.05         0.56        19.96 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33         4.31         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       31.27        25.05         3.72        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
       20.88        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QL 
       14.17         0.53         0.66        32.52         0.46        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        5.13        13.41        13.02        13.18        13.35        11.21 
TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8536 
       12.59         7.17        12.59        11.64        12.07        12.43 
TCGA-CD-A489 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       11.31        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       15.95         1.02         8.05         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 
       19.07        12.03         0.00         9.01        30.97         6.97 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 
        1.02         0.99         6.02         0.99       105.07        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       12.66        19.13        18.84        18.61        17.85        13.35 
TCGA-D7-6815 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       15.98        16.80        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       20.91         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.44        20.32         8.38         4.34        19.96         7.13 
TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 
       14.47        21.27        11.38        19.53        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HU-8238 TCGA-HU-8249 
       59.54         5.03         6.21        77.29         1.51        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
       24.26        22.68        24.20        21.37        29.98         0.10 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
       20.25         0.26         2.10        29.00        23.84        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ 
       14.07        15.68        36.36        18.81         3.39        12.46 
TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X 
       19.53        12.59         6.51        10.62        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        37.64        36.95         3.72        19.73 
TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       45.67         8.52        74.53         4.60         9.24        11.05 
TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
        5.13        37.91        40.64       116.38        71.38        57.44 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8E7 
       35.61        16.87        19.04         5.79         0.92        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       38.14        37.22         7.73        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO 
       16.31        22.19         2.50        12.79         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A91D TCGA-VQ-A91E 
       23.41        15.65        13.35        29.59        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 
       61.22        32.88        60.85         9.50        55.56         9.04 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P 
        2.01        55.43         6.58         5.72        21.04         2.66 
TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        32.94        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       27.55        17.26         0.79 

  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                         0.56                          0.00 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                       122.30                        116.38 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                        13.43                         15.95 
[1] "0.6 - 122.3 (13.4)" "0.0 - 116.4 (15.9)"
[1] "hr=" "1"  
D2V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  2(1Q21.3) MUTATED         1        7       17        9        15
  AMP PEAK  2(1Q21.3) WILD-TYPE       1        9       24       23        25
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  2(1Q21.3) MUTATED          20         1         30         20
  AMP PEAK  2(1Q21.3) WILD-TYPE        36         2         51         43
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK  2(1Q21.3) MUTATED           11       17
  AMP PEAK  2(1Q21.3) WILD-TYPE         28       27
D2V3, multiclass
            clus
vv           AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             7                             9
  STAGE IB                            17                            24
  STAGE II                             9                            23
  STAGE IIA                           15                            25
  STAGE IIB                           20                            36
  STAGE III                            1                             2
  STAGE IIIA                          30                            51
  STAGE IIIB                          20                            43
  STAGE IIIC                          11                            28
  STAGE IV                            17                            27
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  2(1Q21.3) MUTATED    10  36  75  36
  AMP PEAK  2(1Q21.3) WILD-TYPE  13  57 121  83
D2V4, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  T1                          10                            13
  T2                          36                            57
  T3                          75                           121
  T4                          36                            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"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  2(1Q21.3) MUTATED   50 35 30 34
  AMP PEAK  2(1Q21.3) WILD-TYPE 80 84 56 54
D2V5, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  N0                          50                            80
  N1                          35                            84
  N2                          30                            56
  N3                          34                            54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED   139  10
  AMP PEAK  2(1Q21.3) WILD-TYPE 250  20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED    139   10
  AMP PEAK  2(1Q21.3) WILD-TYPE  250   20
   clus
vv  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  0                         139                           250
  1                          10                            20
[1] 2 2
[1] FALSE
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED    57 103
  AMP PEAK  2(1Q21.3) WILD-TYPE 101 180
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     57  103
  AMP PEAK  2(1Q21.3) WILD-TYPE  101  180
        clus
vv       AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  FEMALE                          57                           101
  MALE                           103                           180
[1] 2 2
[1] FALSE
D2V8, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED   111  37
  AMP PEAK  2(1Q21.3) WILD-TYPE 211  39
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED    111   37
  AMP PEAK  2(1Q21.3) WILD-TYPE  211   39
     clus
vv    AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  NO                          111                           211
  YES                          37                            39
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK  2(1Q21.3) MUTATED                                          6
  AMP PEAK  2(1Q21.3) WILD-TYPE                                        7
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK  2(1Q21.3) MUTATED                                      16
  AMP PEAK  2(1Q21.3) WILD-TYPE                                    56
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  2(1Q21.3) MUTATED                                                       59
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                    104
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK  2(1Q21.3) MUTATED                                                   6
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                15
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  2(1Q21.3) MUTATED                                                                  32
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                                50
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK  2(1Q21.3) MUTATED                                                    4
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                  4
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK  2(1Q21.3) MUTATED                                                 34
  AMP PEAK  2(1Q21.3) WILD-TYPE                                               45
D2V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK  2(1Q21.3) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    6
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                      16
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     59
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           6
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          32
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           34
                                                                   clus
vv                                                                  AMP PEAK  2(1Q21.3) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        56
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      104
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            15
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            50
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             45
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  2(1Q21.3) MUTATED   118  10   9   9
  AMP PEAK  2(1Q21.3) WILD-TYPE 231   8  10  16
D2V10, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  R0                         118                           231
  R1                          10                             8
  R2                           9                            10
  RX                           9                            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"
D2V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  2(1Q21.3) MUTATED      35                         5
  AMP PEAK  2(1Q21.3) WILD-TYPE    53                         7
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  2(1Q21.3) MUTATED                                           1    95
  AMP PEAK  2(1Q21.3) WILD-TYPE                                         0   183
D2V12, multiclass
                                           clus
vv                                          AMP PEAK  2(1Q21.3) MUTATED
  ASIAN                                                              35
  BLACK OR AFRICAN AMERICAN                                           5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              95
                                           clus
vv                                          AMP PEAK  2(1Q21.3) WILD-TYPE
  ASIAN                                                                53
  BLACK OR AFRICAN AMERICAN                                             7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               183
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V13, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED     1 115
  AMP PEAK  2(1Q21.3) WILD-TYPE   4 201
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED      1  115
  AMP PEAK  2(1Q21.3) WILD-TYPE    4  201
                        clus
vv                       AMP PEAK  2(1Q21.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         115
                        clus
vv                       AMP PEAK  2(1Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           201
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(1Q42.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  3(1Q42.3) MUTATED    84  57
  AMP PEAK  3(1Q42.3) WILD-TYPE 162 112
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                          141                           274 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                           57                           112 
$`AMP PEAK  3(1Q42.3) MUTATED`
TCGA-CG-4460 TCGA-EQ-A4SO TCGA-3M-AB46 TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4255 
       21.99        16.24        58.03        11.01         6.61         4.08 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-7197 
        9.67         6.18        19.33         9.17        25.61         9.21 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-8059 TCGA-BR-8060 
       33.63        39.78        18.15        28.73        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8297 
        0.69         9.60        29.42         2.66         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8369 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8484 
        6.18        31.10        14.04         7.36         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8680 TCGA-BR-8687 
        9.21        20.22         1.12        12.79        31.96         8.22 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4J9 
        7.53        34.98         0.72        28.34        13.51         0.46 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-CD-5800 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 
       20.42         1.15        13.15        12.10        12.76        12.59 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48C 
       12.33        12.39        15.39         6.31        12.30        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-4466 
        6.58        12.20         7.99        54.08        19.07        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5719 TCGA-CG-5730 TCGA-D7-5578 TCGA-D7-5579 
        7.07        12.00         1.02         4.01        12.66        20.91 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 
       18.84        18.54        17.19        10.26        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-A4YU TCGA-D7-A6EX 
       11.31        12.33        24.72        19.50        16.44        11.31 
TCGA-D7-A6F0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 
       22.29         0.62         7.99        72.23         3.48        14.07 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 
        0.56         5.52        52.21        30.51        26.47         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.39        18.15        28.96         0.76         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4H2 TCGA-HU-A4HD 
       25.81        11.77         0.10         6.51        12.95        33.40 
TCGA-IN-7808 TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-AB1V TCGA-KB-A6F7 
        3.45        13.35        19.53         6.44        15.75        63.62 
TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-VQ-A8DT 
       18.21         6.08       122.30       115.69        35.61        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P5 
        5.46        13.25        13.02        18.48        43.36         7.73 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       12.79         2.70        17.85        14.33        73.41        39.45 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       18.74        20.81        32.88         9.73        55.56         9.04 
TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
        4.54        66.81        21.04        42.54        11.24        18.41 
TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6K 
       38.93        17.13        12.43 

$`AMP PEAK  3(1Q42.3) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       47.05        22.98        79.07         0.23        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
       27.35        26.93        26.70        11.70        19.56         9.47 
TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        4.08         9.34         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       13.87        17.29        13.68        39.12        26.10        32.78 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        44.94        21.90        36.16        35.24        35.84 
TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       15.32         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8296 
       29.59        32.25         8.05         0.56        19.96        15.58 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 
        4.31         3.32        11.80        31.27        14.79        25.05 
TCGA-BR-8384 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        3.72        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 
       26.73        24.79        32.58         9.86        20.88        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       34.13        13.87         6.08         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
       12.89         8.98        14.17         0.53         0.66        32.52 
TCGA-BR-A4PD TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.65        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 
       13.18        13.35        11.21        12.53         7.17        12.30 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A489 
       12.59        11.64        12.07        12.82        12.43        11.31 
TCGA-CD-A48A TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.43        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       15.95         1.02         8.05         4.01        14.01        29.98 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       12.03         0.00         9.01        30.97         6.97        36.00 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10        69.04        21.07         7.99        25.71 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 
       19.13        20.55        18.61        17.85        13.35        15.22 
TCGA-D7-6815 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       15.98        16.80        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 
       26.43        11.24        11.44        20.32        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        4.34        19.96         7.13        14.47        21.27        11.38 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       19.53        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HU-8238 TCGA-HU-8602 TCGA-HU-8604 
        6.21        77.29        63.06         1.51        22.32        22.82 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       21.07        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       21.37        29.98         8.98         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       15.68        36.36        18.81         3.39        18.38        12.46 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X 
        6.74        12.59         6.51        10.62        11.70        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        37.64        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 
       14.04        45.67         8.52        74.53         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         8.61         5.13        16.67        37.91        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        5.79         0.92        21.73        37.41        38.14        37.22 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       30.97        34.29        46.26        16.31        22.19         2.50 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PX TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91V 
       64.57        11.70        21.83        61.22         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
       60.85         9.50         2.01        55.43         6.58         5.72 
TCGA-VQ-A94P TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
        2.66        43.66        28.41        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        27.55        17.26         0.79 

  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                          0.1                           0.0 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                       122.30                        116.38 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                        13.02                         15.95 
[1] "0.1 - 122.3 (13.0)" "0.0 - 116.4 (15.9)"
[1] "hr=" "1.1"
D3V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  3(1Q42.3) MUTATED         0        8       14       10        14
  AMP PEAK  3(1Q42.3) WILD-TYPE       2        8       27       22        26
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  3(1Q42.3) MUTATED          13         2         28         22
  AMP PEAK  3(1Q42.3) WILD-TYPE        43         1         53         41
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK  3(1Q42.3) MUTATED           14       15
  AMP PEAK  3(1Q42.3) WILD-TYPE         25       29
D3V3, multiclass
            clus
vv           AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             8                             8
  STAGE IB                            14                            27
  STAGE II                            10                            22
  STAGE IIA                           14                            26
  STAGE IIB                           13                            43
  STAGE III                            2                             1
  STAGE IIIA                          28                            53
  STAGE IIIB                          22                            41
  STAGE IIIC                          14                            25
  STAGE IV                            15                            29
[1] 11  2
[1] TRUE
[1] "dimension of 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(1Q42.3) MUTATED    10  27  67  43
  AMP PEAK  3(1Q42.3) WILD-TYPE  13  66 129  76
D3V4, multiclass
    clus
vv   AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  T1                          10                            13
  T2                          27                            66
  T3                          67                           129
  T4                          43                            76
[1] 4 2
[1] TRUE
[1] "dimension of 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(1Q42.3) MUTATED   46 33 32 31
  AMP PEAK  3(1Q42.3) WILD-TYPE 84 86 54 57
D3V5, multiclass
    clus
vv   AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  N0                          46                            84
  N1                          33                            86
  N2                          32                            54
  N3                          31                            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"
D3V6, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q42.3) MUTATED   132   9
  AMP PEAK  3(1Q42.3) WILD-TYPE 257  21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED    132    9
  AMP PEAK  3(1Q42.3) WILD-TYPE  257   21
   clus
vv  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  0                         132                           257
  1                           9                            21
[1] 2 2
[1] FALSE
D3V7, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q42.3) MUTATED    52  98
  AMP PEAK  3(1Q42.3) WILD-TYPE 106 185
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED     52   98
  AMP PEAK  3(1Q42.3) WILD-TYPE  106  185
        clus
vv       AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  FEMALE                          52                           106
  MALE                            98                           185
[1] 2 2
[1] FALSE
D3V8, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q42.3) MUTATED   104  33
  AMP PEAK  3(1Q42.3) WILD-TYPE 218  43
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED    104   33
  AMP PEAK  3(1Q42.3) WILD-TYPE  218   43
     clus
vv    AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  NO                          104                           218
  YES                          33                            43
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK  3(1Q42.3) MUTATED                                          5
  AMP PEAK  3(1Q42.3) WILD-TYPE                                        8
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK  3(1Q42.3) MUTATED                                      12
  AMP PEAK  3(1Q42.3) WILD-TYPE                                    60
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  3(1Q42.3) MUTATED                                                       52
  AMP PEAK  3(1Q42.3) WILD-TYPE                                                    111
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK  3(1Q42.3) MUTATED                                                   7
  AMP PEAK  3(1Q42.3) WILD-TYPE                                                14
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  3(1Q42.3) MUTATED                                                                  29
  AMP PEAK  3(1Q42.3) WILD-TYPE                                                                53
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK  3(1Q42.3) MUTATED                                                    3
  AMP PEAK  3(1Q42.3) WILD-TYPE                                                  5
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK  3(1Q42.3) MUTATED                                                 40
  AMP PEAK  3(1Q42.3) WILD-TYPE                                               39
D3V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK  3(1Q42.3) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                      12
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     52
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           7
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          29
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           40
                                                                   clus
vv                                                                  AMP PEAK  3(1Q42.3) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        60
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      111
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            14
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            53
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             39
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  3(1Q42.3) MUTATED   115   8   7   9
  AMP PEAK  3(1Q42.3) WILD-TYPE 234  10  12  16
D3V10, multiclass
    clus
vv   AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  R0                         115                           234
  R1                           8                            10
  R2                           7                            12
  RX                           9                            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"
D3V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  3(1Q42.3) MUTATED      33                         7
  AMP PEAK  3(1Q42.3) WILD-TYPE    55                         5
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  3(1Q42.3) MUTATED                                           0    90
  AMP PEAK  3(1Q42.3) WILD-TYPE                                         1   188
D3V12, multiclass
                                           clus
vv                                          AMP PEAK  3(1Q42.3) MUTATED
  ASIAN                                                              33
  BLACK OR AFRICAN AMERICAN                                           7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              90
                                           clus
vv                                          AMP PEAK  3(1Q42.3) WILD-TYPE
  ASIAN                                                                55
  BLACK OR AFRICAN AMERICAN                                             5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               188
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V13, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q42.3) MUTATED     1 108
  AMP PEAK  3(1Q42.3) WILD-TYPE   4 208
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED      1  108
  AMP PEAK  3(1Q42.3) WILD-TYPE    4  208
                        clus
vv                       AMP PEAK  3(1Q42.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         108
                        clus
vv                       AMP PEAK  3(1Q42.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           208
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(3Q26.2) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(3Q26.2) MUTATED    91  64
  AMP PEAK  4(3Q26.2) WILD-TYPE 155 105
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                          155                           260 
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                           64                           105 
$`AMP PEAK  4(3Q26.2) MUTATED`
TCGA-CG-4444 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-VQ-A8PU TCGA-3M-AB46 TCGA-B7-5816 
       47.05        16.24         0.23        27.35        58.03        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4191 
       11.70        19.56        11.01         9.44         6.61        18.35 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-6456 TCGA-BR-6565 
        4.08         9.67         6.18        34.68        17.29         9.17 
TCGA-BR-6706 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-7196 TCGA-BR-7722 TCGA-BR-7723 
       18.05        40.21        30.90        21.90        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8284 TCGA-BR-8289 
        3.45        29.56        14.43        11.44         8.05         2.66 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8361 TCGA-BR-8367 TCGA-BR-8373 TCGA-BR-8484 
        2.20        15.58        31.10        26.33        14.79        25.18 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8676 TCGA-BR-8687 TCGA-BR-A4CQ 
       12.79        27.12         9.34         7.53         8.22        34.98 
TCGA-BR-A4IU TCGA-BR-A4J4 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI 
       27.55         0.53        32.52        20.65        20.42        21.44 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 
       13.02        13.18        13.35        11.21        12.10        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-A487 
       12.53         7.17        12.33        12.39        15.39        12.30 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4436 
       12.43        11.61        12.20         3.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5719 
        8.05        12.03         0.00        12.00        30.97         1.02 
TCGA-CG-5724 TCGA-CG-5725 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-8570 
       12.03        15.02        18.54        10.26        15.98        24.72 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F0 
       20.91        16.44        14.76        11.24        20.32        22.29 
TCGA-EQ-5647 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8211 
        0.62        21.27         3.48        14.07        22.29        13.58 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.56        26.47         5.92        24.26        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H2 
       22.75        25.81        11.77         8.98         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RL TCGA-IN-A6RN 
       29.00        23.84        21.17        33.40        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-KB-A6F7 TCGA-R5-A7O7 
        6.44        10.62        11.70        15.75        63.62        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-VQ-A8DL 
       18.21         6.08        16.67       115.69        35.61         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       48.79         5.46        13.02        18.48        43.36        21.73 
TCGA-VQ-A8P5 TCGA-VQ-A8PD TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PP 
        7.73        16.31        12.79         2.70        17.85        23.41 
TCGA-VQ-A8PS TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A91S 
       13.35        64.57        73.41        21.83        20.81        32.88 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A928 
        9.73        55.56         9.04         2.01         4.54         5.72 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A 
       66.81        21.04        42.54        18.41        43.66        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       32.94        54.12        27.55        12.43         0.79 

$`AMP PEAK  4(3Q26.2) WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A94U 
       21.99        22.98        79.07        20.15         9.86        26.93 
TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 
        9.47         6.97         4.64         7.43        30.90         4.08 
TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 
        9.34         9.57         6.61        15.95        13.87        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6707 
       19.33        39.12        26.10        32.78        25.61        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7703 
       12.16         8.98        31.20        44.94         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7957 
       35.24        35.84        33.63        39.78        18.15         9.07 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       33.21        37.25         0.69        29.59         9.60        32.25 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 
        0.56        29.42        19.96         7.40         6.18        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8369 
        0.26        22.19        17.52         0.95         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        31.27         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8592 
        5.39         9.21        20.22         1.12        28.14         6.28 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS 
       10.68        34.13        13.87         7.53         6.08         1.48 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 
       28.57        12.89         8.98         0.72        14.17        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM 
        0.66        13.51         0.46         1.15        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-8524 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
       13.41        13.15        12.76        12.30        12.59        11.64 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A4MG 
       12.07        12.82        12.43         6.31        11.31         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4438 
       11.77        12.62        20.02        27.02         1.02        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4465 TCGA-CG-4466 
        4.01        14.01        29.98        19.07         9.01        18.97 
TCGA-CG-4469 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        7.07         6.97        36.00         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
      105.07        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 
       18.84        18.61        17.85        13.35        17.19        15.22 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 
       12.79        12.36        11.31        12.33        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YV 
       17.19        18.21        14.66        21.14        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F2 
       36.43        13.78        26.43        11.31        11.44        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 
        8.38         4.34        19.96         7.13         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       72.23        11.38        19.53        17.06        59.54         5.03 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51        24.39        18.15        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GJ 
       21.07         0.76        24.30         5.59        22.68        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       23.80        14.07        15.68        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
        3.39        18.38        12.46         6.74        12.59         6.51 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        37.64        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 
       19.73        14.04         8.52        74.53         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         8.61         5.13       122.30        37.91        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DV TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
        5.79        13.25        37.41        38.14        37.22        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO 
       34.29        46.26        22.19         2.50         1.87         9.27 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K 
       15.65        29.59        14.33        39.45        11.70        61.22 
TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A924 
       18.74         1.71        42.64        60.85         9.50        55.43 
TCGA-VQ-A927 TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G 
        6.58         2.66        11.24        28.41        17.13        26.04 
TCGA-VQ-AA6I TCGA-ZA-A8F6 
       16.14        17.26 

  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                          0.0                           0.1 
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                       115.69                        122.30 
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                        15.32                         14.40 
[1] "0.0 - 115.7 (15.3)" "0.1 - 122.3 (14.4)"
[1] "hr=" "1"  
D4V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  4(3Q26.2) MUTATED         0        6       15       12        11
  AMP PEAK  4(3Q26.2) WILD-TYPE       2       10       26       20        29
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  4(3Q26.2) MUTATED          23         2         27         23
  AMP PEAK  4(3Q26.2) WILD-TYPE        33         1         54         40
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK  4(3Q26.2) MUTATED           21       16
  AMP PEAK  4(3Q26.2) WILD-TYPE         18       28
D4V3, multiclass
            clus
vv           AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             6                            10
  STAGE IB                            15                            26
  STAGE II                            12                            20
  STAGE IIA                           11                            29
  STAGE IIB                           23                            33
  STAGE III                            2                             1
  STAGE IIIA                          27                            54
  STAGE IIIB                          23                            40
  STAGE IIIC                          21                            18
  STAGE IV                            16                            28
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  4(3Q26.2) MUTATED     9  31  66  54
  AMP PEAK  4(3Q26.2) WILD-TYPE  14  62 130  65
D4V4, multiclass
    clus
vv   AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  T1                           9                            14
  T2                          31                            62
  T3                          66                           130
  T4                          54                            65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  4(3Q26.2) MUTATED   43 46 32 36
  AMP PEAK  4(3Q26.2) WILD-TYPE 87 73 54 52
D4V5, multiclass
    clus
vv   AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  N0                          43                            87
  N1                          46                            73
  N2                          32                            54
  N3                          36                            52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                               cls
clus                              0   1
  AMP PEAK  4(3Q26.2) MUTATED   142  10
  AMP PEAK  4(3Q26.2) WILD-TYPE 247  20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(3Q26.2) MUTATED    142   10
  AMP PEAK  4(3Q26.2) WILD-TYPE  247   20
   clus
vv  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  0                         142                           247
  1                          10                            20
[1] 2 2
[1] FALSE
D4V7, binary
                               cls
clus                              0   1
  AMP PEAK  4(3Q26.2) MUTATED    58 106
  AMP PEAK  4(3Q26.2) WILD-TYPE 100 177
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(3Q26.2) MUTATED     58  106
  AMP PEAK  4(3Q26.2) WILD-TYPE  100  177
        clus
vv       AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  FEMALE                          58                           100
  MALE                           106                           177
[1] 2 2
[1] FALSE
D4V8, binary
                               cls
clus                              0   1
  AMP PEAK  4(3Q26.2) MUTATED   113  39
  AMP PEAK  4(3Q26.2) WILD-TYPE 209  37
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(3Q26.2) MUTATED    113   39
  AMP PEAK  4(3Q26.2) WILD-TYPE  209   37
     clus
vv    AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  NO                          113                           209
  YES                          39                            37
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK  4(3Q26.2) MUTATED                                          5
  AMP PEAK  4(3Q26.2) WILD-TYPE                                        8
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK  4(3Q26.2) MUTATED                                      20
  AMP PEAK  4(3Q26.2) WILD-TYPE                                    52
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  4(3Q26.2) MUTATED                                                       63
  AMP PEAK  4(3Q26.2) WILD-TYPE                                                    100
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK  4(3Q26.2) MUTATED                                                   5
  AMP PEAK  4(3Q26.2) WILD-TYPE                                                16
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  4(3Q26.2) MUTATED                                                                  33
  AMP PEAK  4(3Q26.2) WILD-TYPE                                                                49
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK  4(3Q26.2) MUTATED                                                    3
  AMP PEAK  4(3Q26.2) WILD-TYPE                                                  5
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK  4(3Q26.2) MUTATED                                                 33
  AMP PEAK  4(3Q26.2) WILD-TYPE                                               46
D4V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK  4(3Q26.2) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                      20
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     63
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           5
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          33
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           33
                                                                   clus
vv                                                                  AMP PEAK  4(3Q26.2) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        52
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      100
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            16
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            49
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             46
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  4(3Q26.2) MUTATED   126   7   8   9
  AMP PEAK  4(3Q26.2) WILD-TYPE 223  11  11  16
D4V10, multiclass
    clus
vv   AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  R0                         126                           223
  R1                           7                            11
  R2                           8                            11
  RX                           9                            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"
D4V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  4(3Q26.2) MUTATED      36                         7
  AMP PEAK  4(3Q26.2) WILD-TYPE    52                         5
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  4(3Q26.2) MUTATED                                           0    99
  AMP PEAK  4(3Q26.2) WILD-TYPE                                         1   179
D4V12, multiclass
                                           clus
vv                                          AMP PEAK  4(3Q26.2) MUTATED
  ASIAN                                                              36
  BLACK OR AFRICAN AMERICAN                                           7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              99
                                           clus
vv                                          AMP PEAK  4(3Q26.2) WILD-TYPE
  ASIAN                                                                52
  BLACK OR AFRICAN AMERICAN                                             5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               179
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V13, binary
                               cls
clus                              0   1
  AMP PEAK  4(3Q26.2) MUTATED     4 108
  AMP PEAK  4(3Q26.2) WILD-TYPE   1 208
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(3Q26.2) MUTATED      4  108
  AMP PEAK  4(3Q26.2) WILD-TYPE    1  208
                        clus
vv                       AMP PEAK  4(3Q26.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         108
                        clus
vv                       AMP PEAK  4(3Q26.2) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           208
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(5P15.33) MUTATION ANALYSIS
D5V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  5(5P15.33) MUTATED    71  52
  AMP PEAK  5(5P15.33) WILD-TYPE 175 117
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                           123                            292 
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                            52                            117 
$`AMP PEAK  5(5P15.33) MUTATED`
TCGA-CG-4444 TCGA-CG-4475 TCGA-FP-A8CX TCGA-KB-A93G TCGA-BR-4187 TCGA-BR-7197 
       47.05        22.98         0.23        20.15         4.64         9.21 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-8060 
       35.24        33.63        39.78        18.15         3.45        11.44 
TCGA-BR-8077 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8363 
        0.69         8.05        29.42         2.66        15.58         0.26 
TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8373 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 
       17.52        26.33        14.79         9.21        20.22        24.79 
TCGA-BR-8687 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5804 
        8.22        20.65        21.44        13.15        13.18        12.10 
TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 
       12.59        12.33        12.30        15.39        12.82         6.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4441 
       12.43        11.61        12.20         7.99        54.08        14.01 
TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5722 
       12.03        18.97         7.07        12.00        36.00         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       12.03        15.02         4.01        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 
       19.13        17.19        10.26        15.22        12.36        11.31 
TCGA-D7-8570 TCGA-D7-8576 TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A 
       24.72        14.66        11.31        22.29        15.65        19.96 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 
        0.62         7.99        72.23         3.48        19.53        17.06 
TCGA-HF-7132 TCGA-HU-8238 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4G2 TCGA-HU-A4GC 
       77.29         1.51        18.15        28.96        24.30         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H5 
       22.75        25.81        11.77         6.58         2.10        23.80 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IN-A7NT TCGA-KB-A6F5 
       33.40         3.45        13.35         6.74        10.62         5.56 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8N5 
       14.04        45.67        18.21         8.61       122.30        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        8.94        35.61         5.46        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A91A TCGA-VQ-A91N 
       43.36        21.73        12.79        17.85        39.45        18.74 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 
        1.71        42.64         9.50        55.56         9.04         4.54 
TCGA-VQ-A927 TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6F 
        6.58        11.24        18.41        43.66        38.93        54.12 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       16.14        27.55         0.79 

$`AMP PEAK  5(5P15.33) WILD-TYPE`
TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U 
       21.99        79.07        16.24         9.86        27.35        26.93 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       58.03        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         6.97         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7722 
       31.20        44.94        21.90        36.16        35.84        15.32 
TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       28.73         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 
       29.59         9.60        32.25         0.56        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8366 
        7.40         6.18        31.10        13.08        22.19         0.95 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        31.27         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 
       25.05         3.72         5.39        25.18         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T 
       31.96        32.58         9.86        20.88        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51         0.46        20.42 
TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5802 
        1.15        16.14         5.13        13.41        13.02        13.35 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8531 
       11.21        12.76        12.53         7.17        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG 
       11.64        12.07        12.43        12.30        11.31         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 
        1.02         8.05         4.01        29.98        19.07         0.00 
TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        9.01        30.97         6.97         1.02         0.99         6.02 
TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
      105.07        28.96        65.10        69.04        21.07         7.99 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       15.98        12.79        12.33        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       18.21        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
       36.43        13.78        14.76        26.43        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 
       20.32         8.38         4.34         7.13        14.47        21.27 
TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       11.38        14.07        22.29        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        0.56         5.52         6.21        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       26.47         5.92        24.39        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ 
        0.76         5.59        24.26        22.68        24.20        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        20.25         0.26 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        29.00        23.84        21.17        14.07        15.68 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
       36.36        18.81         3.39        18.38        12.46        19.53 
TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
        6.44        12.59         6.51        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53        63.62        37.64        36.95         3.72        19.73 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        5.13        16.67        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       71.38        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PM 
       46.26        16.31        22.19         2.50         2.70         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q 
       14.33        73.41        11.70        21.83        61.22        20.81 
TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A928 
       32.88        60.85         9.73         2.01        55.43         5.72 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA69 TCGA-VQ-AA6B 
       66.81        21.04         2.66        42.54        28.41        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZA-A8F6 
       17.13        26.04        12.43        17.26 

  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                          0.23                           0.00 
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                        122.30                         116.38 
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                        14.040                         15.665 
[1] "0.2 - 122.3 (14.0)" "0.0 - 116.4 (15.7)"
[1] "hr=" "1.1"
D5V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  5(5P15.33) MUTATED         0        3       12       10        12
  AMP PEAK  5(5P15.33) WILD-TYPE       2       13       29       22        28
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  5(5P15.33) MUTATED          14         0         29         17
  AMP PEAK  5(5P15.33) WILD-TYPE        42         3         52         46
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK  5(5P15.33) MUTATED           10       15
  AMP PEAK  5(5P15.33) WILD-TYPE         29       29
D5V3, multiclass
            clus
vv           AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              3                             13
  STAGE IB                             12                             29
  STAGE II                             10                             22
  STAGE IIA                            12                             28
  STAGE IIB                            14                             42
  STAGE III                             0                              3
  STAGE IIIA                           29                             52
  STAGE IIIB                           17                             46
  STAGE IIIC                           10                             29
  STAGE IV                             15                             29
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK  5(5P15.33) MUTATED     2  30  70  25
  AMP PEAK  5(5P15.33) WILD-TYPE  21  63 126  94
D5V4, multiclass
    clus
vv   AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  T1                            2                             21
  T2                           30                             63
  T3                           70                            126
  T4                           25                             94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK  5(5P15.33) MUTATED   34 34 30 27
  AMP PEAK  5(5P15.33) WILD-TYPE 96 85 56 61
D5V5, multiclass
    clus
vv   AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  N0                           34                             96
  N1                           34                             85
  N2                           30                             56
  N3                           27                             61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                                cls
clus                               0   1
  AMP PEAK  5(5P15.33) MUTATED   113   9
  AMP PEAK  5(5P15.33) WILD-TYPE 276  21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(5P15.33) MUTATED    113    9
  AMP PEAK  5(5P15.33) WILD-TYPE  276   21
   clus
vv  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  0                          113                            276
  1                            9                             21
[1] 2 2
[1] FALSE
D5V7, binary
                                cls
clus                               0   1
  AMP PEAK  5(5P15.33) MUTATED    42  88
  AMP PEAK  5(5P15.33) WILD-TYPE 116 195
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(5P15.33) MUTATED     42   88
  AMP PEAK  5(5P15.33) WILD-TYPE  116  195
        clus
vv       AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  FEMALE                           42                            116
  MALE                             88                            195
[1] 2 2
[1] FALSE
D5V8, binary
                                cls
clus                               0   1
  AMP PEAK  5(5P15.33) MUTATED    94  24
  AMP PEAK  5(5P15.33) WILD-TYPE 228  52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(5P15.33) MUTATED     94   24
  AMP PEAK  5(5P15.33) WILD-TYPE  228   52
     clus
vv    AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  NO                            94                            228
  YES                           24                             52
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK  5(5P15.33) MUTATED                                          3
  AMP PEAK  5(5P15.33) WILD-TYPE                                       10
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK  5(5P15.33) MUTATED                                      12
  AMP PEAK  5(5P15.33) WILD-TYPE                                    60
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  5(5P15.33) MUTATED                                                       41
  AMP PEAK  5(5P15.33) WILD-TYPE                                                    122
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK  5(5P15.33) MUTATED                                                   8
  AMP PEAK  5(5P15.33) WILD-TYPE                                                13
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  5(5P15.33) MUTATED                                                                  31
  AMP PEAK  5(5P15.33) WILD-TYPE                                                                51
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK  5(5P15.33) MUTATED                                                    4
  AMP PEAK  5(5P15.33) WILD-TYPE                                                  4
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK  5(5P15.33) MUTATED                                                 29
  AMP PEAK  5(5P15.33) WILD-TYPE                                               50
D5V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK  5(5P15.33) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       12
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      41
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            8
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           31
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            29
                                                                   clus
vv                                                                  AMP PEAK  5(5P15.33) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         60
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       122
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             13
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             51
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              50
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  5(5P15.33) MUTATED   102   6   7   5
  AMP PEAK  5(5P15.33) WILD-TYPE 247  12  12  20
D5V10, multiclass
    clus
vv   AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  R0                          102                            247
  R1                            6                             12
  R2                            7                             12
  RX                            5                             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"
D5V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  5(5P15.33) MUTATED      27                         5
  AMP PEAK  5(5P15.33) WILD-TYPE    61                         7
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK  5(5P15.33) MUTATED                                           1
  AMP PEAK  5(5P15.33) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK  5(5P15.33) MUTATED      77
  AMP PEAK  5(5P15.33) WILD-TYPE   201
D5V12, multiclass
                                           clus
vv                                          AMP PEAK  5(5P15.33) MUTATED
  ASIAN                                                               27
  BLACK OR AFRICAN AMERICAN                                            5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               77
                                           clus
vv                                          AMP PEAK  5(5P15.33) WILD-TYPE
  ASIAN                                                                 61
  BLACK OR AFRICAN AMERICAN                                              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                201
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V13, binary
                                cls
clus                               0   1
  AMP PEAK  5(5P15.33) MUTATED     1  88
  AMP PEAK  5(5P15.33) WILD-TYPE   4 228
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(5P15.33) MUTATED      1   88
  AMP PEAK  5(5P15.33) WILD-TYPE    4  228
                        clus
vv                       AMP PEAK  5(5P15.33) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           88
                        clus
vv                       AMP PEAK  5(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            228
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(5P13.1) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  6(5P13.1) MUTATED    70  48
  AMP PEAK  6(5P13.1) WILD-TYPE 176 121
  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE 
                          118                           297 
  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE 
                           48                           121 
$`AMP PEAK  6(5P13.1) MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-FP-A8CX TCGA-KB-A93G TCGA-BR-4187 
       47.05        21.99        22.98         0.23        20.15         4.64 
TCGA-BR-6458 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       19.33         9.21        35.24        33.63        39.78        18.15 
TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8284 TCGA-BR-8286 
        3.45        33.21        11.44         0.69         8.05        29.42 
TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8369 
        2.66        15.58         0.26        17.52        26.33        14.04 
TCGA-BR-8373 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8687 TCGA-BR-A4CQ 
       14.79         9.21        20.22        24.79         8.22        34.98 
TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 
       20.65        21.44        13.18        12.10        12.76        12.59 
TCGA-CD-8528 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
       12.33        12.82         6.31        12.43        11.61        12.20 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
        7.99        54.08        12.03        18.97         7.07        12.00 
TCGA-CG-5718 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-D7-5578 
       36.00         0.99        12.03        15.02         4.01        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 
       20.91        19.13        10.26        15.22        12.36        11.31 
TCGA-D7-8570 TCGA-D7-8576 TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-5647 
       24.72        14.66        11.31        22.29        15.65         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-HF-7132 
        7.99        72.23         3.48        19.53        17.06        77.29 
TCGA-HU-8238 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4GC 
        1.51        18.15        28.96        22.82        24.30         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4H0 TCGA-HU-A4H5 TCGA-HU-A4HD 
       22.75        25.81        11.77         2.10        23.80        33.40 
TCGA-IN-7808 TCGA-IN-A6RL TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        3.45        13.35         6.51        10.62        11.70        15.75 
TCGA-KB-A6F5 TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-RD-A8N5 TCGA-RD-A8N6 
        5.56        14.04        45.67        18.21        57.44         8.94 
TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E3 
       35.61         5.46        13.25        13.02        18.48        21.73 
TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91X TCGA-VQ-A91Y 
       12.79        17.85        39.45        18.74         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A927 TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6A 
       55.56         9.04         6.58        11.24        43.66        38.93 
TCGA-VQ-AA6F TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       54.12        27.55        12.43         0.79 

$`AMP PEAK  6(5P13.1) WILD-TYPE`
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 
       79.07        16.24         9.86        27.35        26.93        58.03 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         6.97         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 
       34.68        15.95        13.87        17.29        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 
       21.90        36.16        35.84        15.32        28.73         9.07 
TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       29.56        37.25        14.43        29.59         9.60        32.25 
TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        0.56        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
       13.08        22.19         0.95         4.31         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       31.27         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        31.96        32.58         9.86        20.88 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS 
       10.68        34.13        13.87         7.53         6.08         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.53        28.34         0.66        32.52        13.51         0.46 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 
       13.15        13.35        11.21        12.53         7.17        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 
       12.39        12.59        11.64        15.39        12.07        12.43 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.30        11.31         6.58        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 
        3.02        27.02        15.95         1.02         8.05         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4477 
       14.01        29.98        19.07         0.00         9.01        30.97 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 
        6.97         1.02         0.99         6.02       105.07        28.96 
TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6519 
       65.10        69.04        21.07         7.99        25.71        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       15.98        12.79        12.33        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       18.21        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
       36.43        13.78        14.76        26.43        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 
       20.32         8.38         4.34        19.96         7.13        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
       21.27        11.38        14.07        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 
       13.58         0.56         5.52         6.21        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 
       30.51        26.47         5.92        24.39        22.32        21.07 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ 
        0.76         5.59        24.26        22.68        24.20        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        0.26        12.95        29.00        23.84        21.17        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       15.68        36.36        18.81         3.39        18.38        12.46 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-AB1X TCGA-IP-7968 
       19.53         6.44         6.74        12.59        13.51         2.53 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF 
       63.62        37.64        36.95         3.72        19.73         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
      116.38        71.38        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       48.79        43.36        37.41        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       30.97        34.29        46.26        16.31        22.19         2.50 
TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
        2.70         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E 
       29.59        64.57        14.33        73.41        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       61.22        20.81        32.88         1.71        42.64        60.85 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O 
        2.01        55.43         4.54         5.72        66.81        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D 
        2.66        42.54        18.41        28.41        32.94        17.13 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-ZA-A8F6 
       26.04        16.14        17.26 

  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE 
                         0.23                          0.00 
  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE 
                        77.29                        122.30 
  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE 
                        14.04                         15.65 
[1] "0.2 - 77.3 (14.0)"  "0.0 - 122.3 (15.7)"
[1] "hr=" "1.1"
D6V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  6(5P13.1) MUTATED         0        4       12        9        13
  AMP PEAK  6(5P13.1) WILD-TYPE       2       12       29       23        27
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  6(5P13.1) MUTATED          14         0         23         15
  AMP PEAK  6(5P13.1) WILD-TYPE        42         3         58         48
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK  6(5P13.1) MUTATED           13       15
  AMP PEAK  6(5P13.1) WILD-TYPE         26       29
D6V3, multiclass
            clus
vv           AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             4                            12
  STAGE IB                            12                            29
  STAGE II                             9                            23
  STAGE IIA                           13                            27
  STAGE IIB                           14                            42
  STAGE III                            0                             3
  STAGE IIIA                          23                            58
  STAGE IIIB                          15                            48
  STAGE IIIC                          13                            26
  STAGE IV                            15                            29
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  6(5P13.1) MUTATED     3  28  62  30
  AMP PEAK  6(5P13.1) WILD-TYPE  20  65 134  89
D6V4, multiclass
    clus
vv   AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  T1                           3                            20
  T2                          28                            65
  T3                          62                           134
  T4                          30                            89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  6(5P13.1) MUTATED   34 35 22 30
  AMP PEAK  6(5P13.1) WILD-TYPE 96 84 64 58
D6V5, multiclass
    clus
vv   AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  N0                          34                            96
  N1                          35                            84
  N2                          22                            64
  N3                          30                            58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                               cls
clus                              0   1
  AMP PEAK  6(5P13.1) MUTATED   108  10
  AMP PEAK  6(5P13.1) WILD-TYPE 281  20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(5P13.1) MUTATED    108   10
  AMP PEAK  6(5P13.1) WILD-TYPE  281   20
   clus
vv  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  0                         108                           281
  1                          10                            20
[1] 2 2
[1] FALSE
D6V7, binary
                               cls
clus                              0   1
  AMP PEAK  6(5P13.1) MUTATED    44  82
  AMP PEAK  6(5P13.1) WILD-TYPE 114 201
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(5P13.1) MUTATED     44   82
  AMP PEAK  6(5P13.1) WILD-TYPE  114  201
        clus
vv       AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  FEMALE                          44                           114
  MALE                            82                           201
[1] 2 2
[1] FALSE
D6V8, binary
                               cls
clus                              0   1
  AMP PEAK  6(5P13.1) MUTATED    94  20
  AMP PEAK  6(5P13.1) WILD-TYPE 228  56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(5P13.1) MUTATED     94   20
  AMP PEAK  6(5P13.1) WILD-TYPE  228   56
     clus
vv    AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  NO                           94                           228
  YES                          20                            56
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK  6(5P13.1) MUTATED                                          4
  AMP PEAK  6(5P13.1) WILD-TYPE                                        9
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK  6(5P13.1) MUTATED                                      12
  AMP PEAK  6(5P13.1) WILD-TYPE                                    60
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  6(5P13.1) MUTATED                                                       45
  AMP PEAK  6(5P13.1) WILD-TYPE                                                    118
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK  6(5P13.1) MUTATED                                                   8
  AMP PEAK  6(5P13.1) WILD-TYPE                                                13
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  6(5P13.1) MUTATED                                                                  27
  AMP PEAK  6(5P13.1) WILD-TYPE                                                                55
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK  6(5P13.1) MUTATED                                                    3
  AMP PEAK  6(5P13.1) WILD-TYPE                                                  5
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK  6(5P13.1) MUTATED                                                 25
  AMP PEAK  6(5P13.1) WILD-TYPE                                               54
D6V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK  6(5P13.1) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    4
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                      12
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     45
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           8
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          27
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           25
                                                                   clus
vv                                                                  AMP PEAK  6(5P13.1) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      9
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        60
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      118
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            13
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            55
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             54
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  6(5P13.1) MUTATED    97   7   7   5
  AMP PEAK  6(5P13.1) WILD-TYPE 252  11  12  20
D6V10, multiclass
    clus
vv   AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  R0                          97                           252
  R1                           7                            11
  R2                           7                            12
  RX                           5                            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"
D6V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  6(5P13.1) MUTATED      23                         5
  AMP PEAK  6(5P13.1) WILD-TYPE    65                         7
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  6(5P13.1) MUTATED                                           0    78
  AMP PEAK  6(5P13.1) WILD-TYPE                                         1   200
D6V12, multiclass
                                           clus
vv                                          AMP PEAK  6(5P13.1) MUTATED
  ASIAN                                                              23
  BLACK OR AFRICAN AMERICAN                                           5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              78
                                           clus
vv                                          AMP PEAK  6(5P13.1) WILD-TYPE
  ASIAN                                                                65
  BLACK OR AFRICAN AMERICAN                                             7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               200
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V13, binary
                               cls
clus                              0   1
  AMP PEAK  6(5P13.1) MUTATED     1  87
  AMP PEAK  6(5P13.1) WILD-TYPE   4 229
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(5P13.1) MUTATED      1   87
  AMP PEAK  6(5P13.1) WILD-TYPE    4  229
                        clus
vv                       AMP PEAK  6(5P13.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          87
                        clus
vv                       AMP PEAK  6(5P13.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           229
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(6P21.1) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  7(6P21.1) MUTATED    61  53
  AMP PEAK  7(6P21.1) WILD-TYPE 185 116
  AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE 
                          114                           301 
  AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE 
                           53                           116 
$`AMP PEAK  7(6P21.1) MUTATED`
TCGA-CG-5727 TCGA-VQ-A8PU TCGA-3M-AB46 TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4184 
       79.07        27.35        58.03        11.01         6.61         6.97 
TCGA-BR-4191 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6457 
       18.35         4.08         9.67         6.18        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 
       19.33         9.17         9.21        35.24        33.63        18.15 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8369 
       28.73         3.45        11.44        29.42         2.66        14.04 
TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8683 
       14.79        25.18         9.21        20.22        24.79         9.86 
TCGA-BR-8686 TCGA-BR-A4CQ TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-5799 
       20.88        34.98        20.65        20.42        21.44        13.02 
TCGA-CD-5803 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48C TCGA-CG-4436 
       11.21        12.82         6.31        12.30        11.61         7.99 
TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5718 
       54.08        19.07        12.03        18.97        30.97        36.00 
TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-6518 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
        4.01        69.04        19.13        10.26        15.22        15.98 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YU 
       12.36        11.31        12.33        14.66        14.27        16.44 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-8122 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 
       22.29        15.65         7.99         3.48        19.53        17.06 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-7134 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-A4GF 
        0.56         5.52        52.21         5.92        28.96        25.81 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL 
       23.84        23.80        21.17         3.39        18.38        13.35 
TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IP-7968 TCGA-KB-A93H 
       19.53         6.74        12.59        10.62         2.53        37.64 
TCGA-KB-A93J TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-RD-A7BT TCGA-RD-A8MV 
       36.95        14.04        45.67        18.21         8.61       122.30 
TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
       37.91       115.69         5.46        13.02        18.48        43.36 
TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A91S TCGA-VQ-A91U 
        7.73        22.19         2.70        17.85        32.88         1.71 
TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R 
        9.50         9.04         4.54        66.81        21.04        42.54 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-ZQ-A9CR 
       18.41        43.66        32.94        17.13        26.04         0.79 

$`AMP PEAK  7(6P21.1) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        22.98        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A94U TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
        9.86        26.93        26.70        11.70        19.56         9.47 
TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 
        9.44         4.64         7.43        30.90         4.08         9.34 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6563 
        9.57         6.61        34.68        15.95        13.87        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-7958 
       36.16        35.84        39.78        15.32         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       33.21        37.25        14.43         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
       32.25         8.05         0.56        19.96         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33         4.31         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8487 
       31.27         7.36        25.05         3.72         5.39         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       26.73        31.96        32.58         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       13.87         7.53         6.08         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QL 
        0.66        32.52        13.51         0.46         1.15        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5804 
        5.13        13.41        13.15        13.18        13.35        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 
       12.39        12.59        11.64        15.39        12.07        12.43 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         1.02         8.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
        4.01        14.01        29.98         0.00         9.01         7.07 
TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       12.00         6.97         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 
      105.07        12.03        15.02        28.96        65.10        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 
        7.99        25.71        12.66        20.91        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6817 
       18.54        18.61        17.85        13.35        17.19        12.79 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 
       24.72        16.80        19.50        17.19        18.21        21.14 
TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       20.91         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 
       11.24        11.31        11.44        20.32         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
       19.96         7.13         0.62        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       11.38        14.07        22.29        59.54         5.03        13.58 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        30.51        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        18.15        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       29.00        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V 
       18.81        12.46         6.44         6.51        11.70        15.75 
TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF 
       13.51         5.56        63.62         3.72        19.73         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW 
       74.53         6.08         4.60         9.24        11.05         5.13 
TCGA-RD-A7C1 TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       16.67        40.64       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       35.61        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DV TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       13.25        21.73        37.41        38.14        37.22        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM 
       34.29        46.26        16.31         2.50        12.79         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z 
       18.74        20.81        42.64        60.85         9.73        55.56 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94T 
        2.01        55.43         6.58         5.72         2.66        11.24 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       28.41        38.93        54.12        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE 
                         0.56                          0.00 
  AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE 
                       122.30                        116.38 
  AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE 
                        16.75                         14.17 
[1] "0.6 - 122.3 (16.8)" "0.0 - 116.4 (14.2)"
[1] "hr=" "1.1"
D7V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  7(6P21.1) MUTATED         1        4       16       11        11
  AMP PEAK  7(6P21.1) WILD-TYPE       1       12       25       21        29
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  7(6P21.1) MUTATED          17         0         24         17
  AMP PEAK  7(6P21.1) WILD-TYPE        39         3         57         46
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK  7(6P21.1) MUTATED            6       11
  AMP PEAK  7(6P21.1) WILD-TYPE         33       33
D7V3, multiclass
            clus
vv           AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             4                            12
  STAGE IB                            16                            25
  STAGE II                            11                            21
  STAGE IIA                           11                            29
  STAGE IIB                           17                            39
  STAGE III                            0                             3
  STAGE IIIA                          24                            57
  STAGE IIIB                          17                            46
  STAGE IIIC                           6                            33
  STAGE IV                            11                            33
[1] 11  2
[1] TRUE
[1] "dimension of 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(6P21.1) MUTATED     6  34  54  25
  AMP PEAK  7(6P21.1) WILD-TYPE  17  59 142  94
D7V4, multiclass
    clus
vv   AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE
  T1                           6                            17
  T2                          34                            59
  T3                          54                           142
  T4                          25                            94
[1] 4 2
[1] TRUE
[1] "dimension of 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(6P21.1) MUTATED   37 38 26 19
  AMP PEAK  7(6P21.1) WILD-TYPE 93 81 60 69
D7V5, multiclass
    clus
vv   AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE
  N0                          37                            93
  N1                          38                            81
  N2                          26                            60
  N3                          19                            69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                               cls
clus                              0   1
  AMP PEAK  7(6P21.1) MUTATED   109   5
  AMP PEAK  7(6P21.1) WILD-TYPE 280  25
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(6P21.1) MUTATED    109    5
  AMP PEAK  7(6P21.1) WILD-TYPE  280   25
   clus
vv  AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE
  0                         109                           280
  1                           5                            25
[1] 2 2
[1] FALSE
D7V7, binary
                               cls
clus                              0   1
  AMP PEAK  7(6P21.1) MUTATED    40  84
  AMP PEAK  7(6P21.1) WILD-TYPE 118 199
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(6P21.1) MUTATED     40   84
  AMP PEAK  7(6P21.1) WILD-TYPE  118  199
        clus
vv       AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE
  FEMALE                          40                           118
  MALE                            84                           199
[1] 2 2
[1] FALSE
D7V8, binary
                               cls
clus                              0   1
  AMP PEAK  7(6P21.1) MUTATED    92  23
  AMP PEAK  7(6P21.1) WILD-TYPE 230  53
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(6P21.1) MUTATED     92   23
  AMP PEAK  7(6P21.1) WILD-TYPE  230   53
     clus
vv    AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE
  NO                           92                           230
  YES                          23                            53
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK  7(6P21.1) MUTATED                                          2
  AMP PEAK  7(6P21.1) WILD-TYPE                                       11
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK  7(6P21.1) MUTATED                                       5
  AMP PEAK  7(6P21.1) WILD-TYPE                                    67
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  7(6P21.1) MUTATED                                                       52
  AMP PEAK  7(6P21.1) WILD-TYPE                                                    111
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK  7(6P21.1) MUTATED                                                   3
  AMP PEAK  7(6P21.1) WILD-TYPE                                                18
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  7(6P21.1) MUTATED                                                                  30
  AMP PEAK  7(6P21.1) WILD-TYPE                                                                52
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK  7(6P21.1) MUTATED                                                    2
  AMP PEAK  7(6P21.1) WILD-TYPE                                                  6
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK  7(6P21.1) MUTATED                                                 30
  AMP PEAK  7(6P21.1) WILD-TYPE                                               49
D7V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK  7(6P21.1) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     52
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          30
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           30
                                                                   clus
vv                                                                  AMP PEAK  7(6P21.1) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      111
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            52
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             49
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  7(6P21.1) MUTATED    95   4   5  10
  AMP PEAK  7(6P21.1) WILD-TYPE 254  14  14  15
D7V10, multiclass
    clus
vv   AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE
  R0                          95                           254
  R1                           4                            14
  R2                           5                            14
  RX                          10                            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"
D7V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  7(6P21.1) MUTATED      18                         5
  AMP PEAK  7(6P21.1) WILD-TYPE    70                         7
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  7(6P21.1) MUTATED                                           1    84
  AMP PEAK  7(6P21.1) WILD-TYPE                                         0   194
D7V12, multiclass
                                           clus
vv                                          AMP PEAK  7(6P21.1) MUTATED
  ASIAN                                                              18
  BLACK OR AFRICAN AMERICAN                                           5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              84
                                           clus
vv                                          AMP PEAK  7(6P21.1) WILD-TYPE
  ASIAN                                                                70
  BLACK OR AFRICAN AMERICAN                                             7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               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"
D7V13, binary
                               cls
clus                              0   1
  AMP PEAK  7(6P21.1) MUTATED     2  85
  AMP PEAK  7(6P21.1) WILD-TYPE   3 231
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(6P21.1) MUTATED      2   85
  AMP PEAK  7(6P21.1) WILD-TYPE    3  231
                        clus
vv                       AMP PEAK  7(6P21.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          85
                        clus
vv                       AMP PEAK  7(6P21.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           231
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(6Q12) MUTATION ANALYSIS
D8V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  8(6Q12) MUTATED    43  38
  AMP PEAK  8(6Q12) WILD-TYPE 203 131
  AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE 
                         81                         334 
  AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE 
                         38                         131 
$`AMP PEAK  8(6Q12) MUTATED`
TCGA-MX-A663 TCGA-3M-AB46 TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4255 
        9.86        58.03        11.01         6.61         6.97         4.08 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-7197 TCGA-BR-7704 
        9.67         6.18        17.29        19.33         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7723 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8369 
       33.63        28.73        11.44        29.42         2.66        14.04 
TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-A4J1 
       14.79        25.18         9.21        24.79        20.88         0.72 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5804 
       13.51        20.65        20.42        21.44        13.02        12.10 
TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CG-4436 TCGA-CG-4438 
       15.39         6.31        12.30        12.43         7.99        54.08 
TCGA-CG-4440 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5730 TCGA-D7-6526 
        4.01        18.97        30.97         1.02         4.01        17.19 
TCGA-D7-6527 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8576 TCGA-D7-A4YT 
       10.26        12.36        11.31        12.33        14.66        14.27 
TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-A4BF TCGA-HF-7134 
       22.29         7.99         3.48        19.53         5.52        52.21 
TCGA-HU-A4GF TCGA-HU-A4GT TCGA-HU-A4H6 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL 
       25.81         6.51        21.17         3.39        18.38        13.35 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A666 TCGA-RD-A7BT TCGA-RD-A8MW TCGA-RD-A8N1 
       63.62        37.64        14.04         8.61        37.91       115.69 
TCGA-RD-A8N6 TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PJ 
        8.94        13.25        13.02         7.73        22.19         2.70 
TCGA-VQ-A8PK TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A94R 
       17.85        32.88         1.71         9.50         9.04        42.54 
TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6F 
       43.66        32.94        54.12 

$`AMP PEAK  8(6Q12) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
       20.15        27.35        26.93        26.70        11.70        19.56 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.47         9.44         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        4.08         9.34         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.87        13.68        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        44.94        21.90        36.16        35.84 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       39.78        18.15        15.32         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       33.21        37.25        14.43         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
       32.25         8.05         0.56        19.96         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33         4.31         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8486 
       31.27         7.36        25.05         3.72         5.39        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 
        7.53        26.73        31.96        32.58         9.86         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        1.48        27.55        28.57        12.89         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PF 
        0.53        28.34         0.66        32.52         0.46         1.15 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       16.14         5.13        13.41        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       11.21        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 
       12.30        12.39        12.59        11.64        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       12.43        11.31        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        8.05        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 
        9.01         7.07        12.00         6.97        36.00         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8570 
       17.85        13.35        15.22        15.98        12.79        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19        18.21        21.14        20.91 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        11.44        20.32        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 
        4.34        19.96         7.13         0.62        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       21.27        11.38        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        5.03        13.58         0.56         6.21        77.29        63.06 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       30.51        26.47         1.51         5.92        24.39        18.15 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         0.10         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       18.81        12.46        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE 
        5.56        36.95         3.72        19.73        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
        5.13        16.67       122.30        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       48.79         5.46        18.48        43.36        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       38.14        37.22        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.50        12.79         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       13.35        29.59        64.57        14.33        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V 
       11.70        21.83        61.22        18.74        20.81        42.64 
TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
       60.85         9.73        55.56         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T 
        6.58         5.72        66.81        21.04         2.66        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I 
       18.41        28.41        38.93        17.13        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       27.55        12.43        17.26         0.79 

  AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE 
                       0.72                        0.00 
  AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE 
                     115.69                      122.30 
  AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE 
                      13.51                       15.65 
[1] "0.7 - 115.7 (13.5)" "0.0 - 122.3 (15.7)"
[1] "hr=" "1.3"
D8V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  8(6Q12) MUTATED         1        2       12        6         9
  AMP PEAK  8(6Q12) WILD-TYPE       1       14       29       26        31
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  8(6Q12) MUTATED          12         0         15         12
  AMP PEAK  8(6Q12) WILD-TYPE        44         3         66         51
                             vv
clus                          STAGE IIIC STAGE IV
  AMP PEAK  8(6Q12) MUTATED            4       10
  AMP PEAK  8(6Q12) WILD-TYPE         35       34
D8V3, multiclass
            clus
vv           AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE
  STAGE I                            1                           1
  STAGE IA                           2                          14
  STAGE IB                          12                          29
  STAGE II                           6                          26
  STAGE IIA                          9                          31
  STAGE IIB                         12                          44
  STAGE III                          0                           3
  STAGE IIIA                        15                          66
  STAGE IIIB                        12                          51
  STAGE IIIC                         4                          35
  STAGE IV                          10                          34
[1] 11  2
[1] TRUE
[1] "dimension of 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(6Q12) MUTATED     4  22  41  19
  AMP PEAK  8(6Q12) WILD-TYPE  19  71 155 100
D8V4, multiclass
    clus
vv   AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE
  T1                         4                          19
  T2                        22                          71
  T3                        41                         155
  T4                        19                         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"
                             vv
clus                           N0  N1  N2  N3
  AMP PEAK  8(6Q12) MUTATED    28  26  14  16
  AMP PEAK  8(6Q12) WILD-TYPE 102  93  72  72
D8V5, multiclass
    clus
vv   AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE
  N0                        28                         102
  N1                        26                          93
  N2                        14                          72
  N3                        16                          72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                             cls
clus                            0   1
  AMP PEAK  8(6Q12) MUTATED    76   6
  AMP PEAK  8(6Q12) WILD-TYPE 313  24
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(6Q12) MUTATED     76    6
  AMP PEAK  8(6Q12) WILD-TYPE  313   24
   clus
vv  AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE
  0                        76                         313
  1                         6                          24
[1] 2 2
[1] FALSE
D8V7, binary
                             cls
clus                            0   1
  AMP PEAK  8(6Q12) MUTATED    32  56
  AMP PEAK  8(6Q12) WILD-TYPE 126 227
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(6Q12) MUTATED     32   56
  AMP PEAK  8(6Q12) WILD-TYPE  126  227
        clus
vv       AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE
  FEMALE                        32                         126
  MALE                          56                         227
[1] 2 2
[1] FALSE
D8V8, binary
                             cls
clus                            0   1
  AMP PEAK  8(6Q12) MUTATED    61  18
  AMP PEAK  8(6Q12) WILD-TYPE 261  58
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(6Q12) MUTATED     61   18
  AMP PEAK  8(6Q12) WILD-TYPE  261   58
     clus
vv    AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE
  NO                         61                         261
  YES                        18                          58
[1] 2 2
[1] FALSE
                             vv
clus                          STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK  8(6Q12) MUTATED                                          2
  AMP PEAK  8(6Q12) WILD-TYPE                                       11
                             vv
clus                          STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK  8(6Q12) MUTATED                                       4
  AMP PEAK  8(6Q12) WILD-TYPE                                    68
                             vv
clus                          STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  8(6Q12) MUTATED                                                       38
  AMP PEAK  8(6Q12) WILD-TYPE                                                    125
                             vv
clus                          STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK  8(6Q12) MUTATED                                                   1
  AMP PEAK  8(6Q12) WILD-TYPE                                                20
                             vv
clus                          STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  8(6Q12) MUTATED                                                                  27
  AMP PEAK  8(6Q12) WILD-TYPE                                                                55
                             vv
clus                          STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK  8(6Q12) MUTATED                                                    1
  AMP PEAK  8(6Q12) WILD-TYPE                                                  7
                             vv
clus                          STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK  8(6Q12) MUTATED                                                 15
  AMP PEAK  8(6Q12) WILD-TYPE                                               64
D8V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK  8(6Q12) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                  2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                     4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                   38
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                         1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        27
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                        1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                         15
                                                                   clus
vv                                                                  AMP PEAK  8(6Q12) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                   11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                      68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                    125
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                          20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          55
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           64
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  8(6Q12) MUTATED    65   3   5   8
  AMP PEAK  8(6Q12) WILD-TYPE 284  15  14  17
D8V10, multiclass
    clus
vv   AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE
  R0                        65                         284
  R1                         3                          15
  R2                         5                          14
  RX                         8                          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"
D8V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  8(6Q12) MUTATED      14                         3
  AMP PEAK  8(6Q12) WILD-TYPE    74                         9
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  8(6Q12) MUTATED                                           1    57
  AMP PEAK  8(6Q12) WILD-TYPE                                         0   221
D8V12, multiclass
                                           clus
vv                                          AMP PEAK  8(6Q12) MUTATED
  ASIAN                                                            14
  BLACK OR AFRICAN AMERICAN                                         3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         1
  WHITE                                                            57
                                           clus
vv                                          AMP PEAK  8(6Q12) WILD-TYPE
  ASIAN                                                              74
  BLACK OR AFRICAN AMERICAN                                           9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V13, binary
                             cls
clus                            0   1
  AMP PEAK  8(6Q12) MUTATED     1  61
  AMP PEAK  8(6Q12) WILD-TYPE   4 255
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(6Q12) MUTATED      1   61
  AMP PEAK  8(6Q12) WILD-TYPE    4  255
                        clus
vv                       AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE
  HISPANIC OR LATINO                             1                           4
  NOT HISPANIC OR LATINO                        61                         255
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(6Q21) MUTATION ANALYSIS
D9V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  9(6Q21) MUTATED    41  37
  AMP PEAK  9(6Q21) WILD-TYPE 205 132
  AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE 
                         78                         337 
  AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE 
                         37                         132 
$`AMP PEAK  9(6Q21) MUTATED`
TCGA-CG-4444 TCGA-EQ-A4SO TCGA-MX-A663 TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4184 
       47.05        16.24         9.86        11.01         6.61         6.97 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-6456 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 
        4.08         9.67        17.29         9.21        35.24        33.63 
TCGA-BR-7717 TCGA-BR-8060 TCGA-BR-8289 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8484 
       18.15        11.44         2.66        14.04        14.79        25.18 
TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
        9.21        24.79        20.88         7.53        34.98         1.48 
TCGA-BR-A4J1 TCGA-BR-A4J7 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8528 TCGA-CD-A487 
        0.72        32.52        13.02        13.15        12.33        12.30 
TCGA-CD-A48A TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4466 
       12.43         3.02         7.99        54.08         4.01        18.97 
TCGA-CG-4477 TCGA-CG-5724 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 
       30.97        12.03        18.54        10.26        15.22        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-A4YT TCGA-EQ-8122 TCGA-FP-A4BF TCGA-HU-A4GH 
       11.31        12.33        14.27         7.99         5.52        11.77 
TCGA-HU-A4GT TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        6.51        12.95        21.17         3.45        18.81         3.39 
TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-MX-A666 TCGA-R5-A7O7 TCGA-RD-A7BT TCGA-RD-A7C1 
       11.70         5.56        14.04        45.67         8.61        16.67 
TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
       37.91         8.94         5.46        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A91S TCGA-VQ-A91U 
       43.36        22.19         2.70        17.85        32.88         1.71 
TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-AA6D TCGA-VQ-AA6J 
        9.50         9.04        66.81        42.54        17.13        27.55 

$`AMP PEAK  9(6Q21) WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A8PU 
       21.99        22.98        79.07         0.23        20.15        27.35 
TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
       26.93        58.03        26.70        11.70        19.56         9.47 
TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        9.44         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.34         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.87        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
       40.21        30.90        31.20        44.94        21.90        36.16 
TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       35.84        39.78        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       29.56        33.21        37.25        14.43         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 
        9.60        32.25         8.05         0.56        29.42        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        2.20        15.58         7.40         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        31.27         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        5.39        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 
        9.86         8.22        10.68        34.13        13.87         6.08 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57        12.89         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        13.51         0.46        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 
        1.15        21.44        16.14         5.13        13.41        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.35        11.21        12.10        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        7.17        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48C 
       12.07        12.82        12.43         6.31        11.31        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 
        6.58        12.20        11.77        12.62        20.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
       15.95         1.02         8.05        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 
       12.03         0.00         9.01         7.07        12.00         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 
       18.84        18.61        17.85        13.35        17.19        15.98 
TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.79        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       14.66        21.14        20.91        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        5.03        13.58         0.56         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       18.15        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        21.37        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.58        20.25         0.26         2.10        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-A6RI 
       23.80        14.07        15.68        33.40        36.36        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 
        6.51        10.62        15.75        13.51         2.53        63.62 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZE TCGA-R5-A7ZF 
       37.64        36.95         3.72        19.73        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW 
       74.53         6.08         4.60         9.24        11.05         5.13 
TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
      122.30        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       35.61        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        37.41        38.14        37.22         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM 
       34.29        46.26        16.31         2.50        12.79         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z 
       18.74        20.81        42.64        60.85         9.73        55.56 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O 
        2.01        55.43         4.54         6.58         5.72        21.04 
TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
        2.66        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       32.94        54.12        26.04        16.14        12.43        17.26 
TCGA-ZQ-A9CR 
        0.79 

  AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE 
                       0.72                        0.00 
  AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE 
                      66.81                      122.30 
  AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE 
                      12.69                       15.95 
[1] "0.7 - 66.8 (12.7)"  "0.0 - 122.3 (15.9)"
[1] "hr=" "1.5"
D9V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  9(6Q21) MUTATED         0        1        9        5         5
  AMP PEAK  9(6Q21) WILD-TYPE       2       15       32       27        35
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  9(6Q21) MUTATED           9         0         21         12
  AMP PEAK  9(6Q21) WILD-TYPE        47         3         60         51
                             vv
clus                          STAGE IIIC STAGE IV
  AMP PEAK  9(6Q21) MUTATED            3       12
  AMP PEAK  9(6Q21) WILD-TYPE         36       32
D9V3, multiclass
            clus
vv           AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE
  STAGE I                            0                           2
  STAGE IA                           1                          15
  STAGE IB                           9                          32
  STAGE II                           5                          27
  STAGE IIA                          5                          35
  STAGE IIB                          9                          47
  STAGE III                          0                           3
  STAGE IIIA                        21                          60
  STAGE IIIB                        12                          51
  STAGE IIIC                         3                          36
  STAGE IV                          12                          32
[1] 11  2
[1] TRUE
[1] "dimension of 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(6Q21) MUTATED     1  21  33  25
  AMP PEAK  9(6Q21) WILD-TYPE  22  72 163  94
D9V4, multiclass
    clus
vv   AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE
  T1                         1                          22
  T2                        21                          72
  T3                        33                         163
  T4                        25                          94
[1] 4 2
[1] TRUE
[1] "dimension of 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(6Q21) MUTATED    18  26  18  16
  AMP PEAK  9(6Q21) WILD-TYPE 112  93  68  72
D9V5, multiclass
    clus
vv   AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE
  N0                        18                         112
  N1                        26                          93
  N2                        18                          68
  N3                        16                          72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                             cls
clus                            0   1
  AMP PEAK  9(6Q21) MUTATED    70   8
  AMP PEAK  9(6Q21) WILD-TYPE 319  22
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q21) MUTATED     70    8
  AMP PEAK  9(6Q21) WILD-TYPE  319   22
   clus
vv  AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE
  0                        70                         319
  1                         8                          22
[1] 2 2
[1] FALSE
D9V7, binary
                             cls
clus                            0   1
  AMP PEAK  9(6Q21) MUTATED    25  57
  AMP PEAK  9(6Q21) WILD-TYPE 133 226
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q21) MUTATED     25   57
  AMP PEAK  9(6Q21) WILD-TYPE  133  226
        clus
vv       AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE
  FEMALE                        25                         133
  MALE                          57                         226
[1] 2 2
[1] FALSE
D9V8, binary
                             cls
clus                            0   1
  AMP PEAK  9(6Q21) MUTATED    61  15
  AMP PEAK  9(6Q21) WILD-TYPE 261  61
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q21) MUTATED     61   15
  AMP PEAK  9(6Q21) WILD-TYPE  261   61
     clus
vv    AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE
  NO                         61                         261
  YES                        15                          61
[1] 2 2
[1] FALSE
                             vv
clus                          STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK  9(6Q21) MUTATED                                          2
  AMP PEAK  9(6Q21) WILD-TYPE                                       11
                             vv
clus                          STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK  9(6Q21) MUTATED                                       7
  AMP PEAK  9(6Q21) WILD-TYPE                                    65
                             vv
clus                          STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  9(6Q21) MUTATED                                                       28
  AMP PEAK  9(6Q21) WILD-TYPE                                                    135
                             vv
clus                          STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK  9(6Q21) MUTATED                                                   1
  AMP PEAK  9(6Q21) WILD-TYPE                                                20
                             vv
clus                          STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  9(6Q21) MUTATED                                                                  22
  AMP PEAK  9(6Q21) WILD-TYPE                                                                60
                             vv
clus                          STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK  9(6Q21) MUTATED                                                    2
  AMP PEAK  9(6Q21) WILD-TYPE                                                  6
                             vv
clus                          STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK  9(6Q21) MUTATED                                                 19
  AMP PEAK  9(6Q21) WILD-TYPE                                               60
D9V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK  9(6Q21) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                  2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                     7
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                   28
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                         1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        22
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                         19
                                                                   clus
vv                                                                  AMP PEAK  9(6Q21) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                   11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                      65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                    135
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                          20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          60
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  9(6Q21) MUTATED    61   2   6   6
  AMP PEAK  9(6Q21) WILD-TYPE 288  16  13  19
D9V10, multiclass
    clus
vv   AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE
  R0                        61                         288
  R1                         2                          16
  R2                         6                          13
  RX                         6                          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"
D9V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  9(6Q21) MUTATED      15                         4
  AMP PEAK  9(6Q21) WILD-TYPE    73                         8
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  9(6Q21) MUTATED                                           1    49
  AMP PEAK  9(6Q21) WILD-TYPE                                         0   229
D9V12, multiclass
                                           clus
vv                                          AMP PEAK  9(6Q21) MUTATED
  ASIAN                                                            15
  BLACK OR AFRICAN AMERICAN                                         4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         1
  WHITE                                                            49
                                           clus
vv                                          AMP PEAK  9(6Q21) WILD-TYPE
  ASIAN                                                              73
  BLACK OR AFRICAN AMERICAN                                           8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             229
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V13, binary
                             cls
clus                            0   1
  AMP PEAK  9(6Q21) MUTATED     1  55
  AMP PEAK  9(6Q21) WILD-TYPE   4 261
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q21) MUTATED      1   55
  AMP PEAK  9(6Q21) WILD-TYPE    4  261
                        clus
vv                       AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE
  HISPANIC OR LATINO                             1                           4
  NOT HISPANIC OR LATINO                        55                         261
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(7P22.1) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(7P22.1) MUTATED   129  85
  AMP PEAK 10(7P22.1) WILD-TYPE 117  84
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                          214                           201 
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                           85                            84 
$`AMP PEAK 10(7P22.1) MUTATED`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       21.99        22.98        79.07         0.23        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-B7-5818 TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4184 
       27.35        26.93        11.70        11.01         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4257 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 
        4.64        18.35         9.67        17.29        19.33         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7703 
       32.78        25.61        18.05        40.21         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-7958 
       35.24        33.63        39.78        18.15         3.45        29.56 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8284 TCGA-BR-8285 
       33.21        14.43        11.44         0.69         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       29.42         2.20        15.58         7.40         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8370 TCGA-BR-8373 TCGA-BR-8381 
       13.08        22.19         0.95         3.32        14.79         7.36 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8682 TCGA-BR-8683 
        5.39         9.21        20.22         1.12        32.58         9.86 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
        8.22        10.68        13.87         7.53        34.98         1.48 
TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PE 
       12.89         0.72         0.53        32.52        13.51        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8524 
        1.15        21.44        13.02        13.18        12.10        12.76 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.33        12.39        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        6.31        11.31        12.43        11.61         6.58        12.20 
TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       20.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5724 
        4.01        18.97         7.07        12.00        36.00        12.03 
TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 
       28.96         4.01        21.07         7.99        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 
       19.13        18.84        18.54        17.19        15.22        15.98 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8574 TCGA-D7-8575 
       12.36        11.31        12.33        24.72        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        36.43 
TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
       11.31        22.29        15.65        14.47        72.23         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF 
       19.53        14.07        22.29        17.06         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4G6 
        6.21        52.21        26.47        18.15        28.96        24.26 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        25.81        11.77         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
        6.58        20.25         2.10        12.95        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       21.17        33.40         3.45        18.81         3.39        18.38 
TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-KB-A6F5 
       13.35         6.44        12.59         6.51        11.70         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       63.62        37.64        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 
        6.08         8.61       122.30       115.69        57.44         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        5.79        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PF TCGA-VQ-A8PH 
       21.73        37.41        34.29        46.26         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
        2.70        17.85        14.33        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X 
       21.83        18.74        20.81         1.71        60.85         9.50 
TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T 
        2.01         4.54        66.81        21.04        42.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I 
       18.41        43.66        38.93        32.94        54.12        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       27.55        12.43        17.26         0.79 

$`AMP PEAK 10(7P22.1) WILD-TYPE`
TCGA-CG-4444 TCGA-EQ-A4SO TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK 
       47.05        16.24        58.03        26.70        19.56         9.47 
TCGA-B7-A5TN TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        9.44         7.43        30.90         4.08         4.08         9.34 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       13.68        39.12        26.10        19.89        12.16         8.98 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7707 TCGA-BR-7722 
       30.90        31.20        44.94        21.90        35.84        15.32 
TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       28.73         9.07        37.25        29.59         9.60        32.25 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 
        2.66        19.96         0.26        17.52        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 
       14.04        11.80        31.27        25.05         3.72        25.18 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A453 
       26.73        24.79        31.96        20.88        34.13         6.08 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 
       27.55        28.57         8.98        14.17        28.34         0.66 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 
        0.46        20.65        16.14         5.13        13.41        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 
       13.35        11.21        12.59        12.53         7.17        12.30 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-A487 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 
       12.59        11.64        12.30        11.77        12.62         3.02 
TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        1.02        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        9.01        30.97         6.97         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5732 TCGA-D7-5577 
        0.99       105.07        15.02        65.10        69.04        25.71 
TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6817 
       20.55        18.61        17.85        13.35        10.26        12.79 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.80        19.50         5.92        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.24        11.44        20.32         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-8209 
        7.13         0.62         7.99        21.27        11.38        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB TCGA-HU-8238 
        5.03        13.58        77.29        63.06        30.51         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.30         5.59        22.68        24.20        21.37        29.98 
TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
        6.51         0.26        29.00        14.07        15.68        36.36 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X 
       12.46        19.53         6.74        10.62        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A804 
        2.53        36.95         3.72        19.73        14.04         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 
        9.24        11.05         5.13        16.67        37.91        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL 
      116.38        71.38        35.61        16.87        19.04         0.92 
TCGA-VQ-A8E0 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PD 
       18.48        38.14        37.22         7.73        30.97        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       22.19         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91Y 
       29.59        64.57        61.22        32.88        42.64         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P 
       55.56         9.04        55.43         6.58         5.72         2.66 
TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G 
       28.41        17.13        26.04 

  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                          0.1                           0.0 
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                       122.30                        116.38 
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                       14.565                        15.320 
[1] "0.1 - 122.3 (14.6)" "0.0 - 116.4 (15.3)"
[1] "hr=" "1"  
D10V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 10(7P22.1) MUTATED         2        9       21       15        19
  AMP PEAK 10(7P22.1) WILD-TYPE       0        7       20       17        21
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 10(7P22.1) MUTATED          27         2         43         33
  AMP PEAK 10(7P22.1) WILD-TYPE        29         1         38         30
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 10(7P22.1) MUTATED           24       20
  AMP PEAK 10(7P22.1) WILD-TYPE         15       24
D10V3, multiclass
            clus
vv           AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  STAGE I                              2                             0
  STAGE IA                             9                             7
  STAGE IB                            21                            20
  STAGE II                            15                            17
  STAGE IIA                           19                            21
  STAGE IIB                           27                            29
  STAGE III                            2                             1
  STAGE IIIA                          43                            38
  STAGE IIIB                          33                            30
  STAGE IIIC                          24                            15
  STAGE IV                            20                            24
[1] 11  2
[1] TRUE
[1] "dimension of 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(7P22.1) MUTATED    13  44 107  58
  AMP PEAK 10(7P22.1) WILD-TYPE  10  49  89  61
D10V4, multiclass
    clus
vv   AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  T1                          13                            10
  T2                          44                            49
  T3                         107                            89
  T4                          58                            61
[1] 4 2
[1] TRUE
[1] "dimension of 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(7P22.1) MUTATED   67 56 51 46
  AMP PEAK 10(7P22.1) WILD-TYPE 63 63 35 42
D10V5, multiclass
    clus
vv   AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  N0                          67                            63
  N1                          56                            63
  N2                          51                            35
  N3                          46                            42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P22.1) MUTATED   203  13
  AMP PEAK 10(7P22.1) WILD-TYPE 186  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P22.1) MUTATED    203   13
  AMP PEAK 10(7P22.1) WILD-TYPE  186   17
   clus
vv  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  0                         203                           186
  1                          13                            17
[1] 2 2
[1] FALSE
D10V7, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P22.1) MUTATED    72 157
  AMP PEAK 10(7P22.1) WILD-TYPE  86 126
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P22.1) MUTATED     72  157
  AMP PEAK 10(7P22.1) WILD-TYPE   86  126
        clus
vv       AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  FEMALE                          72                            86
  MALE                           157                           126
[1] 2 2
[1] FALSE
D10V8, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P22.1) MUTATED   171  35
  AMP PEAK 10(7P22.1) WILD-TYPE 151  41
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P22.1) MUTATED    171   35
  AMP PEAK 10(7P22.1) WILD-TYPE  151   41
     clus
vv    AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  NO                          171                           151
  YES                          35                            41
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK 10(7P22.1) MUTATED                                          9
  AMP PEAK 10(7P22.1) WILD-TYPE                                        4
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK 10(7P22.1) MUTATED                                      25
  AMP PEAK 10(7P22.1) WILD-TYPE                                    47
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 10(7P22.1) MUTATED                                                       82
  AMP PEAK 10(7P22.1) WILD-TYPE                                                     81
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK 10(7P22.1) MUTATED                                                   8
  AMP PEAK 10(7P22.1) WILD-TYPE                                                13
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 10(7P22.1) MUTATED                                                                  52
  AMP PEAK 10(7P22.1) WILD-TYPE                                                                30
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK 10(7P22.1) MUTATED                                                    5
  AMP PEAK 10(7P22.1) WILD-TYPE                                                  3
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK 10(7P22.1) MUTATED                                                 46
  AMP PEAK 10(7P22.1) WILD-TYPE                                               33
D10V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK 10(7P22.1) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    9
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                      25
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     82
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           8
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          52
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           46
                                                                   clus
vv                                                                  AMP PEAK 10(7P22.1) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      4
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        47
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       81
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            13
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            30
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             33
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 10(7P22.1) MUTATED   185   9   9  12
  AMP PEAK 10(7P22.1) WILD-TYPE 164   9  10  13
D10V10, multiclass
    clus
vv   AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  R0                         185                           164
  R1                           9                             9
  R2                           9                            10
  RX                          12                            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"
D10V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 10(7P22.1) MUTATED      45                         8
  AMP PEAK 10(7P22.1) WILD-TYPE    43                         4
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 10(7P22.1) MUTATED                                           1   143
  AMP PEAK 10(7P22.1) WILD-TYPE                                         0   135
D10V12, multiclass
                                           clus
vv                                          AMP PEAK 10(7P22.1) MUTATED
  ASIAN                                                              45
  BLACK OR AFRICAN AMERICAN                                           8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             143
                                           clus
vv                                          AMP PEAK 10(7P22.1) WILD-TYPE
  ASIAN                                                                43
  BLACK OR AFRICAN AMERICAN                                             4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               135
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V13, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P22.1) MUTATED     3 159
  AMP PEAK 10(7P22.1) WILD-TYPE   2 157
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P22.1) MUTATED      3  159
  AMP PEAK 10(7P22.1) WILD-TYPE    2  157
                        clus
vv                       AMP PEAK 10(7P22.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         159
                        clus
vv                       AMP PEAK 10(7P22.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           157
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(7P11.2) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 11(7P11.2) MUTATED   114  86
  AMP PEAK 11(7P11.2) WILD-TYPE 132  83
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                          200                           215 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                           86                            83 
$`AMP PEAK 11(7P11.2) MUTATED`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       21.99        22.98        79.07         0.23        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-B7-5818 TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4184 
       27.35        26.93        11.70        11.01         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4257 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 
        4.64        18.35         9.67        17.29        19.33         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7703 
       32.78        25.61        18.05        40.21         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 
       35.24        33.63        18.15         3.45        29.56        33.21 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8295 TCGA-BR-8296 
       14.43         0.69         8.05         0.56         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8370 TCGA-BR-8373 
        7.40        13.08        17.52         0.95         3.32        14.79 
TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8682 TCGA-BR-8683 
        7.36         5.39        20.22         1.12        32.58         9.86 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY 
        8.22        10.68        13.87        34.98         1.48        12.89 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PE 
        0.72        14.17         0.53        32.52        13.51        20.42 
TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8526 TCGA-CD-8528 
       21.44        13.02        13.18        12.10        12.53        12.33 
TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       12.39        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 
       11.61         6.58        12.20        20.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 
        7.99         4.01        18.97         7.07        12.00        36.00 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 
       12.03        28.96        21.07         7.99        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 
       19.13        18.84        18.54        17.19        15.22        15.98 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       11.31        12.33        24.72        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EX TCGA-D7-A6F0 
       21.14        20.91        16.44        36.43        11.31        22.29 
TCGA-D7-A6F2 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       15.65        14.47        72.23         3.48        19.53        14.07 
TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7134 TCGA-HJ-7597 
       17.06         0.56         5.52         6.21        52.21        26.47 
TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GF 
        5.92        28.96        24.30        24.26         3.25        25.81 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 
       11.77         8.98         0.10         6.58        20.25         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 
       12.95        29.00        23.84        33.40         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
        3.39        18.38        13.35         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7ZE 
        6.51        11.70         5.56        63.62        37.64        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV 
        8.52        74.53         6.08         8.61        16.67       122.30 
TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
      115.69        57.44         8.94        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8PB 
       13.02        18.48        43.36        21.73        37.41        34.29 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PY 
        2.50        12.79         2.70        17.85         1.87        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91Q 
       73.41        39.45        11.70        21.83        18.74        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 
        1.71        42.64        60.85         9.50        55.56         9.04 
TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA68 
        2.01         4.54        21.04        42.54        11.24        43.66 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       38.93        32.94        54.12        16.14        27.55        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

$`AMP PEAK 11(7P11.2) WILD-TYPE`
TCGA-CG-4444 TCGA-EQ-A4SO TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK 
       47.05        16.24        58.03        26.70        19.56         9.47 
TCGA-B7-A5TN TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        9.44         7.43        30.90         4.08         4.08         9.34 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       13.68        39.12        26.10        19.89        12.16         8.98 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7707 TCGA-BR-7716 
       30.90        31.20        44.94        21.90        35.84        39.78 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8078 
       15.32        28.73         9.07        37.25        11.44        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8360 
        9.60        32.25        29.42         2.66        19.96         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       31.10         0.26        22.19        26.33         4.31        14.04 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 
       11.80        31.27        25.05         3.72        25.18         9.21 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A452 
       26.73        24.79        31.96        20.88        34.13         7.53 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J5 TCGA-BR-A4J6 
        6.08        27.55        28.57         8.98        28.34         0.66 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.65         1.15        16.14         5.13        13.41 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 
       13.15        13.35        11.21        12.76        12.59         7.17 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.30        12.59        11.64        12.30        11.31        12.43 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 
       11.77        12.62         3.02         1.02         8.05        54.08 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       30.97         6.97         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5577 
      105.07        15.02        65.10         4.01        69.04        25.71 
TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6817 
       20.55        18.61        17.85        13.35        10.26        12.79 
TCGA-D7-6818 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YY 
       12.36        16.80        19.50        14.27         5.92        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 
       14.76        26.43        11.24        11.44        20.32         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-A448 
        4.34        19.96         7.13         0.62         7.99        21.27 
TCGA-F1-A72C TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-7132 
       11.38        22.29        59.54         5.03        13.58        77.29 
TCGA-HF-7133 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       63.06        30.51         1.51        24.39        18.15        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 
       22.82        21.07         0.76         5.59        22.68        24.20 
TCGA-HU-A4GD TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H5 
       22.75        21.37        29.98         6.51         0.26        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-A6RJ TCGA-IN-A6RN 
       21.17        14.07        15.68        36.36        12.46        19.53 
TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A93J TCGA-MX-A5UG 
       10.62        15.75        13.51         2.53        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       19.73        14.04        45.67         4.60         9.24        11.05 
TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 
        5.13        37.91        40.64       116.38        71.38        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       16.87        19.04         5.79         0.92        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PO 
        7.73        30.97        46.26        16.31        22.19         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A91K 
       23.41        15.65        13.35        29.59        64.57        61.22 
TCGA-VQ-A91S TCGA-VQ-A91Y TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
       32.88         9.73        55.43         6.58         5.72        66.81 
TCGA-VQ-A94P TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G 
        2.66        18.41        28.41        17.13        26.04 

  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                          0.1                           0.0 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                       122.30                        116.38 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                       14.565                        15.320 
[1] "0.1 - 122.3 (14.6)" "0.0 - 116.4 (15.3)"
[1] "hr=" "1.2"
D11V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 11(7P11.2) MUTATED         2        9       20       12        16
  AMP PEAK 11(7P11.2) WILD-TYPE       0        7       21       20        24
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 11(7P11.2) MUTATED          26         2         42         31
  AMP PEAK 11(7P11.2) WILD-TYPE        30         1         39         32
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 11(7P11.2) MUTATED           22       19
  AMP PEAK 11(7P11.2) WILD-TYPE         17       25
D11V3, multiclass
            clus
vv           AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  STAGE I                              2                             0
  STAGE IA                             9                             7
  STAGE IB                            20                            21
  STAGE II                            12                            20
  STAGE IIA                           16                            24
  STAGE IIB                           26                            30
  STAGE III                            2                             1
  STAGE IIIA                          42                            39
  STAGE IIIB                          31                            32
  STAGE IIIC                          22                            17
  STAGE IV                            19                            25
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 11(7P11.2) MUTATED    13  38 100  56
  AMP PEAK 11(7P11.2) WILD-TYPE  10  55  96  63
D11V4, multiclass
    clus
vv   AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  T1                          13                            10
  T2                          38                            55
  T3                         100                            96
  T4                          56                            63
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK 11(7P11.2) MUTATED   62 54 45 45
  AMP PEAK 11(7P11.2) WILD-TYPE 68 65 41 43
D11V5, multiclass
    clus
vv   AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  N0                          62                            68
  N1                          54                            65
  N2                          45                            41
  N3                          45                            43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                               cls
clus                              0   1
  AMP PEAK 11(7P11.2) MUTATED   192  11
  AMP PEAK 11(7P11.2) WILD-TYPE 197  19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED    192   11
  AMP PEAK 11(7P11.2) WILD-TYPE  197   19
   clus
vv  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  0                         192                           197
  1                          11                            19
[1] 2 2
[1] FALSE
D11V7, binary
                               cls
clus                              0   1
  AMP PEAK 11(7P11.2) MUTATED    68 146
  AMP PEAK 11(7P11.2) WILD-TYPE  90 137
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED     68  146
  AMP PEAK 11(7P11.2) WILD-TYPE   90  137
        clus
vv       AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  FEMALE                          68                            90
  MALE                           146                           137
[1] 2 2
[1] FALSE
D11V8, binary
                               cls
clus                              0   1
  AMP PEAK 11(7P11.2) MUTATED   159  34
  AMP PEAK 11(7P11.2) WILD-TYPE 163  42
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED    159   34
  AMP PEAK 11(7P11.2) WILD-TYPE  163   42
     clus
vv    AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  NO                          159                           163
  YES                          34                            42
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK 11(7P11.2) MUTATED                                          9
  AMP PEAK 11(7P11.2) WILD-TYPE                                        4
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK 11(7P11.2) MUTATED                                      25
  AMP PEAK 11(7P11.2) WILD-TYPE                                    47
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 11(7P11.2) MUTATED                                                       76
  AMP PEAK 11(7P11.2) WILD-TYPE                                                     87
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK 11(7P11.2) MUTATED                                                   7
  AMP PEAK 11(7P11.2) WILD-TYPE                                                14
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 11(7P11.2) MUTATED                                                                  48
  AMP PEAK 11(7P11.2) WILD-TYPE                                                                34
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK 11(7P11.2) MUTATED                                                    3
  AMP PEAK 11(7P11.2) WILD-TYPE                                                  5
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK 11(7P11.2) MUTATED                                                 44
  AMP PEAK 11(7P11.2) WILD-TYPE                                               35
D11V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK 11(7P11.2) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    9
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                      25
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     76
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           7
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          48
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           44
                                                                   clus
vv                                                                  AMP PEAK 11(7P11.2) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      4
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        47
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       87
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            14
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            34
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             35
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 11(7P11.2) MUTATED   175   9   8  11
  AMP PEAK 11(7P11.2) WILD-TYPE 174   9  11  14
D11V10, multiclass
    clus
vv   AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  R0                         175                           174
  R1                           9                             9
  R2                           8                            11
  RX                          11                            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"
D11V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 11(7P11.2) MUTATED      42                         9
  AMP PEAK 11(7P11.2) WILD-TYPE    46                         3
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 11(7P11.2) MUTATED                                           1   131
  AMP PEAK 11(7P11.2) WILD-TYPE                                         0   147
D11V12, multiclass
                                           clus
vv                                          AMP PEAK 11(7P11.2) MUTATED
  ASIAN                                                              42
  BLACK OR AFRICAN AMERICAN                                           9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             131
                                           clus
vv                                          AMP PEAK 11(7P11.2) WILD-TYPE
  ASIAN                                                                46
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               147
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V13, binary
                               cls
clus                              0   1
  AMP PEAK 11(7P11.2) MUTATED     1 147
  AMP PEAK 11(7P11.2) WILD-TYPE   4 169
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED      1  147
  AMP PEAK 11(7P11.2) WILD-TYPE    4  169
                        clus
vv                       AMP PEAK 11(7P11.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         147
                        clus
vv                       AMP PEAK 11(7P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           169
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(7Q21.2) MUTATION ANALYSIS
D12V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 12(7Q21.2) MUTATED   113  77
  AMP PEAK 12(7Q21.2) WILD-TYPE 133  92
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                          190                           225 
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                           77                            92 
$`AMP PEAK 12(7Q21.2) MUTATED`
TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-B7-5818 
       22.98        79.07         0.23        20.15         9.86        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 
       19.56        11.01         9.44         6.97         4.64        18.35 
TCGA-BR-4257 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
        9.67        17.29        19.33        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       25.61        18.05        40.21         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8284 
       33.63        29.56        33.21        14.43        11.44         8.05 
TCGA-BR-8285 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8365 
        0.56         2.20        15.58         7.40        13.08        17.52 
TCGA-BR-8366 TCGA-BR-8370 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8484 
        0.95         3.32        14.79         7.36         5.39        25.18 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44U 
       20.22         1.12        32.58         9.86        10.68        13.87 
TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4PD 
       12.89         0.72        14.17         0.53        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8527 
       20.42         1.15        13.02        13.18        12.10         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.33        12.30        12.39        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.43         6.31        12.43        11.61         6.58        12.20 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4438 
       20.02         3.02        27.02        15.95         7.99        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
        4.01        14.01        12.03        18.97         7.07        12.00 
TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5733 TCGA-D7-5578 
       36.00        12.03        15.02        28.96        21.07        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 
       20.91        19.13        18.84        18.54        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8573 
       10.26        15.22        15.98        12.79        24.72        19.50 
TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YX 
       17.19        14.66        21.14        20.91        16.44        36.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-F1-6874 TCGA-F1-6875 
       11.24        11.31        22.29        15.65        14.47        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A9TM 
        3.48        19.53        22.29        17.06         0.56         6.21 
TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-A4G2 TCGA-HU-A4G6 
       52.21        26.47         5.92        28.96        24.30        24.26 
TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 
       25.81         8.98         0.10         6.58        20.25         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RP 
       12.95        29.00         3.45         3.39        13.35         6.44 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-R5-A7ZF 
        6.51        10.62        11.70         5.56        63.62         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 
       74.53         6.08         8.61       122.30        37.91       115.69 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 
       57.44         8.94        48.79        13.25        18.48        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PB TCGA-VQ-A8PF TCGA-VQ-A8PH 
       21.73        37.41         7.73        34.29         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
        2.70        17.85         1.87        14.33        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       11.70        21.83        20.81        32.88         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O 
       60.85         9.50         2.01         4.54        66.81        21.04 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       42.54        11.24        18.41        38.93        32.94        54.12 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        27.55        17.26         0.79 

$`AMP PEAK 12(7Q21.2) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-EQ-A4SO TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 
       47.05        21.99        16.24        27.35        26.93        58.03 
TCGA-B7-5816 TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 
       26.70         9.47         6.61         7.43        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6707 TCGA-BR-6709 
       15.95        13.87        13.68        39.12        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7707 
        8.98        30.90        31.20        44.94        21.90        35.84 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8286 
       37.25         0.69        29.59         9.60        32.25        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.66        19.96         6.18        31.10         0.26        22.19 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8382 
       26.33         4.31        14.04        11.80        31.27        25.05 
TCGA-BR-8384 TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        3.72         9.21        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 
        6.28         7.53        26.73        24.79        31.96        20.88 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
        8.22        34.13         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
       27.55        28.57         8.98        28.34         0.66        32.52 
TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 
        0.46        21.44        16.14         5.13        13.41        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8531 
       13.35        11.21        12.76        12.59        12.53        12.59 
TCGA-CD-8532 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4306 
       11.64        12.30        11.31        11.77        12.62         1.02 
TCGA-CG-4437 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4477 
        8.05        29.98        19.07         0.00         9.01        30.97 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.97         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6519 
       65.10         4.01        69.04         7.99        25.71        20.55 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 
       18.61        17.85        12.36        11.31        12.33        16.80 
TCGA-D7-8575 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       18.21        14.27         5.92        13.78        14.76        26.43 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.44        20.32         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8209 
        0.62         7.99        21.27        11.38        14.07        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB 
        5.03        13.58         5.52        77.29        63.06        30.51 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        1.51        24.39        18.15        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        0.76         5.59        22.68        24.20         3.25        22.75 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H4 
       11.77        21.37        29.98         6.51         0.26        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS 
       18.81        18.38        12.46        19.53         6.74        12.59 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG 
       15.75        13.51         2.53        37.64        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A804 TCGA-R5-A805 
       19.73        14.04        45.67        18.21         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
       11.05         5.13        16.67        40.64       116.38        71.38 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU 
       35.61        16.87        19.04         5.79         0.92         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PC TCGA-VQ-A8PD 
       13.02        38.14        37.22        30.97        46.26        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
       22.19         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PX TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       64.57        61.22        18.74         9.73        55.56         9.04 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-AA68 TCGA-VQ-AA69 
       55.43         6.58         5.72         2.66        43.66        28.41 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6K 
       17.13        26.04        12.43 

  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                          0.1                           0.0 
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                       122.30                        116.38 
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                        14.45                         15.68 
[1] "0.1 - 122.3 (14.4)" "0.0 - 116.4 (15.7)"
[1] "hr=" "1"  
D12V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 12(7Q21.2) MUTATED         1        7       20       15        18
  AMP PEAK 12(7Q21.2) WILD-TYPE       1        9       21       17        22
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 12(7Q21.2) MUTATED          24         2         34         33
  AMP PEAK 12(7Q21.2) WILD-TYPE        32         1         47         30
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 12(7Q21.2) MUTATED           19       17
  AMP PEAK 12(7Q21.2) WILD-TYPE         20       27
D12V3, multiclass
            clus
vv           AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             7                             9
  STAGE IB                            20                            21
  STAGE II                            15                            17
  STAGE IIA                           18                            22
  STAGE IIB                           24                            32
  STAGE III                            2                             1
  STAGE IIIA                          34                            47
  STAGE IIIB                          33                            30
  STAGE IIIC                          19                            20
  STAGE IV                            17                            27
[1] 11  2
[1] TRUE
[1] "dimension of 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(7Q21.2) MUTATED    10  43  94  50
  AMP PEAK 12(7Q21.2) WILD-TYPE  13  50 102  69
D12V4, multiclass
    clus
vv   AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  T1                          10                            13
  T2                          43                            50
  T3                          94                           102
  T4                          50                            69
[1] 4 2
[1] TRUE
[1] "dimension of 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(7Q21.2) MUTATED   62 45 46 42
  AMP PEAK 12(7Q21.2) WILD-TYPE 68 74 40 46
D12V5, multiclass
    clus
vv   AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  N0                          62                            68
  N1                          45                            74
  N2                          46                            40
  N3                          42                            46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                               cls
clus                              0   1
  AMP PEAK 12(7Q21.2) MUTATED   181  11
  AMP PEAK 12(7Q21.2) WILD-TYPE 208  19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7Q21.2) MUTATED    181   11
  AMP PEAK 12(7Q21.2) WILD-TYPE  208   19
   clus
vv  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  0                         181                           208
  1                          11                            19
[1] 2 2
[1] FALSE
D12V7, binary
                               cls
clus                              0   1
  AMP PEAK 12(7Q21.2) MUTATED    62 142
  AMP PEAK 12(7Q21.2) WILD-TYPE  96 141
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7Q21.2) MUTATED     62  142
  AMP PEAK 12(7Q21.2) WILD-TYPE   96  141
        clus
vv       AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  FEMALE                          62                            96
  MALE                           142                           141
[1] 2 2
[1] FALSE
D12V8, binary
                               cls
clus                              0   1
  AMP PEAK 12(7Q21.2) MUTATED   144  37
  AMP PEAK 12(7Q21.2) WILD-TYPE 178  39
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7Q21.2) MUTATED    144   37
  AMP PEAK 12(7Q21.2) WILD-TYPE  178   39
     clus
vv    AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  NO                          144                           178
  YES                          37                            39
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK 12(7Q21.2) MUTATED                                          5
  AMP PEAK 12(7Q21.2) WILD-TYPE                                        8
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK 12(7Q21.2) MUTATED                                      26
  AMP PEAK 12(7Q21.2) WILD-TYPE                                    46
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 12(7Q21.2) MUTATED                                                       75
  AMP PEAK 12(7Q21.2) WILD-TYPE                                                     88
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK 12(7Q21.2) MUTATED                                                   8
  AMP PEAK 12(7Q21.2) WILD-TYPE                                                13
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 12(7Q21.2) MUTATED                                                                  50
  AMP PEAK 12(7Q21.2) WILD-TYPE                                                                32
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK 12(7Q21.2) MUTATED                                                    4
  AMP PEAK 12(7Q21.2) WILD-TYPE                                                  4
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK 12(7Q21.2) MUTATED                                                 34
  AMP PEAK 12(7Q21.2) WILD-TYPE                                               45
D12V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK 12(7Q21.2) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                      26
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     75
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           8
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          50
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           34
                                                                   clus
vv                                                                  AMP PEAK 12(7Q21.2) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        46
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       88
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            13
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            32
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             45
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 12(7Q21.2) MUTATED   169   5   7  11
  AMP PEAK 12(7Q21.2) WILD-TYPE 180  13  12  14
D12V10, multiclass
    clus
vv   AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  R0                         169                           180
  R1                           5                            13
  R2                           7                            12
  RX                          11                            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"
D12V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 12(7Q21.2) MUTATED      37                         9
  AMP PEAK 12(7Q21.2) WILD-TYPE    51                         3
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 12(7Q21.2) MUTATED                                           1   126
  AMP PEAK 12(7Q21.2) WILD-TYPE                                         0   152
D12V12, multiclass
                                           clus
vv                                          AMP PEAK 12(7Q21.2) MUTATED
  ASIAN                                                              37
  BLACK OR AFRICAN AMERICAN                                           9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             126
                                           clus
vv                                          AMP PEAK 12(7Q21.2) WILD-TYPE
  ASIAN                                                                51
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               152
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V13, binary
                               cls
clus                              0   1
  AMP PEAK 12(7Q21.2) MUTATED     2 140
  AMP PEAK 12(7Q21.2) WILD-TYPE   3 176
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7Q21.2) MUTATED      2  140
  AMP PEAK 12(7Q21.2) WILD-TYPE    3  176
                        clus
vv                       AMP PEAK 12(7Q21.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         140
                        clus
vv                       AMP PEAK 12(7Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           176
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(7Q22.1) MUTATION ANALYSIS
D13V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 13(7Q22.1) MUTATED   111  77
  AMP PEAK 13(7Q22.1) WILD-TYPE 135  92
  AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE 
                          188                           227 
  AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE 
                           77                            92 
$`AMP PEAK 13(7Q22.1) MUTATED`
TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-B7-5818 TCGA-B7-A5TI 
       79.07         0.23        20.15         9.86        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4255 
       11.01         9.44         6.97         4.64        18.35         4.08 
TCGA-BR-4257 TCGA-BR-6456 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
        9.67        17.29        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       18.05        40.21         9.21        36.16        35.24        33.63 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8284 TCGA-BR-8285 
       29.56        33.21        14.43        11.44         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8365 
       29.42         2.20        15.58         7.40        13.08        17.52 
TCGA-BR-8366 TCGA-BR-8370 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8486 
        0.95         3.32        14.79         7.36         5.39        20.22 
TCGA-BR-8487 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4IY 
        1.12        32.58         9.86        10.68        13.87        12.89 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.72        14.17         0.53        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8527 
       20.42         1.15        21.44        13.18        12.10         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 
       12.33        12.30        12.39        15.39        12.07        12.43 
TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 
        6.31        12.43        11.61         6.58        12.20        20.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       27.02        15.95         7.99         4.01        14.01        29.98 
TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5724 
       12.03        18.97         7.07        12.00        36.00        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5733 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       15.02        28.96        21.07        12.66        20.91        19.13 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.84        18.54        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       15.98        12.79        24.72        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EV 
       14.66        21.14        20.91        16.44        36.43        11.24 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7998 
       22.29        15.65        14.47        72.23         3.48        22.29 
TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8243 
       17.06         0.56         6.21        52.21        26.47         5.92 
TCGA-HU-8249 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GP 
       28.96        24.30        24.26         3.25        25.81         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-IN-7808 
        0.10        20.25         2.10        12.95        29.00         3.45 
TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        3.39        13.35         6.44         6.51        10.62        11.70 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
        5.56        63.62        45.67         8.52        74.53         6.08 
TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-VQ-A8DT 
        8.61       122.30        37.91       115.69        57.44        48.79 
TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P5 
       13.25        18.48        43.36        21.73        37.41         7.73 
TCGA-VQ-A8PB TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       34.29        22.19         2.50         2.70        17.85         1.87 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91Q 
       14.33        73.41        39.45        11.70        21.83        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A923 
       32.88         1.71        42.64        60.85         9.50         2.01 
TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
        4.54        66.81        21.04        42.54        11.24        18.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        17.13        54.12        16.14        27.55 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

$`AMP PEAK 13(7Q22.1) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-VQ-A8PU TCGA-VQ-A94U 
       47.05        21.99        22.98        16.24        27.35        26.93 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4188 TCGA-BR-4201 
       58.03        26.70         9.47         6.61         7.43        30.90 
TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6707 
       15.95        13.87        13.68        19.33        39.12        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
       12.16         8.98        30.90        31.20        44.94        21.90 
TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       35.84        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
        9.07        37.25         0.69        29.59         9.60        32.25 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.66        19.96         6.18        31.10         0.26        22.19 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8382 
       26.33         4.31        14.04        11.80        31.27        25.05 
TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        3.72        25.18         9.21        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       20.88         8.22        34.13         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J5 TCGA-BR-A4J6 
        1.48        27.55        28.57         8.98        28.34         0.66 
TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        0.46        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8531 
       13.35        11.21        12.76        12.59        12.53        12.59 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.64        12.82        12.30        11.31        11.77        12.62 
TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-4462 
        3.02         1.02         8.05        54.08        19.07         0.00 
TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        9.01        30.97         6.97         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
        0.99       105.07        65.10         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6818 TCGA-D7-6820 
       25.71        20.55        18.61        17.85        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 
       12.33        16.80        14.27         5.92        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 
       26.43        11.31        11.44        20.32         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-A448 TCGA-F1-A72C 
       19.96         7.13         0.62         7.99        21.27        11.38 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF 
       19.53        14.07        59.54         5.03        13.58         5.52 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
       77.29        63.06        30.51         1.51        24.39        18.15 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 
       22.32        22.82        21.07         0.76         5.59        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT 
       24.20        22.75        11.77        21.37        29.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        6.58         0.26        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ 
       15.68        33.40        36.36        18.81        18.38        12.46 
TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
       19.53         6.74        12.59        15.75        13.51         2.53 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE 
       37.64        36.95         3.72        19.73        14.04        18.21 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N0 
        4.60         9.24        11.05         5.13        16.67        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38         8.94        35.61        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        5.79         0.92         5.46        13.02        38.14        37.22 
TCGA-VQ-A8P8 TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PH TCGA-VQ-A8PO TCGA-VQ-A8PP 
       30.97        46.26        16.31        12.79         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A91K TCGA-VQ-A91N 
       15.65        13.35        29.59        64.57        61.22        18.74 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
        9.73        55.56         9.04        55.43         6.58         5.72 
TCGA-VQ-A94P TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6G TCGA-VQ-AA6K 
        2.66        43.66        28.41        26.04        12.43 

  AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE 
                          0.1                           0.0 
  AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE 
                       122.30                        116.38 
  AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE 
                        15.12                         14.27 
[1] "0.1 - 122.3 (15.1)" "0.0 - 116.4 (14.3)"
[1] "hr=" "1"  
D13V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 13(7Q22.1) MUTATED         1        8       20       15        19
  AMP PEAK 13(7Q22.1) WILD-TYPE       1        8       21       17        21
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 13(7Q22.1) MUTATED          21         2         33         34
  AMP PEAK 13(7Q22.1) WILD-TYPE        35         1         48         29
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 13(7Q22.1) MUTATED           19       16
  AMP PEAK 13(7Q22.1) WILD-TYPE         20       28
D13V3, multiclass
            clus
vv           AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             8                             8
  STAGE IB                            20                            21
  STAGE II                            15                            17
  STAGE IIA                           19                            21
  STAGE IIB                           21                            35
  STAGE III                            2                             1
  STAGE IIIA                          33                            48
  STAGE IIIB                          34                            29
  STAGE IIIC                          19                            20
  STAGE IV                            16                            28
[1] 11  2
[1] TRUE
[1] "dimension of 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(7Q22.1) MUTATED    11  41  93  50
  AMP PEAK 13(7Q22.1) WILD-TYPE  12  52 103  69
D13V4, multiclass
    clus
vv   AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE
  T1                          11                            12
  T2                          41                            52
  T3                          93                           103
  T4                          50                            69
[1] 4 2
[1] TRUE
[1] "dimension of 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(7Q22.1) MUTATED   65 40 45 42
  AMP PEAK 13(7Q22.1) WILD-TYPE 65 79 41 46
D13V5, multiclass
    clus
vv   AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE
  N0                          65                            65
  N1                          40                            79
  N2                          45                            41
  N3                          42                            46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                               cls
clus                              0   1
  AMP PEAK 13(7Q22.1) MUTATED   179  11
  AMP PEAK 13(7Q22.1) WILD-TYPE 210  19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7Q22.1) MUTATED    179   11
  AMP PEAK 13(7Q22.1) WILD-TYPE  210   19
   clus
vv  AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE
  0                         179                           210
  1                          11                            19
[1] 2 2
[1] FALSE
D13V7, binary
                               cls
clus                              0   1
  AMP PEAK 13(7Q22.1) MUTATED    61 141
  AMP PEAK 13(7Q22.1) WILD-TYPE  97 142
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7Q22.1) MUTATED     61  141
  AMP PEAK 13(7Q22.1) WILD-TYPE   97  142
        clus
vv       AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE
  FEMALE                          61                            97
  MALE                           141                           142
[1] 2 2
[1] FALSE
D13V8, binary
                               cls
clus                              0   1
  AMP PEAK 13(7Q22.1) MUTATED   144  36
  AMP PEAK 13(7Q22.1) WILD-TYPE 178  40
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7Q22.1) MUTATED    144   36
  AMP PEAK 13(7Q22.1) WILD-TYPE  178   40
     clus
vv    AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE
  NO                          144                           178
  YES                          36                            40
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK 13(7Q22.1) MUTATED                                          5
  AMP PEAK 13(7Q22.1) WILD-TYPE                                        8
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK 13(7Q22.1) MUTATED                                      26
  AMP PEAK 13(7Q22.1) WILD-TYPE                                    46
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 13(7Q22.1) MUTATED                                                       74
  AMP PEAK 13(7Q22.1) WILD-TYPE                                                     89
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK 13(7Q22.1) MUTATED                                                   8
  AMP PEAK 13(7Q22.1) WILD-TYPE                                                13
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 13(7Q22.1) MUTATED                                                                  48
  AMP PEAK 13(7Q22.1) WILD-TYPE                                                                34
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK 13(7Q22.1) MUTATED                                                    4
  AMP PEAK 13(7Q22.1) WILD-TYPE                                                  4
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK 13(7Q22.1) MUTATED                                                 36
  AMP PEAK 13(7Q22.1) WILD-TYPE                                               43
D13V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK 13(7Q22.1) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                      26
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     74
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           8
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          48
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           36
                                                                   clus
vv                                                                  AMP PEAK 13(7Q22.1) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        46
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       89
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            13
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            34
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             43
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 13(7Q22.1) MUTATED   168   4   6  12
  AMP PEAK 13(7Q22.1) WILD-TYPE 181  14  13  13
D13V10, multiclass
    clus
vv   AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE
  R0                         168                           181
  R1                           4                            14
  R2                           6                            13
  RX                          12                            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"
D13V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 13(7Q22.1) MUTATED      36                         9
  AMP PEAK 13(7Q22.1) WILD-TYPE    52                         3
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 13(7Q22.1) MUTATED                                           1   126
  AMP PEAK 13(7Q22.1) WILD-TYPE                                         0   152
D13V12, multiclass
                                           clus
vv                                          AMP PEAK 13(7Q22.1) MUTATED
  ASIAN                                                              36
  BLACK OR AFRICAN AMERICAN                                           9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             126
                                           clus
vv                                          AMP PEAK 13(7Q22.1) WILD-TYPE
  ASIAN                                                                52
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               152
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V13, binary
                               cls
clus                              0   1
  AMP PEAK 13(7Q22.1) MUTATED     3 138
  AMP PEAK 13(7Q22.1) WILD-TYPE   2 178
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7Q22.1) MUTATED      3  138
  AMP PEAK 13(7Q22.1) WILD-TYPE    2  178
                        clus
vv                       AMP PEAK 13(7Q22.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         138
                        clus
vv                       AMP PEAK 13(7Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           178
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(8P23.1) MUTATION ANALYSIS
D14V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 14(8P23.1) MUTATED   100  64
  AMP PEAK 14(8P23.1) WILD-TYPE 146 105
  AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE 
                          164                           251 
  AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE 
                           64                           105 
$`AMP PEAK 14(8P23.1) MUTATED`
TCGA-CG-4460 TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-B7-5816 
       21.99        20.15         9.86        27.35        26.93        26.70 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4201 
       11.01         9.47         6.61         6.97         4.64        30.90 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        4.08         9.34         9.67        34.68        15.95        13.87 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6802 TCGA-BR-6803 
       13.68        19.33        25.61        19.89        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7957 TCGA-BR-8060 
       44.94        35.24        35.84        18.15         9.07        11.44 
TCGA-BR-8078 TCGA-BR-8284 TCGA-BR-8289 TCGA-BR-8297 TCGA-BR-8368 TCGA-BR-8369 
       29.59         8.05         2.66         7.40         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8484 
        3.32        31.27         7.36        25.05         5.39        25.18 
TCGA-BR-8486 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-A4CQ TCGA-BR-A4CS 
       20.22         9.34        28.14         7.53        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE 
       27.55        14.17        28.34        32.52         0.46        20.42 
TCGA-BR-A4QL TCGA-CD-5799 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8530 TCGA-CD-8536 
       16.14        13.02        11.21        12.76        12.39        12.43 
TCGA-CD-A487 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4441 
       12.30        11.61         6.58        12.62        15.95        14.01 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5722 
       12.03         0.00        18.97         7.07        12.00         0.99 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6524 
       28.96        65.10        21.07        12.66        20.91        17.85 
TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8575 
       10.26        12.79        12.36        11.31        12.33        18.21 
TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6EV 
       14.66        20.91         5.92        36.43        14.76        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-F1-A448 
       11.31        11.44        22.29         8.38         4.34        21.27 
TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 
       19.53        17.06         5.52         6.21        77.29        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-A4G2 TCGA-HU-A4G6 
       30.51        26.47        24.39        22.32        24.30        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP 
       22.68        24.20         3.25        25.81        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        0.10         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-A6RL TCGA-IN-A6RS TCGA-IN-A7NT 
       23.80        14.07        15.68        13.35        12.59        10.62 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZI TCGA-R5-A7ZR 
       63.62        37.64        19.73        45.67        74.53         6.08 
TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DT 
       16.67       115.69        35.61        16.87        19.04        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE 
        5.46        38.14        30.97        34.29        16.31        22.19 
TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY 
        2.70         9.27        23.41        29.59        64.57        14.33 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W 
       21.83        61.22        18.74        20.81        42.64        60.85 
TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA6I TCGA-VQ-AA6J 
        4.54         5.72        21.04        42.54        16.14        27.55 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

$`AMP PEAK 14(8P23.1) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-3M-AB46 
       47.05        22.98        79.07        16.24         0.23        58.03 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
       11.70        19.56         9.44         7.43        18.35         4.08 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6456 TCGA-BR-6563 TCGA-BR-6564 
        6.18         9.57         6.61        17.29        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
        9.17        32.78        18.05        12.16         8.98        40.21 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 
       21.90         9.21        36.16        33.63        39.78        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       28.73         3.45        29.56        33.21        37.25        14.43 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 
        0.69         9.60        32.25         0.56        29.42        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
        2.20        15.58         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8371 TCGA-BR-8373 
       22.19        17.52         0.95        26.33        11.80        14.79 
TCGA-BR-8384 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8592 
        3.72         9.21         1.12        12.79        27.12         6.28 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J6 
       28.57        12.89         8.98         0.72         0.53         0.66 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       13.51        20.65         1.15        21.44         5.13        13.41 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8526 
       13.15        13.18        13.35        12.10        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        7.17        12.33        12.30        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH 
       12.07        12.82         6.31        11.31        12.43        12.20 
TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       11.77        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4465 
        8.05        54.08         4.01        29.98        19.07         9.01 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
      105.07        12.03        15.02         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       25.71        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-8570 TCGA-D7-8572 
       13.35        17.19        15.22        15.98        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YY 
       19.50        17.19        21.14        14.27        16.44        13.78 
TCGA-D7-A6ET TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       26.43        20.32        15.65        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 
        7.99        14.47        72.23        11.38         3.48        14.07 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-7133 
       22.29        59.54         5.03        13.58         0.56        63.06 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        18.15        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GT 
        0.76         5.59        22.75        11.77        21.37         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
        6.58        20.25        21.17        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP 
       18.81         3.39        18.38        12.46        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.74         6.51        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        5.56        36.95         3.72        14.04        18.21         8.52 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV 
        4.60         9.24        11.05         8.61         5.13       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       37.91        40.64       116.38        71.38        57.44         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
        5.79         0.92        13.25        13.02        18.48        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PF 
       21.73        37.41        37.22         7.73        46.26         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PZ 
       12.79        17.85         1.87        15.65        13.35        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y 
       39.45        11.70        32.88         1.71         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A92D 
       55.56         9.04         2.01        55.43         6.58        66.81 
TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
        2.66        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6K 
       32.94        17.13        54.12        26.04        12.43 

  AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE 
                         0.00                          0.23 
  AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE 
                       115.69                        122.30 
  AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE 
                        16.77                         13.78 
[1] "0.0 - 115.7 (16.8)" "0.2 - 122.3 (13.8)"
[1] "hr=" "1.2"
D14V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 14(8P23.1) MUTATED         0        8       19       13        13
  AMP PEAK 14(8P23.1) WILD-TYPE       2        8       22       19        27
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 14(8P23.1) MUTATED          29         1         31         19
  AMP PEAK 14(8P23.1) WILD-TYPE        27         2         50         44
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 14(8P23.1) MUTATED           15       18
  AMP PEAK 14(8P23.1) WILD-TYPE         24       26
D14V3, multiclass
            clus
vv           AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             8                             8
  STAGE IB                            19                            22
  STAGE II                            13                            19
  STAGE IIA                           13                            27
  STAGE IIB                           29                            27
  STAGE III                            1                             2
  STAGE IIIA                          31                            50
  STAGE IIIB                          19                            44
  STAGE IIIC                          15                            24
  STAGE IV                            18                            26
[1] 11  2
[1] TRUE
[1] "dimension of 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(8P23.1) MUTATED    12  41  69  49
  AMP PEAK 14(8P23.1) WILD-TYPE  11  52 127  70
D14V4, multiclass
    clus
vv   AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE
  T1                          12                            11
  T2                          41                            52
  T3                          69                           127
  T4                          49                            70
[1] 4 2
[1] TRUE
[1] "dimension of 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(8P23.1) MUTATED   51 49 31 35
  AMP PEAK 14(8P23.1) WILD-TYPE 79 70 55 53
D14V5, multiclass
    clus
vv   AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE
  N0                          51                            79
  N1                          49                            70
  N2                          31                            55
  N3                          35                            53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                               cls
clus                              0   1
  AMP PEAK 14(8P23.1) MUTATED   160  10
  AMP PEAK 14(8P23.1) WILD-TYPE 229  20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(8P23.1) MUTATED    160   10
  AMP PEAK 14(8P23.1) WILD-TYPE  229   20
   clus
vv  AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE
  0                         160                           229
  1                          10                            20
[1] 2 2
[1] FALSE
D14V7, binary
                               cls
clus                              0   1
  AMP PEAK 14(8P23.1) MUTATED    76 101
  AMP PEAK 14(8P23.1) WILD-TYPE  82 182
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(8P23.1) MUTATED     76  101
  AMP PEAK 14(8P23.1) WILD-TYPE   82  182
        clus
vv       AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE
  FEMALE                          76                            82
  MALE                           101                           182
[1] 2 2
[1] FALSE
D14V8, binary
                               cls
clus                              0   1
  AMP PEAK 14(8P23.1) MUTATED   130  30
  AMP PEAK 14(8P23.1) WILD-TYPE 192  46
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(8P23.1) MUTATED    130   30
  AMP PEAK 14(8P23.1) WILD-TYPE  192   46
     clus
vv    AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE
  NO                          130                           192
  YES                          30                            46
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK 14(8P23.1) MUTATED                                          5
  AMP PEAK 14(8P23.1) WILD-TYPE                                        8
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK 14(8P23.1) MUTATED                                      30
  AMP PEAK 14(8P23.1) WILD-TYPE                                    42
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 14(8P23.1) MUTATED                                                       59
  AMP PEAK 14(8P23.1) WILD-TYPE                                                    104
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK 14(8P23.1) MUTATED                                                  10
  AMP PEAK 14(8P23.1) WILD-TYPE                                                11
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 14(8P23.1) MUTATED                                                                  34
  AMP PEAK 14(8P23.1) WILD-TYPE                                                                48
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK 14(8P23.1) MUTATED                                                    5
  AMP PEAK 14(8P23.1) WILD-TYPE                                                  3
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK 14(8P23.1) MUTATED                                                 33
  AMP PEAK 14(8P23.1) WILD-TYPE                                               46
D14V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK 14(8P23.1) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                      30
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     59
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                          10
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          34
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           33
                                                                   clus
vv                                                                  AMP PEAK 14(8P23.1) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        42
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      104
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            11
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            48
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             46
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 14(8P23.1) MUTATED   138   8   6  14
  AMP PEAK 14(8P23.1) WILD-TYPE 211  10  13  11
D14V10, multiclass
    clus
vv   AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE
  R0                         138                           211
  R1                           8                            10
  R2                           6                            13
  RX                          14                            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"
D14V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 14(8P23.1) MUTATED      34                         4
  AMP PEAK 14(8P23.1) WILD-TYPE    54                         8
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 14(8P23.1) MUTATED                                           0   112
  AMP PEAK 14(8P23.1) WILD-TYPE                                         1   166
D14V12, multiclass
                                           clus
vv                                          AMP PEAK 14(8P23.1) MUTATED
  ASIAN                                                              34
  BLACK OR AFRICAN AMERICAN                                           4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             112
                                           clus
vv                                          AMP PEAK 14(8P23.1) WILD-TYPE
  ASIAN                                                                54
  BLACK OR AFRICAN AMERICAN                                             8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V13, binary
                               cls
clus                              0   1
  AMP PEAK 14(8P23.1) MUTATED     3 125
  AMP PEAK 14(8P23.1) WILD-TYPE   2 191
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(8P23.1) MUTATED      3  125
  AMP PEAK 14(8P23.1) WILD-TYPE    2  191
                        clus
vv                       AMP PEAK 14(8P23.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         125
                        clus
vv                       AMP PEAK 14(8P23.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           191
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(8Q24.21) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 15(8Q24.21) MUTATED   174 116
  AMP PEAK 15(8Q24.21) WILD-TYPE  72  53
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                           290                            125 
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                           116                             53 
$`AMP PEAK 15(8Q24.21) MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 
       20.15         9.86        27.35        26.93        58.03        26.70 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 
       11.01         9.47         9.44         6.97         4.64        18.35 
TCGA-BR-4201 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6565 
       34.68        15.95        13.87        17.29        13.68         9.17 
TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       25.61        19.89        12.16        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       44.94         9.21        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       18.15        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69        29.59         9.60         8.05        29.42 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 
        2.66         2.20        15.58         7.40         6.18        13.08 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8381 
       26.33         4.31        14.04         3.32        31.27         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
       25.05         3.72         5.39         9.21        20.22        12.79 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8687 
        9.34        28.14         7.53        24.79        32.58         8.22 
TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       10.68        13.87         7.53        34.98         1.48        27.55 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI 
        0.72        14.17        28.34         0.46        20.42        21.44 
TCGA-BR-A4QL TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 
       16.14        13.15        13.35        11.21        12.10        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8535 
       12.53         7.17        12.33        12.39        15.39        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
       12.43         6.31        12.30        12.43        11.61         6.58 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       12.62        20.02         3.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 
        0.00        18.97         7.07        12.00         6.97        36.00 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
        0.99        12.03        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 
       21.07         7.99        12.66        20.91        19.13        18.84 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        17.19        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8576 TCGA-D7-8579 
       12.36        11.31        12.33        24.72        14.66        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6EV 
       14.27        16.44         5.92        36.43        14.76        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        11.44        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
       19.96         0.62         7.99        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       19.53        17.06         0.56         5.52         6.21        77.29 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       52.21        30.51        26.47         5.92        24.39        18.15 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 
       28.96        22.32         0.76        24.30        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51         6.58         0.26         2.10 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        23.80        14.07        15.68        33.40 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG 
       15.75         2.53         5.56        63.62        37.64         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7C1 
        6.08         4.60         9.24        11.05         8.61        16.67 
TCGA-RD-A8N1 TCGA-RD-A8N4 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
      115.69        71.38         8.94        35.61        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       18.48        43.36        37.41        38.14         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       34.29        16.31        22.19        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A91A 
        1.87         9.27        23.41        29.59        64.57        39.45 
TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       21.83        18.74        32.88         1.71        42.64        60.85 
TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        9.50        55.56         9.04         4.54         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       66.81        21.04        42.54        11.24        18.41        43.66 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        17.13        54.12        16.14        27.55        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

$`AMP PEAK 15(8Q24.21) WILD-TYPE`
TCGA-B7-5818 TCGA-B7-A5TI TCGA-BR-4183 TCGA-BR-4188 TCGA-BR-4253 TCGA-BR-4280 
       11.70        19.56         6.61         7.43         4.08         6.61 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6710 
       19.33        39.12        26.10        32.78        18.05         8.98 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7722 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8081 
       21.90        36.16        15.32        37.25        11.44        32.25 
TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        0.56        19.96        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8589 
        0.95        11.80        14.79        25.18         1.12        27.12 
TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-A44T 
        6.28        26.73        31.96         9.86        20.88        34.13 
TCGA-BR-A453 TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J4 TCGA-BR-A4J6 
        6.08        28.57        12.89         8.98         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QM TCGA-CD-5798 
       32.52        13.51        20.65         1.15         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
       13.02        13.18        12.76        12.30        12.59        11.64 
TCGA-CD-8534 TCGA-CD-A489 TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4304 TCGA-CG-4306 
       12.07        11.31        12.20        11.77        27.02         1.02 
TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 
        9.01        30.97         1.02         0.99         6.02       105.07 
TCGA-CG-5725 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6527 
       15.02        25.71        20.55        18.54        18.61        10.26 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YY 
       16.80        19.50        17.19        18.21        21.14        13.78 
TCGA-D7-A6ET TCGA-D7-A6EZ TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A72C TCGA-FP-7916 
       26.43        20.32         7.13        14.47        11.38        14.07 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-7133 TCGA-HU-8238 
       22.29        59.54         5.03        13.58        63.06         1.51 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G3 TCGA-HU-A4GJ TCGA-HU-A4GX TCGA-HU-A4H2 
       22.82        21.07         5.59        21.37        20.25        12.95 
TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-AB1X TCGA-KB-A93J TCGA-RD-A7BW 
       21.17        36.36        18.81        13.51        36.95         5.13 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N5 TCGA-VQ-A8E3 
      122.30        37.91        40.64       116.38        57.44        21.73 
TCGA-VQ-A8P3 TCGA-VQ-A8PC TCGA-VQ-A8PF TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PY 
       37.22        46.26         2.50        15.65        13.35        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91Y TCGA-VQ-A923 
       73.41        11.70        61.22        20.81         9.73         2.01 
TCGA-VQ-A924 TCGA-VQ-A94P TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6G 
       55.43         2.66        28.41        38.93        26.04 

  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                          0.00                           0.26 
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                        115.69                         122.30 
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                         14.22                          16.80 
[1] "0.0 - 115.7 (14.2)" "0.3 - 122.3 (16.8)"
[1] "hr=" "1"  
D15V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 15(8Q24.21) MUTATED         2       15       28       22        25
  AMP PEAK 15(8Q24.21) WILD-TYPE       0        1       13       10        15
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 15(8Q24.21) MUTATED          41         2         58         41
  AMP PEAK 15(8Q24.21) WILD-TYPE        15         1         23         22
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 15(8Q24.21) MUTATED           26       31
  AMP PEAK 15(8Q24.21) WILD-TYPE         13       13
D15V3, multiclass
            clus
vv           AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  STAGE I                               2                              0
  STAGE IA                             15                              1
  STAGE IB                             28                             13
  STAGE II                             22                             10
  STAGE IIA                            25                             15
  STAGE IIB                            41                             15
  STAGE III                             2                              1
  STAGE IIIA                           58                             23
  STAGE IIIB                           41                             22
  STAGE IIIC                           26                             13
  STAGE IV                             31                             13
[1] 11  2
[1] TRUE
[1] "dimension of 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(8Q24.21) MUTATED    22  65 135  78
  AMP PEAK 15(8Q24.21) WILD-TYPE   1  28  61  41
D15V4, multiclass
    clus
vv   AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  T1                           22                              1
  T2                           65                             28
  T3                          135                             61
  T4                           78                             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"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 15(8Q24.21) MUTATED   89 85 56 64
  AMP PEAK 15(8Q24.21) WILD-TYPE 41 34 30 24
D15V5, multiclass
    clus
vv   AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  N0                           89                             41
  N1                           85                             34
  N2                           56                             30
  N3                           64                             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"
D15V6, binary
                                cls
clus                               0   1
  AMP PEAK 15(8Q24.21) MUTATED   271  20
  AMP PEAK 15(8Q24.21) WILD-TYPE 118  10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8Q24.21) MUTATED    271   20
  AMP PEAK 15(8Q24.21) WILD-TYPE  118   10
   clus
vv  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  0                          271                            118
  1                           20                             10
[1] 2 2
[1] FALSE
D15V7, binary
                                cls
clus                               0   1
  AMP PEAK 15(8Q24.21) MUTATED   110 199
  AMP PEAK 15(8Q24.21) WILD-TYPE  48  84
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8Q24.21) MUTATED    110  199
  AMP PEAK 15(8Q24.21) WILD-TYPE   48   84
        clus
vv       AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  FEMALE                          110                             48
  MALE                            199                             84
[1] 2 2
[1] FALSE
D15V8, binary
                                cls
clus                               0   1
  AMP PEAK 15(8Q24.21) MUTATED   226  51
  AMP PEAK 15(8Q24.21) WILD-TYPE  96  25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8Q24.21) MUTATED    226   51
  AMP PEAK 15(8Q24.21) WILD-TYPE   96   25
     clus
vv    AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  NO                           226                             96
  YES                           51                             25
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK 15(8Q24.21) MUTATED                                          9
  AMP PEAK 15(8Q24.21) WILD-TYPE                                        4
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK 15(8Q24.21) MUTATED                                      41
  AMP PEAK 15(8Q24.21) WILD-TYPE                                    31
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 15(8Q24.21) MUTATED                                                      114
  AMP PEAK 15(8Q24.21) WILD-TYPE                                                     49
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK 15(8Q24.21) MUTATED                                                  16
  AMP PEAK 15(8Q24.21) WILD-TYPE                                                 5
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 15(8Q24.21) MUTATED                                                                  62
  AMP PEAK 15(8Q24.21) WILD-TYPE                                                                20
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK 15(8Q24.21) MUTATED                                                    6
  AMP PEAK 15(8Q24.21) WILD-TYPE                                                  2
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK 15(8Q24.21) MUTATED                                                 58
  AMP PEAK 15(8Q24.21) WILD-TYPE                                               21
D15V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK 15(8Q24.21) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     9
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       41
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     114
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           16
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            58
                                                                   clus
vv                                                                  AMP PEAK 15(8Q24.21) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                       4
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         31
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                        49
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              21
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 15(8Q24.21) MUTATED   240  15  12  20
  AMP PEAK 15(8Q24.21) WILD-TYPE 109   3   7   5
D15V10, multiclass
    clus
vv   AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  R0                          240                            109
  R1                           15                              3
  R2                           12                              7
  RX                           20                              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"
D15V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 15(8Q24.21) MUTATED      57                        12
  AMP PEAK 15(8Q24.21) WILD-TYPE    31                         0
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 15(8Q24.21) MUTATED                                           1
  AMP PEAK 15(8Q24.21) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 15(8Q24.21) MUTATED     193
  AMP PEAK 15(8Q24.21) WILD-TYPE    85
D15V12, multiclass
                                           clus
vv                                          AMP PEAK 15(8Q24.21) MUTATED
  ASIAN                                                               57
  BLACK OR AFRICAN AMERICAN                                           12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              193
                                           clus
vv                                          AMP PEAK 15(8Q24.21) WILD-TYPE
  ASIAN                                                                 31
  BLACK OR AFRICAN AMERICAN                                              0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                 85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V13, binary
                                cls
clus                               0   1
  AMP PEAK 15(8Q24.21) MUTATED     4 217
  AMP PEAK 15(8Q24.21) WILD-TYPE   1  99
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8Q24.21) MUTATED      4  217
  AMP PEAK 15(8Q24.21) WILD-TYPE    1   99
                        clus
vv                       AMP PEAK 15(8Q24.21) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          217
                        clus
vv                       AMP PEAK 15(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                             99
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(9P24.1) MUTATION ANALYSIS
D16V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 16(9P24.1) MUTATED    38  21
  AMP PEAK 16(9P24.1) WILD-TYPE 208 148
  AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE 
                           59                           356 
  AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE 
                           21                           148 
$`AMP PEAK 16(9P24.1) MUTATED`
TCGA-CG-4460 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-B7-A5TK TCGA-BR-4267 
       21.99        16.24         0.23        20.15         9.47         6.18 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-7707 TCGA-BR-8059 TCGA-BR-8080 
       18.05        19.89        12.16        35.84        14.43         9.60 
TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8588 TCGA-BR-8678 TCGA-BR-A4IY 
        0.56         2.66         2.20        12.79        24.79        12.89 
TCGA-BR-A4J4 TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-8535 TCGA-CD-A48A 
        0.53        21.44        13.41        13.18        12.82        12.43 
TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4477 TCGA-D7-6528 TCGA-D7-6818 
       12.20         7.99         8.05        30.97        15.22        12.36 
TCGA-D7-6822 TCGA-D7-A4YT TCGA-D7-A6EY TCGA-EQ-5647 TCGA-F1-6875 TCGA-F1-A448 
       12.33        14.27        11.44         0.62        72.23        21.27 
TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
       77.29        52.21        30.51        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.76        24.26        22.75         8.98         2.10        12.95 
TCGA-HU-A4H5 TCGA-IN-8663 TCGA-KB-A6F7 TCGA-R5-A7ZI TCGA-VQ-A8DU TCGA-VQ-A8PC 
       23.80         3.39        63.62        74.53         5.46        46.26 
TCGA-VQ-A8PP TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A94T TCGA-VQ-AA6D 
       23.41        32.88        42.64        11.24        17.13 

$`AMP PEAK 16(9P24.1) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U 
       47.05        22.98        79.07         9.86        27.35        26.93 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN 
       58.03        26.70        11.70        19.56        11.01         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         9.67         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6710 
       39.12        26.10         9.17        32.78        25.61         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.24        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       11.44         0.69        29.59        32.25         8.05        29.42 
TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       19.96        15.58         7.40         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        1.48        27.55        28.57         8.98         0.72        14.17 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
       28.34         0.66        32.52        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 
       20.42         1.15        16.14         5.13        13.02        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.35        11.21        12.10        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.43         6.31        12.30        11.31 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       27.02        15.95         1.02        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        12.00         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
       18.61        17.85        13.35        17.19        10.26        15.98 
TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       12.79        11.31        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV 
       18.21        14.66        21.14        20.91        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.13         7.99        14.47        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8238 
        0.56         5.52         6.21        63.06        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-A4G2 TCGA-HU-A4G3 
        5.92        24.39        18.15        22.32        24.30         5.59 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       22.68        24.20         3.25        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       36.36         3.45        18.81        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H 
       11.70        15.75        13.51         2.53         5.56        37.64 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      116.38        71.38        57.44         8.94        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       19.04         5.79         0.92        48.79        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       18.48        43.36        21.73        37.41        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
        7.73        30.97        34.29        16.31        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ 
       12.79         2.70        17.85         1.87         9.27        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       13.35        29.59        64.57        14.33        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U 
       11.70        21.83        61.22        18.74        20.81         1.71 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
       60.85         9.50         9.73        55.56         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O 
       55.43         4.54         6.58         5.72        66.81        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
        2.66        42.54        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

  AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE 
                         0.23                          0.00 
  AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE 
                        77.29                        122.30 
  AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE 
                        14.27                         15.17 
[1] "0.2 - 77.3 (14.3)"  "0.0 - 122.3 (15.2)"
[1] "hr=" "1.2"
D16V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 16(9P24.1) MUTATED         0        4       10        3         6
  AMP PEAK 16(9P24.1) WILD-TYPE       2       12       31       29        34
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 16(9P24.1) MUTATED           5         1         12         10
  AMP PEAK 16(9P24.1) WILD-TYPE        51         2         69         53
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 16(9P24.1) MUTATED            6        5
  AMP PEAK 16(9P24.1) WILD-TYPE         33       39
D16V3, multiclass
            clus
vv           AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             4                            12
  STAGE IB                            10                            31
  STAGE II                             3                            29
  STAGE IIA                            6                            34
  STAGE IIB                            5                            51
  STAGE III                            1                             2
  STAGE IIIA                          12                            69
  STAGE IIIB                          10                            53
  STAGE IIIC                           6                            33
  STAGE IV                             5                            39
[1] 11  2
[1] TRUE
[1] "dimension of 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(9P24.1) MUTATED     5  16  22  21
  AMP PEAK 16(9P24.1) WILD-TYPE  18  77 174  98
D16V4, multiclass
    clus
vv   AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE
  T1                           5                            18
  T2                          16                            77
  T3                          22                           174
  T4                          21                            98
[1] 4 2
[1] TRUE
[1] "dimension of 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(9P24.1) MUTATED    22  18   8  14
  AMP PEAK 16(9P24.1) WILD-TYPE 108 101  78  74
D16V5, multiclass
    clus
vv   AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE
  N0                          22                           108
  N1                          18                           101
  N2                           8                            78
  N3                          14                            74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                               cls
clus                              0   1
  AMP PEAK 16(9P24.1) MUTATED    57   4
  AMP PEAK 16(9P24.1) WILD-TYPE 332  26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(9P24.1) MUTATED     57    4
  AMP PEAK 16(9P24.1) WILD-TYPE  332   26
   clus
vv  AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE
  0                          57                           332
  1                           4                            26
[1] 2 2
[1] FALSE
D16V7, binary
                               cls
clus                              0   1
  AMP PEAK 16(9P24.1) MUTATED    23  42
  AMP PEAK 16(9P24.1) WILD-TYPE 135 241
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(9P24.1) MUTATED     23   42
  AMP PEAK 16(9P24.1) WILD-TYPE  135  241
        clus
vv       AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE
  FEMALE                          23                           135
  MALE                            42                           241
[1] 2 2
[1] FALSE
D16V8, binary
                               cls
clus                              0   1
  AMP PEAK 16(9P24.1) MUTATED    45  15
  AMP PEAK 16(9P24.1) WILD-TYPE 277  61
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(9P24.1) MUTATED     45   15
  AMP PEAK 16(9P24.1) WILD-TYPE  277   61
     clus
vv    AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE
  NO                           45                           277
  YES                          15                            61
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK 16(9P24.1) MUTATED                                          3
  AMP PEAK 16(9P24.1) WILD-TYPE                                       10
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK 16(9P24.1) MUTATED                                       6
  AMP PEAK 16(9P24.1) WILD-TYPE                                    66
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 16(9P24.1) MUTATED                                                       24
  AMP PEAK 16(9P24.1) WILD-TYPE                                                    139
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK 16(9P24.1) MUTATED                                                   5
  AMP PEAK 16(9P24.1) WILD-TYPE                                                16
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 16(9P24.1) MUTATED                                                                  10
  AMP PEAK 16(9P24.1) WILD-TYPE                                                                72
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK 16(9P24.1) MUTATED                                                    2
  AMP PEAK 16(9P24.1) WILD-TYPE                                                  6
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK 16(9P24.1) MUTATED                                                 14
  AMP PEAK 16(9P24.1) WILD-TYPE                                               65
D16V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK 16(9P24.1) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     24
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           5
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          10
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           14
                                                                   clus
vv                                                                  AMP PEAK 16(9P24.1) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      139
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            16
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            72
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             65
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 16(9P24.1) MUTATED    50   4   2   4
  AMP PEAK 16(9P24.1) WILD-TYPE 299  14  17  21
D16V10, multiclass
    clus
vv   AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE
  R0                          50                           299
  R1                           4                            14
  R2                           2                            17
  RX                           4                            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"
D16V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 16(9P24.1) MUTATED      17                         2
  AMP PEAK 16(9P24.1) WILD-TYPE    71                        10
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 16(9P24.1) MUTATED                                           0    33
  AMP PEAK 16(9P24.1) WILD-TYPE                                         1   245
D16V12, multiclass
                                           clus
vv                                          AMP PEAK 16(9P24.1) MUTATED
  ASIAN                                                              17
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              33
                                           clus
vv                                          AMP PEAK 16(9P24.1) WILD-TYPE
  ASIAN                                                                71
  BLACK OR AFRICAN AMERICAN                                            10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               245
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V13, binary
                               cls
clus                              0   1
  AMP PEAK 16(9P24.1) MUTATED     2  46
  AMP PEAK 16(9P24.1) WILD-TYPE   3 270
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(9P24.1) MUTATED      2   46
  AMP PEAK 16(9P24.1) WILD-TYPE    3  270
                        clus
vv                       AMP PEAK 16(9P24.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          46
                        clus
vv                       AMP PEAK 16(9P24.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           270
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(9P13.2) MUTATION ANALYSIS
D17V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 17(9P13.2) MUTATED    54  33
  AMP PEAK 17(9P13.2) WILD-TYPE 192 136
  AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE 
                           87                           328 
  AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE 
                           33                           136 
$`AMP PEAK 17(9P13.2) MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-FP-A8CX TCGA-KB-A93G TCGA-3M-AB46 TCGA-B7-A5TK 
       47.05        21.99         0.23        20.15        58.03         9.47 
TCGA-BR-4183 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7959 
        6.61        19.89        12.16        35.84        18.15        33.21 
TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8486 
        9.60        29.42         2.66        19.96         2.20        20.22 
TCGA-BR-8588 TCGA-BR-8678 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4J4 
       12.79        24.79        13.87         7.53        34.98         0.53 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-8526 TCGA-CD-8535 
       20.42        21.44        13.41        13.18        12.53        12.82 
TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4466 TCGA-CG-4477 TCGA-D7-5579 
       12.20         7.99         8.05        18.97        30.97        20.91 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8575 
       17.19        10.26        15.22        12.36        12.33        18.21 
TCGA-D7-A4YT TCGA-D7-A4Z0 TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A747 
       14.27        14.76        11.31        11.44        22.29         8.38 
TCGA-EQ-5647 TCGA-F1-A448 TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8249 
        0.62        21.27        77.29        52.21        30.51        28.96 
TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4H2 TCGA-HU-A4H5 
        0.76        24.26        22.75         8.98        12.95        23.80 
TCGA-HU-A4H6 TCGA-IN-8663 TCGA-IN-AB1V TCGA-KB-A6F7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       21.17         3.39        15.75        63.62        18.21         8.52 
TCGA-R5-A7ZI TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DU 
       74.53       122.30       115.69        35.61        48.79         5.46 
TCGA-VQ-A8PC TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PP TCGA-VQ-A8PS TCGA-VQ-A91N 
       46.26         2.70        17.85        23.41        13.35        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A92D 
       20.81        32.88         1.71         9.50        55.56        66.81 
TCGA-VQ-A94T TCGA-VQ-AA6D TCGA-VQ-AA6F 
       11.24        17.13        54.12 

$`AMP PEAK 17(9P13.2) WILD-TYPE`
TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U 
       22.98        79.07        16.24         9.86        27.35        26.93 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4184 
       26.70        11.70        19.56        11.01         9.44         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6710 
       26.10         9.17        32.78        25.61        18.05         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       36.16        35.24        33.63        39.78        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        3.45         9.07        29.56        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8296 
        0.69        29.59        32.25         8.05         0.56        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 
        5.39        25.18         9.21         1.12        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A453 
        9.86        20.88         8.22        10.68        34.13         6.08 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
       14.17        28.34         0.66        32.52        13.51         0.46 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 
       20.65         1.15        16.14         5.13        13.02        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 
       13.35        11.21        12.10        12.76        12.59         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       27.02        15.95         1.02        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
       29.98        19.07        12.03         0.00         9.01         7.07 
TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       12.00         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 
       13.35        15.98        12.79        11.31        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU 
       19.50        17.19        14.66        21.14        20.91        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EZ 
        5.92        36.43        13.78        26.43        11.24        20.32 
TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 
       15.65         4.34        19.96         7.13         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        6.21        63.06        26.47         1.51         5.92        24.39 
TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 
       18.15        22.32        22.82        21.07        24.30         5.59 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       22.68        24.20         3.25        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
        2.10        29.00        23.84        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       36.36         3.45        18.81        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J 
       11.70        13.51         2.53         5.56        37.64        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZR TCGA-R5-A804 
        3.72        19.73        14.04        45.67         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW 
        9.24        11.05         8.61         5.13        16.67        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB 
       40.64       116.38        71.38        57.44         8.94        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
       19.04         5.79         0.92        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       43.36        21.73        37.41        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH 
       30.97        34.29        16.31        22.19         2.50        12.79 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY 
        1.87         9.27        15.65        29.59        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91V 
       73.41        39.45        11.70        21.83        61.22        42.64 
TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
       60.85         9.73         9.04         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA64 
        6.58         5.72        21.04         2.66        42.54        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-VQ-AA6I 
       43.66        28.41        38.93        32.94        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       27.55        12.43        17.26         0.79 

  AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE 
                         0.23                          0.00 
  AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE 
                       122.30                        116.38 
  AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE 
                        18.15                         14.12 
[1] "0.2 - 122.3 (18.1)" "0.0 - 116.4 (14.1)"
[1] "hr=" "1.3"
D17V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 17(9P13.2) MUTATED         0        5       15        6         4
  AMP PEAK 17(9P13.2) WILD-TYPE       2       11       26       26        36
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 17(9P13.2) MUTATED           8         0         24         14
  AMP PEAK 17(9P13.2) WILD-TYPE        48         3         57         49
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 17(9P13.2) MUTATED            3       10
  AMP PEAK 17(9P13.2) WILD-TYPE         36       34
D17V3, multiclass
            clus
vv           AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             5                            11
  STAGE IB                            15                            26
  STAGE II                             6                            26
  STAGE IIA                            4                            36
  STAGE IIB                            8                            48
  STAGE III                            0                             3
  STAGE IIIA                          24                            57
  STAGE IIIB                          14                            49
  STAGE IIIC                           3                            36
  STAGE IV                            10                            34
[1] 11  2
[1] TRUE
[1] "dimension of 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(9P13.2) MUTATED     7  24  38  21
  AMP PEAK 17(9P13.2) WILD-TYPE  16  69 158  98
D17V4, multiclass
    clus
vv   AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE
  T1                           7                            16
  T2                          24                            69
  T3                          38                           158
  T4                          21                            98
[1] 4 2
[1] TRUE
[1] "dimension of 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(9P13.2) MUTATED    26  29  18  16
  AMP PEAK 17(9P13.2) WILD-TYPE 104  90  68  72
D17V5, multiclass
    clus
vv   AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE
  N0                          26                           104
  N1                          29                            90
  N2                          18                            68
  N3                          16                            72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                               cls
clus                              0   1
  AMP PEAK 17(9P13.2) MUTATED    81   6
  AMP PEAK 17(9P13.2) WILD-TYPE 308  24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9P13.2) MUTATED     81    6
  AMP PEAK 17(9P13.2) WILD-TYPE  308   24
   clus
vv  AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE
  0                          81                           308
  1                           6                            24
[1] 2 2
[1] FALSE
D17V7, binary
                               cls
clus                              0   1
  AMP PEAK 17(9P13.2) MUTATED    36  55
  AMP PEAK 17(9P13.2) WILD-TYPE 122 228
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9P13.2) MUTATED     36   55
  AMP PEAK 17(9P13.2) WILD-TYPE  122  228
        clus
vv       AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE
  FEMALE                          36                           122
  MALE                            55                           228
[1] 2 2
[1] FALSE
D17V8, binary
                               cls
clus                              0   1
  AMP PEAK 17(9P13.2) MUTATED    66  21
  AMP PEAK 17(9P13.2) WILD-TYPE 256  55
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9P13.2) MUTATED     66   21
  AMP PEAK 17(9P13.2) WILD-TYPE  256   55
     clus
vv    AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE
  NO                           66                           256
  YES                          21                            55
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK 17(9P13.2) MUTATED                                          3
  AMP PEAK 17(9P13.2) WILD-TYPE                                       10
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK 17(9P13.2) MUTATED                                       9
  AMP PEAK 17(9P13.2) WILD-TYPE                                    63
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 17(9P13.2) MUTATED                                                       26
  AMP PEAK 17(9P13.2) WILD-TYPE                                                    137
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK 17(9P13.2) MUTATED                                                   8
  AMP PEAK 17(9P13.2) WILD-TYPE                                                13
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 17(9P13.2) MUTATED                                                                  18
  AMP PEAK 17(9P13.2) WILD-TYPE                                                                64
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK 17(9P13.2) MUTATED                                                    3
  AMP PEAK 17(9P13.2) WILD-TYPE                                                  5
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK 17(9P13.2) MUTATED                                                 24
  AMP PEAK 17(9P13.2) WILD-TYPE                                               55
D17V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK 17(9P13.2) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       9
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     26
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           8
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          18
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           24
                                                                   clus
vv                                                                  AMP PEAK 17(9P13.2) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        63
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      137
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            13
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             55
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 17(9P13.2) MUTATED    73   5   3   3
  AMP PEAK 17(9P13.2) WILD-TYPE 276  13  16  22
D17V10, multiclass
    clus
vv   AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE
  R0                          73                           276
  R1                           5                            13
  R2                           3                            16
  RX                           3                            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"
D17V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 17(9P13.2) MUTATED      17                         2
  AMP PEAK 17(9P13.2) WILD-TYPE    71                        10
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 17(9P13.2) MUTATED                                           0    54
  AMP PEAK 17(9P13.2) WILD-TYPE                                         1   224
D17V12, multiclass
                                           clus
vv                                          AMP PEAK 17(9P13.2) MUTATED
  ASIAN                                                              17
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              54
                                           clus
vv                                          AMP PEAK 17(9P13.2) WILD-TYPE
  ASIAN                                                                71
  BLACK OR AFRICAN AMERICAN                                            10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V13, binary
                               cls
clus                              0   1
  AMP PEAK 17(9P13.2) MUTATED     3  59
  AMP PEAK 17(9P13.2) WILD-TYPE   2 257
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9P13.2) MUTATED      3   59
  AMP PEAK 17(9P13.2) WILD-TYPE    2  257
                        clus
vv                       AMP PEAK 17(9P13.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          59
                        clus
vv                       AMP PEAK 17(9P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           257
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(9Q34.3) MUTATION ANALYSIS
D18V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 18(9Q34.3) MUTATED    73  41
  AMP PEAK 18(9Q34.3) WILD-TYPE 173 128
  AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE 
                          114                           301 
  AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE 
                           41                           128 
$`AMP PEAK 18(9Q34.3) MUTATED`
TCGA-EQ-A4SO TCGA-KB-A93G TCGA-VQ-A8PU TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       16.24        20.15        27.35         9.47         9.44         6.61 
TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6564 TCGA-BR-6707 TCGA-BR-7197 TCGA-BR-7704 
       18.35        17.29        26.10        19.89         9.21        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8080 
       35.84        33.63        18.15        33.21        11.44         9.60 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8486 TCGA-BR-8588 
        2.66         2.20         6.18        31.10        20.22        12.79 
TCGA-BR-8682 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4J4 TCGA-BR-A4J9 TCGA-BR-A4PD 
       32.58        13.87        34.98         0.53         0.46        20.65 
TCGA-BR-A4PE TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8535 TCGA-CD-A486 
       20.42        13.15        13.18        12.10        12.82         6.31 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4466 
       12.30        12.43         3.02        27.02         7.99        18.97 
TCGA-CG-4477 TCGA-CG-5718 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6528 
       30.97        36.00        12.66        20.91        17.19        15.22 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-A4YT TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6EX 
       12.36        11.31        14.27        36.43        14.76        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-EQ-5647 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-A4BF TCGA-HF-7132 TCGA-HF-7133 
        0.62        72.23        21.27         5.52        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8610 
       52.21        30.51        26.47         1.51        28.96         0.76 
TCGA-HU-A4G6 TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H5 TCGA-HU-A4HD 
       24.26        25.81         8.98         6.58        23.80        33.40 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RS TCGA-KB-A6F5 TCGA-KB-A6F7 
        3.45        18.81         3.39        12.59         5.56        63.62 
TCGA-R5-A7O7 TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A8MV TCGA-RD-A8N1 
       45.67        74.53         4.60        11.05       122.30       115.69 
TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8E7 TCGA-VQ-A8PC 
       35.61        48.79         5.46        18.48        37.41        46.26 
TCGA-VQ-A8PY TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       14.33        18.74        20.81        32.88         1.71        42.64 
TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94T 
        9.50        55.56         9.04         5.72        66.81        11.24 
TCGA-VQ-AA68 TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       43.66        17.13        54.12        27.55        12.43         0.79 

$`AMP PEAK 18(9Q34.3) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-MX-A663 
       47.05        21.99        22.98        79.07         0.23         9.86 
TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       26.93        58.03        26.70        11.70        19.56        11.01 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 
       15.95        13.87        13.68        19.33        39.12         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7716 
       30.90        31.20        44.94        21.90        36.16        39.78 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
       15.32        28.73         3.45         9.07        29.56        37.25 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       14.43         0.69        29.59        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8363 
       29.42        19.96        15.58         7.40        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8589 
        3.72         5.39        25.18         9.21         1.12        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       31.96         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        7.53         6.08         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       13.51         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.02        13.35        11.21        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG 
       15.39        12.07        12.43        11.31        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4305 TCGA-CG-4306 
       12.20        11.77        12.62        20.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 
       12.03         0.00         9.01         7.07        12.00         6.97 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
        7.99        25.71        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
       18.61        17.85        13.35        10.26        15.98        12.79 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YY 
       14.66        21.14        20.91        16.44         5.92        13.78 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 
       26.43        11.24        19.96         7.13         7.99        14.47 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HU-8243 
       59.54         5.03        13.58         0.56         6.21         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 
       24.39        18.15        22.32        22.82        21.07        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH 
        5.59        22.68        24.20         3.25        22.75        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       21.37        29.98         0.10         6.51        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        29.00        23.84        21.17        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       15.68        36.36        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.44         6.74         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
       13.51         2.53        37.64        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BT 
       14.04        18.21         8.52         6.08         9.24         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
        5.13        16.67        37.91        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        21.73        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
        7.73        30.97        34.29        16.31        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       12.79         2.70        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        13.35        29.59        64.57        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A923 
       11.70        21.83        61.22        60.85         9.73         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
       55.43         4.54         6.58        21.04         2.66        42.54 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-VQ-AA6I 
       18.41        28.41        38.93        32.94        26.04        16.14 
TCGA-ZA-A8F6 
       17.26 

  AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE 
                         0.46                          0.00 
  AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE 
                       122.30                        116.38 
  AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE 
                        17.24                         14.07 
[1] "0.5 - 122.3 (17.2)" "0.0 - 116.4 (14.1)"
[1] "hr=" "1.4"
D18V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 18(9Q34.3) MUTATED         0        7       14        6         8
  AMP PEAK 18(9Q34.3) WILD-TYPE       2        9       27       26        32
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 18(9Q34.3) MUTATED          16         0         27         14
  AMP PEAK 18(9Q34.3) WILD-TYPE        40         3         54         49
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 18(9Q34.3) MUTATED            7       14
  AMP PEAK 18(9Q34.3) WILD-TYPE         32       30
D18V3, multiclass
            clus
vv           AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             7                             9
  STAGE IB                            14                            27
  STAGE II                             6                            26
  STAGE IIA                            8                            32
  STAGE IIB                           16                            40
  STAGE III                            0                             3
  STAGE IIIA                          27                            54
  STAGE IIIB                          14                            49
  STAGE IIIC                           7                            32
  STAGE IV                            14                            30
[1] 11  2
[1] TRUE
[1] "dimension of 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(9Q34.3) MUTATED     8  26  55  29
  AMP PEAK 18(9Q34.3) WILD-TYPE  15  67 141  90
D18V4, multiclass
    clus
vv   AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE
  T1                           8                            15
  T2                          26                            67
  T3                          55                           141
  T4                          29                            90
[1] 4 2
[1] TRUE
[1] "dimension of 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(9Q34.3) MUTATED   34 36 27 20
  AMP PEAK 18(9Q34.3) WILD-TYPE 96 83 59 68
D18V5, multiclass
    clus
vv   AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE
  N0                          34                            96
  N1                          36                            83
  N2                          27                            59
  N3                          20                            68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                               cls
clus                              0   1
  AMP PEAK 18(9Q34.3) MUTATED   108   9
  AMP PEAK 18(9Q34.3) WILD-TYPE 281  21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(9Q34.3) MUTATED    108    9
  AMP PEAK 18(9Q34.3) WILD-TYPE  281   21
   clus
vv  AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE
  0                         108                           281
  1                           9                            21
[1] 2 2
[1] FALSE
D18V7, binary
                               cls
clus                              0   1
  AMP PEAK 18(9Q34.3) MUTATED    42  80
  AMP PEAK 18(9Q34.3) WILD-TYPE 116 203
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(9Q34.3) MUTATED     42   80
  AMP PEAK 18(9Q34.3) WILD-TYPE  116  203
        clus
vv       AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE
  FEMALE                          42                           116
  MALE                            80                           203
[1] 2 2
[1] FALSE
D18V8, binary
                               cls
clus                              0   1
  AMP PEAK 18(9Q34.3) MUTATED    85  28
  AMP PEAK 18(9Q34.3) WILD-TYPE 237  48
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(9Q34.3) MUTATED     85   28
  AMP PEAK 18(9Q34.3) WILD-TYPE  237   48
     clus
vv    AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE
  NO                           85                           237
  YES                          28                            48
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK 18(9Q34.3) MUTATED                                          5
  AMP PEAK 18(9Q34.3) WILD-TYPE                                        8
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK 18(9Q34.3) MUTATED                                      15
  AMP PEAK 18(9Q34.3) WILD-TYPE                                    57
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 18(9Q34.3) MUTATED                                                       40
  AMP PEAK 18(9Q34.3) WILD-TYPE                                                    123
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK 18(9Q34.3) MUTATED                                                   9
  AMP PEAK 18(9Q34.3) WILD-TYPE                                                12
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 18(9Q34.3) MUTATED                                                                  20
  AMP PEAK 18(9Q34.3) WILD-TYPE                                                                62
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK 18(9Q34.3) MUTATED                                                    4
  AMP PEAK 18(9Q34.3) WILD-TYPE                                                  4
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK 18(9Q34.3) MUTATED                                                 28
  AMP PEAK 18(9Q34.3) WILD-TYPE                                               51
D18V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK 18(9Q34.3) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                      15
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     40
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           9
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          20
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           28
                                                                   clus
vv                                                                  AMP PEAK 18(9Q34.3) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        57
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      123
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            12
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             51
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 18(9Q34.3) MUTATED    99   6   2   7
  AMP PEAK 18(9Q34.3) WILD-TYPE 250  12  17  18
D18V10, multiclass
    clus
vv   AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE
  R0                          99                           250
  R1                           6                            12
  R2                           2                            17
  RX                           7                            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"
D18V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 18(9Q34.3) MUTATED      21                         5
  AMP PEAK 18(9Q34.3) WILD-TYPE    67                         7
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 18(9Q34.3) MUTATED                                           0    76
  AMP PEAK 18(9Q34.3) WILD-TYPE                                         1   202
D18V12, multiclass
                                           clus
vv                                          AMP PEAK 18(9Q34.3) MUTATED
  ASIAN                                                              21
  BLACK OR AFRICAN AMERICAN                                           5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              76
                                           clus
vv                                          AMP PEAK 18(9Q34.3) WILD-TYPE
  ASIAN                                                                67
  BLACK OR AFRICAN AMERICAN                                             7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               202
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V13, binary
                               cls
clus                              0   1
  AMP PEAK 18(9Q34.3) MUTATED     3  82
  AMP PEAK 18(9Q34.3) WILD-TYPE   2 234
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(9Q34.3) MUTATED      3   82
  AMP PEAK 18(9Q34.3) WILD-TYPE    2  234
                        clus
vv                       AMP PEAK 18(9Q34.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          82
                        clus
vv                       AMP PEAK 18(9Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           234
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(10P11.22) MUTATION ANALYSIS
D19V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 19(10P11.22) MUTATED    67  46
  AMP PEAK 19(10P11.22) WILD-TYPE 179 123
  AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE 
                            113                             302 
  AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE 
                             46                             123 
$`AMP PEAK 19(10P11.22) MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-FP-A8CX TCGA-MX-A663 TCGA-VQ-A94U TCGA-3M-AB46 
       47.05        21.99         0.23         9.86        26.93        58.03 
TCGA-BR-4183 TCGA-BR-4255 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6565 TCGA-BR-6801 
        6.61         4.08        17.29        13.68         9.17        40.21 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 
        9.21        35.24        33.63        39.78        18.15        28.73 
TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8483 
        0.69         2.66         2.20        15.58         7.40         5.39 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-A4IY TCGA-BR-A4J1 
        9.21        20.22        32.58         9.86        12.89         0.72 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5801 
       32.52        13.51        20.65         1.15        21.44        13.18 
TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C 
       12.76        12.53        12.39        12.30        12.43        11.61 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4440 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5730 
       12.20        20.02         4.01        12.00        30.97         4.01 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-8578 
       19.13        20.55        17.19        15.22        12.36        21.14 
TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 
       16.44        11.24        11.31        15.65        19.96         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-HU-8238 
        7.99        72.23         3.48        19.53        17.06         1.51 
TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4G9 
        5.92        28.96        22.32         0.76        24.26        24.20 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H2 
       22.75        25.81        11.77         8.98         6.58        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI 
       23.84        21.17        33.40         3.45         3.39        18.38 
TCGA-IN-A6RR TCGA-IN-A7NR TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR 
        6.74         6.51        37.64        45.67        18.21         6.08 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-VQ-A8DU TCGA-VQ-A8E3 
       11.05         8.61        16.67       122.30         5.46        21.73 
TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PX 
        7.73        46.26        22.19        12.79        17.85        64.57 
TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U 
       14.33        39.45        21.83        18.74        32.88         1.71 
TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-AA6I TCGA-VQ-AA6J 
        9.50         9.04        21.04        16.14        27.55 

$`AMP PEAK 19(10P11.22) WILD-TYPE`
TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-VQ-A8PU TCGA-B7-5816 
       22.98        79.07        16.24        20.15        27.35        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 
       11.70        19.56        11.01         9.47         9.44         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 
        4.64         7.43        18.35        30.90         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
       13.87        19.33        39.12        26.10        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89        12.16         8.98        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7901 
       44.94        21.90        36.16        35.84        15.32         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
       19.96         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       25.18         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 
        6.28         7.53        26.73        24.79        31.96        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 
       34.98         1.48        27.55        28.57         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL 
        0.53        28.34         0.66         0.46        20.42        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13        13.41        13.02        13.15        13.35        11.21 
TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 
       12.10        12.59         7.17        12.33        12.30        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
       11.31         6.58        11.77        12.62         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 
       15.95         1.02         7.99         8.05        54.08        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        7.07         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 
       18.84        18.54        18.61        17.85        13.35        10.26 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       15.98        12.79        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19        18.21        14.66        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY 
        5.92        36.43        13.78        14.76        26.43        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6874 
       20.32        22.29         8.38         4.34         7.13        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
       21.27        11.38        14.07        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8604 
       52.21        30.51        26.47        24.39        18.15        22.82 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GJ 
       21.07        24.30         5.59        22.68         3.25        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
       29.98         0.10         6.51        20.25         0.26         2.10 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 
       29.00        23.80        14.07        15.68        36.36        18.81 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NT 
       12.46        13.35        19.53         6.44        12.59        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZF TCGA-R5-A7ZI 
       36.95         3.72        19.73        14.04         8.52        74.53 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        4.60         9.24         5.13        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      116.38        71.38        57.44         8.94        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       19.04         5.79         0.92        48.79        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       18.48        43.36        37.41        38.14        37.22        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO 
       34.29        16.31         2.50         2.70         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91D 
       23.41        15.65        13.35        29.59        73.41        11.70 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z 
       61.22        20.81        42.64        60.85         9.73        55.56 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
        2.01        55.43         4.54         6.58         5.72        66.81 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
        2.66        42.54        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6K 
       38.93        32.94        17.13        54.12        26.04        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

  AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE 
                           0.23                            0.00 
  AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE 
                         122.30                          116.38 
  AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE 
                         15.220                          14.775 
[1] "0.2 - 122.3 (15.2)" "0.0 - 116.4 (14.8)"
[1] "hr=" "1.1"
D19V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 19(10P11.22) MUTATED         1        7        8        4        12
  AMP PEAK 19(10P11.22) WILD-TYPE       1        9       33       28        28
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 19(10P11.22) MUTATED          20         1         22         19
  AMP PEAK 19(10P11.22) WILD-TYPE        36         2         59         44
                                 vv
clus                              STAGE IIIC STAGE IV
  AMP PEAK 19(10P11.22) MUTATED            7       13
  AMP PEAK 19(10P11.22) WILD-TYPE         32       31
D19V3, multiclass
            clus
vv           AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE
  STAGE I                                1                               1
  STAGE IA                               7                               9
  STAGE IB                               8                              33
  STAGE II                               4                              28
  STAGE IIA                             12                              28
  STAGE IIB                             20                              36
  STAGE III                              1                               2
  STAGE IIIA                            22                              59
  STAGE IIIB                            19                              44
  STAGE IIIC                             7                              32
  STAGE IV                              13                              31
[1] 11  2
[1] TRUE
[1] "dimension of 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(10P11.22) MUTATED     7  18  63  30
  AMP PEAK 19(10P11.22) WILD-TYPE  16  75 133  89
D19V4, multiclass
    clus
vv   AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE
  T1                             7                              16
  T2                            18                              75
  T3                            63                             133
  T4                            30                              89
[1] 4 2
[1] TRUE
[1] "dimension of 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(10P11.22) MUTATED   39 30 23 24
  AMP PEAK 19(10P11.22) WILD-TYPE 91 89 63 64
D19V5, multiclass
    clus
vv   AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE
  N0                            39                              91
  N1                            30                              89
  N2                            23                              63
  N3                            24                              64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                                 cls
clus                                0   1
  AMP PEAK 19(10P11.22) MUTATED   104   8
  AMP PEAK 19(10P11.22) WILD-TYPE 285  22
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(10P11.22) MUTATED    104    8
  AMP PEAK 19(10P11.22) WILD-TYPE  285   22
   clus
vv  AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE
  0                           104                             285
  1                             8                              22
[1] 2 2
[1] FALSE
D19V7, binary
                                 cls
clus                                0   1
  AMP PEAK 19(10P11.22) MUTATED    44  75
  AMP PEAK 19(10P11.22) WILD-TYPE 114 208
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(10P11.22) MUTATED     44   75
  AMP PEAK 19(10P11.22) WILD-TYPE  114  208
        clus
vv       AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE
  FEMALE                            44                             114
  MALE                              75                             208
[1] 2 2
[1] FALSE
D19V8, binary
                                 cls
clus                                0   1
  AMP PEAK 19(10P11.22) MUTATED    88  21
  AMP PEAK 19(10P11.22) WILD-TYPE 234  55
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(10P11.22) MUTATED     88   21
  AMP PEAK 19(10P11.22) WILD-TYPE  234   55
     clus
vv    AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE
  NO                             88                             234
  YES                            21                              55
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK 19(10P11.22) MUTATED                                          3
  AMP PEAK 19(10P11.22) WILD-TYPE                                       10
                                 vv
clus                              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK 19(10P11.22) MUTATED                                      14
  AMP PEAK 19(10P11.22) WILD-TYPE                                    58
                                 vv
clus                              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 19(10P11.22) MUTATED                                                       42
  AMP PEAK 19(10P11.22) WILD-TYPE                                                    121
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK 19(10P11.22) MUTATED                                                   4
  AMP PEAK 19(10P11.22) WILD-TYPE                                                17
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 19(10P11.22) MUTATED                                                                  23
  AMP PEAK 19(10P11.22) WILD-TYPE                                                                59
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK 19(10P11.22) MUTATED                                                    1
  AMP PEAK 19(10P11.22) WILD-TYPE                                                  7
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK 19(10P11.22) MUTATED                                                 31
  AMP PEAK 19(10P11.22) WILD-TYPE                                               48
D19V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK 19(10P11.22) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        14
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       42
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            23
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             31
                                                                   clus
vv                                                                  AMP PEAK 19(10P11.22) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                       10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                          58
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                        121
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                              17
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                              59
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                              7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                               48
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 19(10P11.22) MUTATED    97   3   5   5
  AMP PEAK 19(10P11.22) WILD-TYPE 252  15  14  20
D19V10, multiclass
    clus
vv   AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE
  R0                            97                             252
  R1                             3                              15
  R2                             5                              14
  RX                             5                              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"
D19V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 19(10P11.22) MUTATED      31                         6
  AMP PEAK 19(10P11.22) WILD-TYPE    57                         6
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 19(10P11.22) MUTATED                                           1
  AMP PEAK 19(10P11.22) WILD-TYPE                                         0
                                 vv
clus                              WHITE
  AMP PEAK 19(10P11.22) MUTATED      68
  AMP PEAK 19(10P11.22) WILD-TYPE   210
D19V12, multiclass
                                           clus
vv                                          AMP PEAK 19(10P11.22) MUTATED
  ASIAN                                                                31
  BLACK OR AFRICAN AMERICAN                                             6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                68
                                           clus
vv                                          AMP PEAK 19(10P11.22) WILD-TYPE
  ASIAN                                                                  57
  BLACK OR AFRICAN AMERICAN                                               6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               0
  WHITE                                                                 210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V13, binary
                                 cls
clus                                0   1
  AMP PEAK 19(10P11.22) MUTATED     2  86
  AMP PEAK 19(10P11.22) WILD-TYPE   3 230
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(10P11.22) MUTATED      2   86
  AMP PEAK 19(10P11.22) WILD-TYPE    3  230
                        clus
vv                       AMP PEAK 19(10P11.22) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            86
                        clus
vv                       AMP PEAK 19(10P11.22) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             230
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(10Q22.2) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 20(10Q22.2) MUTATED    46  38
  AMP PEAK 20(10Q22.2) WILD-TYPE 200 131
  AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE 
                            84                            331 
  AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE 
                            38                            131 
$`AMP PEAK 20(10Q22.2) MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-EQ-A4SO TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-BR-4183 
       47.05        21.99        16.24        27.35        26.93         6.61 
TCGA-BR-4191 TCGA-BR-4255 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-7197 
       18.35         4.08        17.29        19.33        26.10         9.21 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8286 
       35.24        33.63        18.15        14.43         0.69        29.42 
TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8369 TCGA-BR-8485 TCGA-BR-8682 
        2.66        15.58         7.40        14.04         9.21        32.58 
TCGA-BR-8683 TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PF 
        9.86        12.89         0.72        32.52        20.65         1.15 
TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8530 TCGA-CD-8533 TCGA-CG-4300 TCGA-CG-4449 
       13.18        12.76        12.39        15.39        20.02        19.07 
TCGA-CG-4477 TCGA-CG-5732 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6818 TCGA-D7-6822 
       30.97        69.04        20.55        18.84        12.36        12.33 
TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A74A 
       18.21        16.44        11.24        11.31        20.32        19.96 
TCGA-F1-6875 TCGA-FP-8631 TCGA-HU-8238 TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G6 
       72.23         0.56         1.51        22.32         0.76        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7808 
       24.20         8.98         6.58        21.17        33.40         3.45 
TCGA-IN-8663 TCGA-IN-A6RP TCGA-IN-A7NU TCGA-R5-A7ZE TCGA-R5-A805 TCGA-RD-A7BS 
        3.39         6.44        11.70        18.21         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8N9 TCGA-VQ-A8E3 TCGA-VQ-A8PC TCGA-VQ-A8PH 
        8.61       122.30        35.61        21.73        46.26        12.79 
TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91E 
        1.87        13.35        64.57        14.33        39.45        21.83 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-AA64 
       18.74        20.81         4.54         5.72        66.81        18.41 

$`AMP PEAK 20(10Q22.2) WILD-TYPE`
TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-3M-AB46 
       22.98        79.07         0.23        20.15         9.86        58.03 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 
        6.97         4.64         7.43        30.90         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.87        13.68        39.12         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 
       31.20        44.94        21.90        36.16        35.84        39.78 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       37.25        11.44        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        0.56        19.96         2.20         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        3.72         5.39        25.18        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       24.79        31.96        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       28.57         8.98        14.17         0.53        28.34         0.66 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       13.51         0.46        20.42        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.41        13.02        13.15        13.35        11.21        12.10 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 
       12.59        12.53         7.17        12.33        12.30        12.59 
TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       11.64        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       12.62         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 
        8.05        54.08         4.01        14.01        29.98        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        12.00         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 
       12.03        15.02        28.96        65.10         4.01        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 
        7.99        25.71        12.66        20.91        19.13        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       15.98        12.79        11.31        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       17.19        14.66        21.14        20.91        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6F0 
       36.43        13.78        14.76        26.43        11.44        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
       15.65         8.38         4.34         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF 
       22.29        17.06        59.54         5.03        13.58         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        18.15        28.96        22.82        21.07 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.30         5.59        22.68         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       11.77        21.37        29.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ 
       14.07        15.68        36.36        18.81        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       13.35        19.53         6.74        12.59         6.51        10.62 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
       15.75        13.51         2.53         5.56        63.62        37.64 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF 
       36.95         3.72        19.73        14.04        45.67         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW 
       74.53         6.08         4.60         5.13        16.67        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       16.87        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.25        13.02        18.48        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE 
       37.22         7.73        30.97        34.29        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.50         2.70        17.85         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91U 
       29.59        73.41        11.70        61.22        32.88         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       42.64        60.85         9.50         9.73        55.56         9.04 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
        2.01        55.43         6.58        21.04         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       11.24        43.66        28.41        38.93        32.94        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 
TCGA-ZQ-A9CR 
        0.79 

  AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE 
                          0.56                           0.00 
  AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE 
                        122.30                         116.38 
  AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE 
                        16.865                         14.270 
[1] "0.6 - 122.3 (16.9)" "0.0 - 116.4 (14.3)"
[1] "hr=" "1.1"
D20V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 20(10Q22.2) MUTATED         0        5        4        8         3
  AMP PEAK 20(10Q22.2) WILD-TYPE       2       11       37       24        37
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 20(10Q22.2) MUTATED          11         1         21         15
  AMP PEAK 20(10Q22.2) WILD-TYPE        45         2         60         48
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 20(10Q22.2) MUTATED            4       10
  AMP PEAK 20(10Q22.2) WILD-TYPE         35       34
D20V3, multiclass
            clus
vv           AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              5                             11
  STAGE IB                              4                             37
  STAGE II                              8                             24
  STAGE IIA                             3                             37
  STAGE IIB                            11                             45
  STAGE III                             1                              2
  STAGE IIIA                           21                             60
  STAGE IIIB                           15                             48
  STAGE IIIC                            4                             35
  STAGE IV                             10                             34
[1] 11  2
[1] TRUE
[1] "dimension of 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(10Q22.2) MUTATED     5  15  42  23
  AMP PEAK 20(10Q22.2) WILD-TYPE  18  78 154  96
D20V4, multiclass
    clus
vv   AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE
  T1                            5                             18
  T2                           15                             78
  T3                           42                            154
  T4                           23                             96
[1] 4 2
[1] TRUE
[1] "dimension of 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(10Q22.2) MUTATED    23  21  24  17
  AMP PEAK 20(10Q22.2) WILD-TYPE 107  98  62  71
D20V5, multiclass
    clus
vv   AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE
  N0                           23                            107
  N1                           21                             98
  N2                           24                             62
  N3                           17                             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                                cls
clus                               0   1
  AMP PEAK 20(10Q22.2) MUTATED    80   3
  AMP PEAK 20(10Q22.2) WILD-TYPE 309  27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(10Q22.2) MUTATED     80    3
  AMP PEAK 20(10Q22.2) WILD-TYPE  309   27
   clus
vv  AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE
  0                           80                            309
  1                            3                             27
[1] 2 2
[1] FALSE
D20V7, binary
                                cls
clus                               0   1
  AMP PEAK 20(10Q22.2) MUTATED    30  56
  AMP PEAK 20(10Q22.2) WILD-TYPE 128 227
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(10Q22.2) MUTATED     30   56
  AMP PEAK 20(10Q22.2) WILD-TYPE  128  227
        clus
vv       AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE
  FEMALE                           30                            128
  MALE                             56                            227
[1] 2 2
[1] FALSE
D20V8, binary
                                cls
clus                               0   1
  AMP PEAK 20(10Q22.2) MUTATED    61  19
  AMP PEAK 20(10Q22.2) WILD-TYPE 261  57
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(10Q22.2) MUTATED     61   19
  AMP PEAK 20(10Q22.2) WILD-TYPE  261   57
     clus
vv    AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE
  NO                            61                            261
  YES                           19                             57
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK 20(10Q22.2) MUTATED                                          3
  AMP PEAK 20(10Q22.2) WILD-TYPE                                       10
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK 20(10Q22.2) MUTATED                                      12
  AMP PEAK 20(10Q22.2) WILD-TYPE                                    60
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 20(10Q22.2) MUTATED                                                       25
  AMP PEAK 20(10Q22.2) WILD-TYPE                                                    138
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK 20(10Q22.2) MUTATED                                                   4
  AMP PEAK 20(10Q22.2) WILD-TYPE                                                17
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 20(10Q22.2) MUTATED                                                                  18
  AMP PEAK 20(10Q22.2) WILD-TYPE                                                                64
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK 20(10Q22.2) MUTATED                                                    2
  AMP PEAK 20(10Q22.2) WILD-TYPE                                                  6
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK 20(10Q22.2) MUTATED                                                 21
  AMP PEAK 20(10Q22.2) WILD-TYPE                                               58
D20V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK 20(10Q22.2) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       12
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      25
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           18
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            21
                                                                   clus
vv                                                                  AMP PEAK 20(10Q22.2) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         60
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       138
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             17
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 20(10Q22.2) MUTATED    75   1   3   4
  AMP PEAK 20(10Q22.2) WILD-TYPE 274  17  16  21
D20V10, multiclass
    clus
vv   AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE
  R0                           75                            274
  R1                            1                             17
  R2                            3                             16
  RX                            4                             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"
D20V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 20(10Q22.2) MUTATED      19                         1
  AMP PEAK 20(10Q22.2) WILD-TYPE    69                        11
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 20(10Q22.2) MUTATED                                           1
  AMP PEAK 20(10Q22.2) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 20(10Q22.2) MUTATED      55
  AMP PEAK 20(10Q22.2) WILD-TYPE   223
D20V12, multiclass
                                           clus
vv                                          AMP PEAK 20(10Q22.2) MUTATED
  ASIAN                                                               19
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               55
                                           clus
vv                                          AMP PEAK 20(10Q22.2) WILD-TYPE
  ASIAN                                                                 69
  BLACK OR AFRICAN AMERICAN                                             11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V13, binary
                                cls
clus                               0   1
  AMP PEAK 20(10Q22.2) MUTATED     0  62
  AMP PEAK 20(10Q22.2) WILD-TYPE   5 254
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(10Q22.2) MUTATED      0   62
  AMP PEAK 20(10Q22.2) WILD-TYPE    5  254
                        clus
vv                       AMP PEAK 20(10Q22.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           62
                        clus
vv                       AMP PEAK 20(10Q22.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            254
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(10Q26.13) MUTATION ANALYSIS
D21V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 21(10Q26.13) MUTATED    47  38
  AMP PEAK 21(10Q26.13) WILD-TYPE 199 131
  AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE 
                             85                             330 
  AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE 
                             38                             131 
$`AMP PEAK 21(10Q26.13) MUTATED`
TCGA-VQ-A94U TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4255 TCGA-BR-6456 
       26.93         6.61         4.64        18.35         4.08        17.29 
TCGA-BR-6457 TCGA-BR-6564 TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 
       13.68        26.10        31.20         9.21        35.24        33.63 
TCGA-BR-7716 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 
       39.78         0.69         9.60        29.42         2.66        15.58 
TCGA-BR-8297 TCGA-BR-8682 TCGA-BR-A4J1 TCGA-BR-A4J7 TCGA-BR-A4PF TCGA-CD-5801 
        7.40        32.58         0.72        32.52         1.15        13.18 
TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8533 TCGA-CG-4300 TCGA-CG-4304 
       12.59         7.17        12.39        15.39        20.02        27.02 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5718 
       29.98        19.07         7.07        12.00        30.97        36.00 
TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6528 
        4.01        69.04        20.55        18.84        17.19        15.22 
TCGA-D7-6818 TCGA-D7-8572 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6EX 
       12.36        16.80        14.27        16.44        11.24        11.31 
TCGA-D7-A6EZ TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-8099 
       20.32         0.62         7.99        72.23         3.48        17.06 
TCGA-HU-8238 TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GY 
        1.51        22.32         0.76        24.26        24.20         0.26 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RP TCGA-KB-A6F5 
       23.80        21.17         3.39        18.38         6.44         5.56 
TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BS TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8E3 
       18.21         6.08        11.05         5.46        18.48        21.73 
TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91N 
       46.26        12.79        64.57        14.33        21.83        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91Y TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A92D 
       20.81        32.88         9.73         4.54         5.72        66.81 
TCGA-VQ-AA64 
       18.41 

$`AMP PEAK 21(10Q26.13) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
       20.15         9.86        27.35        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4188 
       19.56        11.01         9.47         9.44         6.97         7.43 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6563 
        6.61        34.68        15.95        13.87        19.33        39.12 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
        8.98        40.21        30.90        44.94        21.90        36.16 
TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       35.84        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 
       29.56        33.21        37.25        14.43        11.44        29.59 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8360 
       32.25         8.05         0.56        19.96         2.20         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       31.10        13.08         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         8.98        14.17         0.53        28.34         0.66 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51         0.46        20.65        20.42        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13        13.41        13.02        13.15        13.35        11.21 
TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 
       12.10        12.76        12.53        12.33        12.30        12.59 
TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       11.64        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       12.62         3.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       54.08         4.01        14.01        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       18.97         6.97         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 
      105.07        12.03        15.02        28.96        65.10        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 
        7.99        25.71        12.66        20.91        19.13        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
       18.61        17.85        13.35        10.26        15.98        12.79 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        12.33        24.72        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       14.66        21.14        20.91         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       14.76        26.43        11.44        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        4.34        19.96         7.13        14.47        21.27        11.38 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       19.53        14.07        22.29        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
       30.51        26.47         5.92        24.39        18.15        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GC 
       22.82        21.07        24.30         5.59        22.68         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.58        20.25         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       29.00        23.84        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR 
        3.45        18.81        12.46        13.35        19.53         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53        63.62        37.64        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 
       14.04        45.67         8.52        74.53         4.60         9.24 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV 
       16.87        19.04         5.79         0.92        48.79        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       13.02        43.36        37.41        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PJ 
       30.97        34.29        16.31        22.19         2.50         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       17.85         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91U 
       29.59        73.41        39.45        11.70        61.22         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
       42.64        60.85         9.50        55.56         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
       55.43         6.58        21.04         2.66        42.54        11.24 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       43.66        28.41        38.93        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        27.55        12.43        17.26         0.79 

  AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE 
                           0.26                            0.00 
  AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE 
                          72.23                          122.30 
  AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE 
                          16.44                           14.45 
[1] "0.3 - 72.2 (16.4)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.2"
D21V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 21(10Q26.13) MUTATED         1        6        7        8         5
  AMP PEAK 21(10Q26.13) WILD-TYPE       1       10       34       24        35
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 21(10Q26.13) MUTATED          10         1         21          9
  AMP PEAK 21(10Q26.13) WILD-TYPE        46         2         60         54
                                 vv
clus                              STAGE IIIC STAGE IV
  AMP PEAK 21(10Q26.13) MUTATED            5       10
  AMP PEAK 21(10Q26.13) WILD-TYPE         34       34
D21V3, multiclass
            clus
vv           AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE
  STAGE I                                1                               1
  STAGE IA                               6                              10
  STAGE IB                               7                              34
  STAGE II                               8                              24
  STAGE IIA                              5                              35
  STAGE IIB                             10                              46
  STAGE III                              1                               2
  STAGE IIIA                            21                              60
  STAGE IIIB                             9                              54
  STAGE IIIC                             5                              34
  STAGE IV                              10                              34
[1] 11  2
[1] TRUE
[1] "dimension of 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(10Q26.13) MUTATED     7  20  39  19
  AMP PEAK 21(10Q26.13) WILD-TYPE  16  73 157 100
D21V4, multiclass
    clus
vv   AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE
  T1                             7                              16
  T2                            20                              73
  T3                            39                             157
  T4                            19                             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"
                                 vv
clus                               N0  N1  N2  N3
  AMP PEAK 21(10Q26.13) MUTATED    28  20  21  15
  AMP PEAK 21(10Q26.13) WILD-TYPE 102  99  65  73
D21V5, multiclass
    clus
vv   AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE
  N0                            28                             102
  N1                            20                              99
  N2                            21                              65
  N3                            15                              73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                                 cls
clus                                0   1
  AMP PEAK 21(10Q26.13) MUTATED    81   3
  AMP PEAK 21(10Q26.13) WILD-TYPE 308  27
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(10Q26.13) MUTATED     81    3
  AMP PEAK 21(10Q26.13) WILD-TYPE  308   27
   clus
vv  AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE
  0                            81                             308
  1                             3                              27
[1] 2 2
[1] FALSE
D21V7, binary
                                 cls
clus                                0   1
  AMP PEAK 21(10Q26.13) MUTATED    33  55
  AMP PEAK 21(10Q26.13) WILD-TYPE 125 228
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(10Q26.13) MUTATED     33   55
  AMP PEAK 21(10Q26.13) WILD-TYPE  125  228
        clus
vv       AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE
  FEMALE                            33                             125
  MALE                              55                             228
[1] 2 2
[1] FALSE
D21V8, binary
                                 cls
clus                                0   1
  AMP PEAK 21(10Q26.13) MUTATED    62  17
  AMP PEAK 21(10Q26.13) WILD-TYPE 260  59
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(10Q26.13) MUTATED     62   17
  AMP PEAK 21(10Q26.13) WILD-TYPE  260   59
     clus
vv    AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE
  NO                             62                             260
  YES                            17                              59
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK 21(10Q26.13) MUTATED                                          2
  AMP PEAK 21(10Q26.13) WILD-TYPE                                       11
                                 vv
clus                              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK 21(10Q26.13) MUTATED                                       9
  AMP PEAK 21(10Q26.13) WILD-TYPE                                    63
                                 vv
clus                              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 21(10Q26.13) MUTATED                                                       28
  AMP PEAK 21(10Q26.13) WILD-TYPE                                                    135
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK 21(10Q26.13) MUTATED                                                   5
  AMP PEAK 21(10Q26.13) WILD-TYPE                                                16
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 21(10Q26.13) MUTATED                                                                  18
  AMP PEAK 21(10Q26.13) WILD-TYPE                                                                64
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK 21(10Q26.13) MUTATED                                                    3
  AMP PEAK 21(10Q26.13) WILD-TYPE                                                  5
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK 21(10Q26.13) MUTATED                                                 22
  AMP PEAK 21(10Q26.13) WILD-TYPE                                               57
D21V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK 21(10Q26.13) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         9
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       28
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            18
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             22
                                                                   clus
vv                                                                  AMP PEAK 21(10Q26.13) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                       11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                          63
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                        135
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                              16
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                              64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 21(10Q26.13) MUTATED    73   2   4   6
  AMP PEAK 21(10Q26.13) WILD-TYPE 276  16  15  19
D21V10, multiclass
    clus
vv   AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE
  R0                            73                             276
  R1                             2                              16
  R2                             4                              15
  RX                             6                              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"
D21V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 21(10Q26.13) MUTATED      16                         5
  AMP PEAK 21(10Q26.13) WILD-TYPE    72                         7
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 21(10Q26.13) MUTATED                                           0
  AMP PEAK 21(10Q26.13) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  AMP PEAK 21(10Q26.13) MUTATED      52
  AMP PEAK 21(10Q26.13) WILD-TYPE   226
D21V12, multiclass
                                           clus
vv                                          AMP PEAK 21(10Q26.13) MUTATED
  ASIAN                                                                16
  BLACK OR AFRICAN AMERICAN                                             5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                52
                                           clus
vv                                          AMP PEAK 21(10Q26.13) WILD-TYPE
  ASIAN                                                                  72
  BLACK OR AFRICAN AMERICAN                                               7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 226
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V13, binary
                                 cls
clus                                0   1
  AMP PEAK 21(10Q26.13) MUTATED     0  59
  AMP PEAK 21(10Q26.13) WILD-TYPE   5 257
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(10Q26.13) MUTATED      0   59
  AMP PEAK 21(10Q26.13) WILD-TYPE    5  257
                        clus
vv                       AMP PEAK 21(10Q26.13) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            59
                        clus
vv                       AMP PEAK 21(10Q26.13) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             257
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 22(11P13) MUTATION ANALYSIS
D22V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 22(11P13) MUTATED    45  36
  AMP PEAK 22(11P13) WILD-TYPE 201 133
  AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE 
                          81                          334 
  AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE 
                          36                          133 
$`AMP PEAK 22(11P13) MUTATED`
TCGA-FP-A8CX TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5818 TCGA-B7-A5TJ 
        0.23        27.35        26.93        58.03        11.70        11.01 
TCGA-B7-A5TN TCGA-BR-4257 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 
        9.44         9.67        13.87        17.29        19.33        26.10 
TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8296 
       18.15         3.45        11.44         0.69         9.60        15.58 
TCGA-BR-8297 TCGA-BR-8485 TCGA-BR-8590 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-A44T 
        7.40         9.21         9.34        24.79        20.88        34.13 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J2 TCGA-BR-A4J8 TCGA-CD-8525 
        6.08        34.98        12.89        14.17        13.51        12.59 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-A487 TCGA-CD-A4MH TCGA-CG-4300 
       12.33        12.39        15.39        12.30        12.20        20.02 
TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5722 TCGA-D7-6822 
       54.08        19.07        12.00         6.97         0.99        12.33 
TCGA-D7-8576 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 
       14.66         0.62         7.99        14.07        17.06         0.56 
TCGA-HF-7133 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-A4G2 TCGA-HU-A4HD TCGA-IN-7808 
       63.06         5.92        28.96        24.30        33.40         3.45 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H 
       18.38        12.46        10.62        11.70         5.56        37.64 
TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N5 
       18.21        74.53         8.61        16.67       115.69        57.44 
TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PJ 
        5.46        13.02        18.48        43.36        22.19         2.70 
TCGA-VQ-A8PX TCGA-VQ-A91S TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A925 
       64.57        32.88         9.50         9.73         9.04         4.54 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6K 
       32.94        54.12        12.43 

$`AMP PEAK 22(11P13) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G 
       47.05        21.99        22.98        79.07        16.24        20.15 
TCGA-MX-A663 TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 
        9.86        26.70        19.56         9.47         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.34         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.68        39.12         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 
       33.63        39.78        15.32        28.73         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       33.21        37.25        14.43        29.59        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8360 
        0.56        29.42         2.66        19.96         2.20         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       31.10        13.08         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8592 
       20.22         1.12        12.79        27.12        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 
        7.53        26.73        31.96        32.58         9.86         8.22 
TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       10.68        13.87         7.53         1.48        27.55        28.57 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72         0.53        28.34         0.66        32.52 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
        0.46        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 
       11.21        12.10        12.76        12.53         7.17        12.30 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       12.59        11.64        12.07        12.82        12.43         6.31 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        11.77        12.62 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
        4.01        14.01        29.98        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       18.97         7.07        30.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.79        12.36        11.31        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       17.19        18.21        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        4.34        19.96         7.13        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
       11.38         3.48        19.53        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB 
       13.58         5.52         6.21        77.29        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 
       26.47         1.51        24.39        18.15        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       21.07         0.76         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RL 
       14.07        15.68        36.36        18.81         3.39        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V 
       19.53         6.44         6.74        12.59         6.51        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
       13.51         2.53        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       14.04        45.67         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 
       11.05         5.13       122.30        37.91        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38         8.94        35.61        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        0.92        48.79        13.25        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       37.22         7.73        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
        2.50        12.79        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        13.35        29.59        14.33        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U 
       11.70        21.83        61.22        18.74        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
       42.64        60.85        55.56         2.01        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
        5.72        66.81        21.04         2.66        42.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G 
       18.41        43.66        28.41        38.93        17.13        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        27.55        17.26         0.79 

  AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE 
                        0.23                         0.00 
  AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE 
                      115.69                       122.30 
  AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE 
                      13.020                       15.665 
[1] "0.2 - 115.7 (13.0)" "0.0 - 122.3 (15.7)"
[1] "hr=" "1.2"
D22V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 22(11P13) MUTATED         1        3        6        4         3
  AMP PEAK 22(11P13) WILD-TYPE       1       13       35       28        37
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 22(11P13) MUTATED          16         0         15         12
  AMP PEAK 22(11P13) WILD-TYPE        40         3         66         51
                              vv
clus                           STAGE IIIC STAGE IV
  AMP PEAK 22(11P13) MUTATED           10       13
  AMP PEAK 22(11P13) WILD-TYPE         29       31
D22V3, multiclass
            clus
vv           AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE
  STAGE I                             1                            1
  STAGE IA                            3                           13
  STAGE IB                            6                           35
  STAGE II                            4                           28
  STAGE IIA                           3                           37
  STAGE IIB                          16                           40
  STAGE III                           0                            3
  STAGE IIIA                         15                           66
  STAGE IIIB                         12                           51
  STAGE IIIC                         10                           29
  STAGE IV                           13                           31
[1] 11  2
[1] TRUE
[1] "dimension of 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(11P13) MUTATED     4  10  40  31
  AMP PEAK 22(11P13) WILD-TYPE  19  83 156  88
D22V4, multiclass
    clus
vv   AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE
  T1                          4                           19
  T2                         10                           83
  T3                         40                          156
  T4                         31                           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"
                              vv
clus                            N0  N1  N2  N3
  AMP PEAK 22(11P13) MUTATED    19  25  21  18
  AMP PEAK 22(11P13) WILD-TYPE 111  94  65  70
D22V5, multiclass
    clus
vv   AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE
  N0                         19                          111
  N1                         25                           94
  N2                         21                           65
  N3                         18                           70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                              cls
clus                             0   1
  AMP PEAK 22(11P13) MUTATED    74   7
  AMP PEAK 22(11P13) WILD-TYPE 315  23
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(11P13) MUTATED     74    7
  AMP PEAK 22(11P13) WILD-TYPE  315   23
   clus
vv  AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE
  0                         74                          315
  1                          7                           23
[1] 2 2
[1] FALSE
D22V7, binary
                              cls
clus                             0   1
  AMP PEAK 22(11P13) MUTATED    26  62
  AMP PEAK 22(11P13) WILD-TYPE 132 221
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(11P13) MUTATED     26   62
  AMP PEAK 22(11P13) WILD-TYPE  132  221
        clus
vv       AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE
  FEMALE                         26                          132
  MALE                           62                          221
[1] 2 2
[1] FALSE
D22V8, binary
                              cls
clus                             0   1
  AMP PEAK 22(11P13) MUTATED    59  19
  AMP PEAK 22(11P13) WILD-TYPE 263  57
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(11P13) MUTATED     59   19
  AMP PEAK 22(11P13) WILD-TYPE  263   57
     clus
vv    AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE
  NO                          59                          263
  YES                         19                           57
[1] 2 2
[1] FALSE
                              vv
clus                           STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK 22(11P13) MUTATED                                          5
  AMP PEAK 22(11P13) WILD-TYPE                                        8
                              vv
clus                           STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK 22(11P13) MUTATED                                      13
  AMP PEAK 22(11P13) WILD-TYPE                                    59
                              vv
clus                           STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 22(11P13) MUTATED                                                       33
  AMP PEAK 22(11P13) WILD-TYPE                                                    130
                              vv
clus                           STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK 22(11P13) MUTATED                                                   5
  AMP PEAK 22(11P13) WILD-TYPE                                                16
                              vv
clus                           STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 22(11P13) MUTATED                                                                  14
  AMP PEAK 22(11P13) WILD-TYPE                                                                68
                              vv
clus                           STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK 22(11P13) MUTATED                                                    0
  AMP PEAK 22(11P13) WILD-TYPE                                                  8
                              vv
clus                           STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK 22(11P13) MUTATED                                                 17
  AMP PEAK 22(11P13) WILD-TYPE                                               62
D22V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK 22(11P13) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                   5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                     13
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                    33
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                          5
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         14
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                         0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                          17
                                                                   clus
vv                                                                  AMP PEAK 22(11P13) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       59
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     130
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           16
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           8
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            62
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 22(11P13) MUTATED    64   4   7   5
  AMP PEAK 22(11P13) WILD-TYPE 285  14  12  20
D22V10, multiclass
    clus
vv   AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE
  R0                         64                          285
  R1                          4                           14
  R2                          7                           12
  RX                          5                           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"
D22V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 22(11P13) MUTATED      18                         3
  AMP PEAK 22(11P13) WILD-TYPE    70                         9
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 22(11P13) MUTATED                                           1    54
  AMP PEAK 22(11P13) WILD-TYPE                                         0   224
D22V12, multiclass
                                           clus
vv                                          AMP PEAK 22(11P13) MUTATED
  ASIAN                                                             18
  BLACK OR AFRICAN AMERICAN                                          3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                             54
                                           clus
vv                                          AMP PEAK 22(11P13) WILD-TYPE
  ASIAN                                                               70
  BLACK OR AFRICAN AMERICAN                                            9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V13, binary
                              cls
clus                             0   1
  AMP PEAK 22(11P13) MUTATED     2  59
  AMP PEAK 22(11P13) WILD-TYPE   3 257
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(11P13) MUTATED      2   59
  AMP PEAK 22(11P13) WILD-TYPE    3  257
                        clus
vv                       AMP PEAK 22(11P13) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         59
                        clus
vv                       AMP PEAK 22(11P13) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          257
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 23(11P11.2) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 23(11P11.2) MUTATED    50  35
  AMP PEAK 23(11P11.2) WILD-TYPE 196 134
  AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE 
                            85                            330 
  AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE 
                            35                            134 
$`AMP PEAK 23(11P11.2) MUTATED`
TCGA-CG-4444 TCGA-FP-A8CX TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-A5TJ 
       47.05         0.23        27.35        26.93        58.03        11.01 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4257 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6458 
        9.44         6.61         9.67        13.87        17.29        19.33 
TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8296 TCGA-BR-8485 
       18.15         3.45        11.44         0.69        15.58         9.21 
TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY 
       24.79        20.88         8.22        34.98         1.48        12.89 
TCGA-BR-A4J8 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-A487 TCGA-CD-A4MH 
       13.51        12.59        12.33        12.39        12.30        12.20 
TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5722 
       20.02        54.08         4.01        12.00         6.97         0.99 
TCGA-D7-6520 TCGA-D7-6822 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A6F2 
       18.84        12.33        14.66        21.14        14.27        15.65 
TCGA-EQ-8122 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 TCGA-HF-7133 TCGA-HU-8243 
        7.99        14.07        17.06         0.56        63.06         5.92 
TCGA-HU-8249 TCGA-HU-A4G2 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RI 
       28.96        24.30        23.80        33.40         3.45        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-KB-A6F5 
       12.46        19.53        10.62        11.70        15.75         5.56 
TCGA-KB-A93H TCGA-R5-A7ZI TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N6 
       37.64        74.53         8.61        16.67       115.69         8.94 
TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PJ 
        5.46        13.02        18.48        43.36        22.19         2.70 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X 
       64.57        14.33        21.83        32.88         1.71         9.50 
TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-AA6B TCGA-VQ-AA6D 
        9.73         9.04         4.54        66.81        32.94        17.13 
TCGA-VQ-AA6F 
       54.12 

$`AMP PEAK 23(11P11.2) WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 
       21.99        22.98        79.07        16.24        20.15         9.86 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 
       26.70        11.70        19.56         9.47         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6457 
        6.18         9.57         6.61        34.68        15.95        13.68 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 
       33.63        39.78        15.32        28.73         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       33.21        37.25        14.43        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        9.34        28.14         6.28         7.53        26.73        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       32.58         9.86        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        6.08        27.55        28.57         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
       12.76        12.53         7.17        12.30        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 
       15.39        12.07        12.82        12.43         6.31        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 
       12.43        11.61         6.58        11.77        12.62         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 
       27.02        15.95         1.02         7.99         8.05        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        7.07        30.97        36.00         1.02         0.99         6.02 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        20.55        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 
        8.38         4.34        19.96         7.13         0.62        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
       72.23        21.27        11.38         3.48        19.53        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       59.54         5.03        13.58         5.52         6.21        77.29 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
       52.21        30.51        26.47         1.51        24.39        18.15 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.32        22.82        21.07         0.76         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 
       21.17        14.07        15.68        36.36        18.81         3.39 
TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1X 
       13.35         6.44         6.74        12.59         6.51        13.51 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        2.53        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 
       11.05         5.13       122.30        37.91        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44        35.61        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        0.92        48.79        13.25        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       37.22         7.73        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
        2.50        12.79        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       15.65        13.35        29.59        73.41        39.45        11.70 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Z 
       61.22        18.74        20.81        42.64        60.85        55.56 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P 
        2.01        55.43         6.58         5.72        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       42.54        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        27.55        12.43        17.26         0.79 

  AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE 
                          0.23                           0.00 
  AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE 
                        115.69                         122.30 
  AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE 
                        14.070                         15.355 
[1] "0.2 - 115.7 (14.1)" "0.0 - 122.3 (15.4)"
[1] "hr=" "1"  
D23V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 23(11P11.2) MUTATED         1        4        9        2         3
  AMP PEAK 23(11P11.2) WILD-TYPE       1       12       32       30        37
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 23(11P11.2) MUTATED          15         0         19         14
  AMP PEAK 23(11P11.2) WILD-TYPE        41         3         62         49
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 23(11P11.2) MUTATED            8       12
  AMP PEAK 23(11P11.2) WILD-TYPE         31       32
D23V3, multiclass
            clus
vv           AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                              4                             12
  STAGE IB                              9                             32
  STAGE II                              2                             30
  STAGE IIA                             3                             37
  STAGE IIB                            15                             41
  STAGE III                             0                              3
  STAGE IIIA                           19                             62
  STAGE IIIB                           14                             49
  STAGE IIIC                            8                             31
  STAGE IV                             12                             32
[1] 11  2
[1] TRUE
[1] "dimension of 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(11P11.2) MUTATED     6  16  39  28
  AMP PEAK 23(11P11.2) WILD-TYPE  17  77 157  91
D23V4, multiclass
    clus
vv   AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE
  T1                            6                             17
  T2                           16                             77
  T3                           39                            157
  T4                           28                             91
[1] 4 2
[1] TRUE
[1] "dimension of 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(11P11.2) MUTATED    21  26  24  16
  AMP PEAK 23(11P11.2) WILD-TYPE 109  93  62  72
D23V5, multiclass
    clus
vv   AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE
  N0                           21                            109
  N1                           26                             93
  N2                           24                             62
  N3                           16                             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                                cls
clus                               0   1
  AMP PEAK 23(11P11.2) MUTATED    79   6
  AMP PEAK 23(11P11.2) WILD-TYPE 310  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(11P11.2) MUTATED     79    6
  AMP PEAK 23(11P11.2) WILD-TYPE  310   24
   clus
vv  AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE
  0                           79                            310
  1                            6                             24
[1] 2 2
[1] FALSE
D23V7, binary
                                cls
clus                               0   1
  AMP PEAK 23(11P11.2) MUTATED    29  63
  AMP PEAK 23(11P11.2) WILD-TYPE 129 220
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(11P11.2) MUTATED     29   63
  AMP PEAK 23(11P11.2) WILD-TYPE  129  220
        clus
vv       AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE
  FEMALE                           29                            129
  MALE                             63                            220
[1] 2 2
[1] FALSE
D23V8, binary
                                cls
clus                               0   1
  AMP PEAK 23(11P11.2) MUTATED    60  21
  AMP PEAK 23(11P11.2) WILD-TYPE 262  55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(11P11.2) MUTATED     60   21
  AMP PEAK 23(11P11.2) WILD-TYPE  262   55
     clus
vv    AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE
  NO                            60                            262
  YES                           21                             55
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK 23(11P11.2) MUTATED                                          3
  AMP PEAK 23(11P11.2) WILD-TYPE                                       10
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK 23(11P11.2) MUTATED                                       9
  AMP PEAK 23(11P11.2) WILD-TYPE                                    63
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 23(11P11.2) MUTATED                                                       36
  AMP PEAK 23(11P11.2) WILD-TYPE                                                    127
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK 23(11P11.2) MUTATED                                                   2
  AMP PEAK 23(11P11.2) WILD-TYPE                                                19
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 23(11P11.2) MUTATED                                                                  17
  AMP PEAK 23(11P11.2) WILD-TYPE                                                                65
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK 23(11P11.2) MUTATED                                                    1
  AMP PEAK 23(11P11.2) WILD-TYPE                                                  7
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK 23(11P11.2) MUTATED                                                 23
  AMP PEAK 23(11P11.2) WILD-TYPE                                               56
D23V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK 23(11P11.2) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        9
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      36
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           17
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            23
                                                                   clus
vv                                                                  AMP PEAK 23(11P11.2) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         63
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       127
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 23(11P11.2) MUTATED    68   4   7   6
  AMP PEAK 23(11P11.2) WILD-TYPE 281  14  12  19
D23V10, multiclass
    clus
vv   AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE
  R0                           68                            281
  R1                            4                             14
  R2                            7                             12
  RX                            6                             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"
D23V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 23(11P11.2) MUTATED      17                         3
  AMP PEAK 23(11P11.2) WILD-TYPE    71                         9
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 23(11P11.2) MUTATED                                           1
  AMP PEAK 23(11P11.2) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 23(11P11.2) MUTATED      57
  AMP PEAK 23(11P11.2) WILD-TYPE   221
D23V12, multiclass
                                           clus
vv                                          AMP PEAK 23(11P11.2) MUTATED
  ASIAN                                                               17
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               57
                                           clus
vv                                          AMP PEAK 23(11P11.2) WILD-TYPE
  ASIAN                                                                 71
  BLACK OR AFRICAN AMERICAN                                              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V13, binary
                                cls
clus                               0   1
  AMP PEAK 23(11P11.2) MUTATED     2  58
  AMP PEAK 23(11P11.2) WILD-TYPE   3 258
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(11P11.2) MUTATED      2   58
  AMP PEAK 23(11P11.2) WILD-TYPE    3  258
                        clus
vv                       AMP PEAK 23(11P11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           58
                        clus
vv                       AMP PEAK 23(11P11.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            258
[1] 2 2
[1] FALSE

Clustering(24) Variable = AMP PEAK 24(11Q13.3) MUTATION ANALYSIS
D24V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 24(11Q13.3) MUTATED    62  43
  AMP PEAK 24(11Q13.3) WILD-TYPE 184 126
  AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE 
                           105                            310 
  AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE 
                            43                            126 
$`AMP PEAK 24(11Q13.3) MUTATED`
TCGA-CG-4444 TCGA-MX-A663 TCGA-VQ-A8PU TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4257 
       47.05         9.86        27.35        11.01         9.44         9.67 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-7704 TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-8058 
       13.87        13.68        35.24        18.15         3.45        37.25 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8296 TCGA-BR-8361 TCGA-BR-8365 
       11.44         0.69         9.60        15.58        31.10        17.52 
TCGA-BR-8485 TCGA-BR-8589 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A4CQ 
        9.21        27.12        24.79        20.88         8.22        34.98 
TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-8525 
        1.48        12.89         1.15        21.44        13.02        12.59 
TCGA-CD-8528 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-A487 TCGA-CD-A48C 
       12.33        11.64        15.39        12.07        12.30        11.61 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4472 
       12.20        20.02        54.08        19.07        12.03        12.00 
TCGA-CG-5722 TCGA-CG-5724 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A6EV TCGA-D7-A6F0 
        0.99        12.03        18.21        14.66        11.24        22.29 
TCGA-D7-A6F2 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-8099 TCGA-FP-8631 TCGA-HF-7133 
       15.65         7.99        72.23        17.06         0.56        63.06 
TCGA-HF-7134 TCGA-HU-8243 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4GC TCGA-HU-A4GY 
       52.21         5.92         0.76        24.30         3.25         0.26 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-8663 TCGA-IN-A6RJ 
       23.84        23.80        21.17        33.40         3.39        12.46 
TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 
       13.35         6.44         6.74        10.62        11.70         5.56 
TCGA-KB-A93H TCGA-R5-A7ZI TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N1 
       37.64        74.53         8.61        16.67       122.30       115.69 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-VQ-A8DU TCGA-VQ-A8DZ 
       57.44         8.94        35.61        19.04         5.46        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PX TCGA-VQ-A8PY 
       18.48        43.36        22.19         2.70        64.57        14.33 
TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91Y 
       39.45        21.83        18.74        32.88         1.71         9.73 
TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B 
        4.54        66.81        11.24        43.66        38.93        32.94 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       27.55        12.43         0.79 

$`AMP PEAK 24(11Q13.3) WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       21.99        22.98        79.07        16.24         0.23        20.15 
TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
       26.93        58.03        26.70        11.70        19.56         9.47 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       34.68        15.95        17.29        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 
        9.21        36.16        35.84        33.63        39.78        15.32 
TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8078 
       28.73         9.07        29.56        33.21        14.43        29.59 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        13.08         0.26        22.19 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
       25.18        20.22         1.12        12.79         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        31.96        32.58         9.86 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU 
       10.68        34.13        13.87         7.53         6.08        27.55 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.66        32.52        13.51         0.46        20.65        20.42 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       16.14         5.13        13.41        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 
       11.21        12.10        12.76        12.53         7.17        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 
       12.39        12.59        12.82        12.43         6.31        11.31 
TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
       12.43         6.58        11.77        12.62         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         7.99         8.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       29.98         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         6.02       105.07 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8578 
       12.33        24.72        16.80        19.50        17.19        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 
       14.76        26.43        11.31        11.44        20.32         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-A448 
        4.34        19.96         7.13         0.62        14.47        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
       11.38         3.48        19.53        14.07        22.29        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-A5NB 
        5.03        13.58         5.52         6.21        77.29        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51        24.39        18.15        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       22.82        21.07         5.59        24.26        22.68        24.20 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.58        20.25         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       29.00        14.07        15.68        36.36         3.45        18.81 
TCGA-IN-A6RI TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X 
       18.38        19.53        12.59         6.51        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        2.53        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
       11.05         5.13        37.91        40.64       116.38        71.38 
TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E3 
       16.87         5.79         0.92        48.79        13.25        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM 
       46.26        16.31         2.50        12.79        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ 
        9.27        23.41        15.65        13.35        29.59        73.41 
TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       11.70        61.22        20.81        42.64        60.85         9.50 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
       55.56         9.04         2.01        55.43         6.58         5.72 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6D 
       21.04         2.66        42.54        18.41        28.41        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-ZA-A8F6 
       54.12        26.04        16.14        17.26 

  AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE 
                          0.26                           0.00 
  AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE 
                        122.30                         116.38 
  AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE 
                         13.87                          15.27 
[1] "0.3 - 122.3 (13.9)" "0.0 - 116.4 (15.3)"
[1] "hr=" "1"  
D24V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 24(11Q13.3) MUTATED         0        6        8        8         7
  AMP PEAK 24(11Q13.3) WILD-TYPE       2       10       33       24        33
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 24(11Q13.3) MUTATED          15         0         20         20
  AMP PEAK 24(11Q13.3) WILD-TYPE        41         3         61         43
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 24(11Q13.3) MUTATED           14       12
  AMP PEAK 24(11Q13.3) WILD-TYPE         25       32
D24V3, multiclass
            clus
vv           AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              6                             10
  STAGE IB                              8                             33
  STAGE II                              8                             24
  STAGE IIA                             7                             33
  STAGE IIB                            15                             41
  STAGE III                             0                              3
  STAGE IIIA                           20                             61
  STAGE IIIB                           20                             43
  STAGE IIIC                           14                             25
  STAGE IV                             12                             32
[1] 11  2
[1] TRUE
[1] "dimension of 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(11Q13.3) MUTATED     6  21  47  37
  AMP PEAK 24(11Q13.3) WILD-TYPE  17  72 149  82
D24V4, multiclass
    clus
vv   AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE
  T1                            6                             17
  T2                           21                             72
  T3                           47                            149
  T4                           37                             82
[1] 4 2
[1] TRUE
[1] "dimension of 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(11Q13.3) MUTATED    28  29  32  20
  AMP PEAK 24(11Q13.3) WILD-TYPE 102  90  54  68
D24V5, multiclass
    clus
vv   AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE
  N0                           28                            102
  N1                           29                             90
  N2                           32                             54
  N3                           20                             68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                                cls
clus                               0   1
  AMP PEAK 24(11Q13.3) MUTATED   105   5
  AMP PEAK 24(11Q13.3) WILD-TYPE 284  25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(11Q13.3) MUTATED    105    5
  AMP PEAK 24(11Q13.3) WILD-TYPE  284   25
   clus
vv  AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE
  0                          105                            284
  1                            5                             25
[1] 2 2
[1] FALSE
D24V7, binary
                                cls
clus                               0   1
  AMP PEAK 24(11Q13.3) MUTATED    39  76
  AMP PEAK 24(11Q13.3) WILD-TYPE 119 207
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(11Q13.3) MUTATED     39   76
  AMP PEAK 24(11Q13.3) WILD-TYPE  119  207
        clus
vv       AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE
  FEMALE                           39                            119
  MALE                             76                            207
[1] 2 2
[1] FALSE
D24V8, binary
                                cls
clus                               0   1
  AMP PEAK 24(11Q13.3) MUTATED    79  24
  AMP PEAK 24(11Q13.3) WILD-TYPE 243  52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(11Q13.3) MUTATED     79   24
  AMP PEAK 24(11Q13.3) WILD-TYPE  243   52
     clus
vv    AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE
  NO                            79                            243
  YES                           24                             52
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK 24(11Q13.3) MUTATED                                          2
  AMP PEAK 24(11Q13.3) WILD-TYPE                                       11
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK 24(11Q13.3) MUTATED                                      14
  AMP PEAK 24(11Q13.3) WILD-TYPE                                    58
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 24(11Q13.3) MUTATED                                                       45
  AMP PEAK 24(11Q13.3) WILD-TYPE                                                    118
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK 24(11Q13.3) MUTATED                                                   7
  AMP PEAK 24(11Q13.3) WILD-TYPE                                                14
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 24(11Q13.3) MUTATED                                                                  21
  AMP PEAK 24(11Q13.3) WILD-TYPE                                                                61
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK 24(11Q13.3) MUTATED                                                    1
  AMP PEAK 24(11Q13.3) WILD-TYPE                                                  7
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK 24(11Q13.3) MUTATED                                                 24
  AMP PEAK 24(11Q13.3) WILD-TYPE                                               55
D24V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK 24(11Q13.3) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       14
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      45
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            7
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           21
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            24
                                                                   clus
vv                                                                  AMP PEAK 24(11Q13.3) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         58
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       118
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             14
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             61
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              55
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 24(11Q13.3) MUTATED    91   5   7   6
  AMP PEAK 24(11Q13.3) WILD-TYPE 258  13  12  19
D24V10, multiclass
    clus
vv   AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE
  R0                           91                            258
  R1                            5                             13
  R2                            7                             12
  RX                            6                             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"
D24V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 24(11Q13.3) MUTATED      25                         5
  AMP PEAK 24(11Q13.3) WILD-TYPE    63                         7
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 24(11Q13.3) MUTATED                                           1
  AMP PEAK 24(11Q13.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 24(11Q13.3) MUTATED      67
  AMP PEAK 24(11Q13.3) WILD-TYPE   211
D24V12, multiclass
                                           clus
vv                                          AMP PEAK 24(11Q13.3) MUTATED
  ASIAN                                                               25
  BLACK OR AFRICAN AMERICAN                                            5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               67
                                           clus
vv                                          AMP PEAK 24(11Q13.3) WILD-TYPE
  ASIAN                                                                 63
  BLACK OR AFRICAN AMERICAN                                              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V13, binary
                                cls
clus                               0   1
  AMP PEAK 24(11Q13.3) MUTATED     1  77
  AMP PEAK 24(11Q13.3) WILD-TYPE   4 239
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(11Q13.3) MUTATED      1   77
  AMP PEAK 24(11Q13.3) WILD-TYPE    4  239
                        clus
vv                       AMP PEAK 24(11Q13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           77
                        clus
vv                       AMP PEAK 24(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            239
[1] 2 2
[1] FALSE

Clustering(25) Variable = AMP PEAK 25(12P12.1) MUTATION ANALYSIS
D25V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 25(12P12.1) MUTATED    74  47
  AMP PEAK 25(12P12.1) WILD-TYPE 172 122
  AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE 
                           121                            294 
  AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE 
                            47                            122 
$`AMP PEAK 25(12P12.1) MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-B7-A5TK TCGA-BR-4183 
       47.05        21.99        79.07        16.24         9.47         6.61 
TCGA-BR-4255 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6709 TCGA-BR-6801 
        4.08        39.12        32.78        25.61        12.16        40.21 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8078 TCGA-BR-8295 TCGA-BR-8297 
       28.73         3.45        33.21        29.59         2.20         7.40 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8369 TCGA-BR-8370 
       31.10        13.08         0.26         0.95        14.04         3.32 
TCGA-BR-8381 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8678 TCGA-BR-8687 TCGA-BR-A452 
        7.36        20.22        27.12        24.79         8.22         7.53 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4PF TCGA-CD-5798 
       34.98         1.48         0.72        14.17         1.15        13.41 
TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 
       13.02        13.35        12.76        12.53         7.17        12.39 
TCGA-CD-8531 TCGA-CD-A48A TCGA-CD-A48C TCGA-CG-4300 TCGA-CG-4472 TCGA-CG-5722 
       12.59        12.43        11.61        20.02        12.00         0.99 
TCGA-CG-5724 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6526 
       12.03        12.66        19.13        20.55        18.54        17.19 
TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-A4YV TCGA-D7-A6EX 
       12.79        11.31        19.50        18.21         5.92        11.31 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A74A TCGA-EQ-5647 TCGA-F1-A72C 
       22.29        15.65         8.38        19.96         0.62        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HU-8238 
        3.48        19.53        22.29         5.52         6.21         1.51 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       28.96        22.82        24.30         3.25        22.75        25.81 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4HB TCGA-HU-A4HD 
        8.98         6.51         6.58        20.25        15.68        33.40 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR 
        3.45         3.39        12.46         6.44         6.74         6.51 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7ZE 
       11.70        15.75         2.53        63.62        37.64        18.21 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8N6 TCGA-SW-A7EB 
       74.53         6.08        11.05        16.67         8.94         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        0.92        48.79        13.25        18.48        43.36        21.73 
TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91E 
        7.73        22.19        17.85        14.33        39.45        21.83 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A94T 
       18.74        20.81        42.64         4.54         5.72        11.24 
TCGA-VQ-AA6K 
       12.43 

$`AMP PEAK 25(12P12.1) WILD-TYPE`
TCGA-CG-4475 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U 
       22.98         0.23        20.15         9.86        27.35        26.93 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN 
       58.03        26.70        11.70        19.56        11.01         9.44 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 
       15.95        13.87        17.29        13.68        19.33        26.10 
TCGA-BR-6565 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 
        9.17        18.05        19.89         8.98        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-7958 
       33.63        39.78        18.15        15.32         9.07        29.56 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 
        8.05         0.56        29.42         2.66        19.96        15.58 
TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8371 
        6.18        22.19        17.52        26.33         4.31        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       31.27        14.79        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        9.21         1.12        12.79         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        31.96        32.58         9.86        20.88 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
       10.68        34.13        13.87         6.08        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
       12.89         8.98         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51         0.46        20.65        20.42        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 
        5.13        13.15        13.18        11.21        12.10        12.59 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.33        12.30        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MH 
       12.43         6.31        12.30        11.31         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        12.62         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6522 
       21.07         7.99        25.71        20.91        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 
       17.85        13.35        10.26        15.22        15.98        12.36 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 
       12.33        24.72        16.80        17.19        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27        16.44        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74B 
       26.43        11.24        11.44        20.32         4.34         7.13 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7916 TCGA-FP-8099 
        7.99        14.47        72.23        21.27        14.07        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-7132 TCGA-HF-7133 
       59.54         5.03        13.58         0.56        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       52.21        30.51        26.47         5.92        24.39        18.15 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       22.32        21.07         0.76         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GY 
       24.20        11.77        21.37        29.98         0.10         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN 
       14.07        36.36        18.81        18.38        13.35        19.53 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A93J TCGA-MX-A5UG 
       12.59        10.62        13.51         5.56        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A804 TCGA-R5-A805 
       19.73        14.04        45.67         8.52         4.60         9.24 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        8.61         5.13       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44        35.61        16.87        19.04 
TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
        5.46        13.02        37.41        38.14        37.22        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       34.29        46.26        16.31         2.50        12.79         2.70 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91U 
       64.57        73.41        11.70        61.22        32.88         1.71 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
       60.85         9.50         9.73        55.56         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
       55.43         6.58        66.81        21.04         2.66        42.54 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       18.41        43.66        28.41        38.93        32.94        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       54.12        26.04        16.14        27.55        17.26         0.79 

  AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE 
                          0.26                           0.00 
  AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE 
                         79.07                         122.30 
  AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE 
                         13.02                          15.95 
[1] "0.3 - 79.1 (13.0)"  "0.0 - 122.3 (15.9)"
[1] "hr=" "1.1"
D25V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 25(12P12.1) MUTATED         0        3        9        7        14
  AMP PEAK 25(12P12.1) WILD-TYPE       2       13       32       25        26
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 25(12P12.1) MUTATED          17         1         29         20
  AMP PEAK 25(12P12.1) WILD-TYPE        39         2         52         43
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 25(12P12.1) MUTATED           10       12
  AMP PEAK 25(12P12.1) WILD-TYPE         29       32
D25V3, multiclass
            clus
vv           AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              3                             13
  STAGE IB                              9                             32
  STAGE II                              7                             25
  STAGE IIA                            14                             26
  STAGE IIB                            17                             39
  STAGE III                             1                              2
  STAGE IIIA                           29                             52
  STAGE IIIB                           20                             43
  STAGE IIIC                           10                             29
  STAGE IV                             12                             32
[1] 11  2
[1] TRUE
[1] "dimension of 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(12P12.1) MUTATED     6  20  72  29
  AMP PEAK 25(12P12.1) WILD-TYPE  17  73 124  90
D25V4, multiclass
    clus
vv   AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE
  T1                            6                             17
  T2                           20                             73
  T3                           72                            124
  T4                           29                             90
[1] 4 2
[1] TRUE
[1] "dimension of 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(12P12.1) MUTATED   33 35 32 26
  AMP PEAK 25(12P12.1) WILD-TYPE 97 84 54 62
D25V5, multiclass
    clus
vv   AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE
  N0                           33                             97
  N1                           35                             84
  N2                           32                             54
  N3                           26                             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"
D25V6, binary
                                cls
clus                               0   1
  AMP PEAK 25(12P12.1) MUTATED   116   8
  AMP PEAK 25(12P12.1) WILD-TYPE 273  22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(12P12.1) MUTATED    116    8
  AMP PEAK 25(12P12.1) WILD-TYPE  273   22
   clus
vv  AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE
  0                          116                            273
  1                            8                             22
[1] 2 2
[1] FALSE
D25V7, binary
                                cls
clus                               0   1
  AMP PEAK 25(12P12.1) MUTATED    46  82
  AMP PEAK 25(12P12.1) WILD-TYPE 112 201
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(12P12.1) MUTATED     46   82
  AMP PEAK 25(12P12.1) WILD-TYPE  112  201
        clus
vv       AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE
  FEMALE                           46                            112
  MALE                             82                            201
[1] 2 2
[1] FALSE
D25V8, binary
                                cls
clus                               0   1
  AMP PEAK 25(12P12.1) MUTATED    96  24
  AMP PEAK 25(12P12.1) WILD-TYPE 226  52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(12P12.1) MUTATED     96   24
  AMP PEAK 25(12P12.1) WILD-TYPE  226   52
     clus
vv    AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE
  NO                            96                            226
  YES                           24                             52
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK 25(12P12.1) MUTATED                                          2
  AMP PEAK 25(12P12.1) WILD-TYPE                                       11
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK 25(12P12.1) MUTATED                                      24
  AMP PEAK 25(12P12.1) WILD-TYPE                                    48
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 25(12P12.1) MUTATED                                                       46
  AMP PEAK 25(12P12.1) WILD-TYPE                                                    117
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK 25(12P12.1) MUTATED                                                   5
  AMP PEAK 25(12P12.1) WILD-TYPE                                                16
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 25(12P12.1) MUTATED                                                                  18
  AMP PEAK 25(12P12.1) WILD-TYPE                                                                64
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK 25(12P12.1) MUTATED                                                    1
  AMP PEAK 25(12P12.1) WILD-TYPE                                                  7
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK 25(12P12.1) MUTATED                                                 30
  AMP PEAK 25(12P12.1) WILD-TYPE                                               49
D25V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK 25(12P12.1) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       24
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      46
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           18
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            30
                                                                   clus
vv                                                                  AMP PEAK 25(12P12.1) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         48
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       117
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             16
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              49
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 25(12P12.1) MUTATED   103   6   6   4
  AMP PEAK 25(12P12.1) WILD-TYPE 246  12  13  21
D25V10, multiclass
    clus
vv   AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE
  R0                          103                            246
  R1                            6                             12
  R2                            6                             13
  RX                            4                             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"
D25V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 25(12P12.1) MUTATED      29                         3
  AMP PEAK 25(12P12.1) WILD-TYPE    59                         9
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 25(12P12.1) MUTATED                                           0
  AMP PEAK 25(12P12.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 25(12P12.1) MUTATED      81
  AMP PEAK 25(12P12.1) WILD-TYPE   197
D25V12, multiclass
                                           clus
vv                                          AMP PEAK 25(12P12.1) MUTATED
  ASIAN                                                               29
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               81
                                           clus
vv                                          AMP PEAK 25(12P12.1) WILD-TYPE
  ASIAN                                                                 59
  BLACK OR AFRICAN AMERICAN                                              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                197
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V13, binary
                                cls
clus                               0   1
  AMP PEAK 25(12P12.1) MUTATED     2  96
  AMP PEAK 25(12P12.1) WILD-TYPE   3 220
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(12P12.1) MUTATED      2   96
  AMP PEAK 25(12P12.1) WILD-TYPE    3  220
                        clus
vv                       AMP PEAK 25(12P12.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           96
                        clus
vv                       AMP PEAK 25(12P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            220
[1] 2 2
[1] FALSE

Clustering(26) Variable = AMP PEAK 26(12Q15) MUTATION ANALYSIS
D26V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 26(12Q15) MUTATED    63  40
  AMP PEAK 26(12Q15) WILD-TYPE 183 129
  AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE 
                         103                          312 
  AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE 
                          40                          129 
$`AMP PEAK 26(12Q15) MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-B7-A5TK 
       47.05        21.99        22.98        79.07         0.23         9.47 
TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-7723 
        6.61        18.35         6.18        39.12        32.78        28.73 
TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8295 TCGA-BR-8297 
       33.21        11.44         0.69        29.59         2.20         7.40 
TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8370 TCGA-BR-8381 TCGA-BR-8484 TCGA-BR-8589 
        0.26         0.95         3.32         7.36        25.18        27.12 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A4CS TCGA-BR-A4J1 
       20.88         8.22        34.13         7.53         1.48         0.72 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5802 
        0.53         0.66         1.15        13.41        13.02        13.35 
TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A48A 
       12.53        12.39        12.59        12.82        12.30        12.43 
TCGA-CG-4301 TCGA-CG-4455 TCGA-CG-4472 TCGA-CG-5722 TCGA-CG-5725 TCGA-CG-5732 
        3.02        12.03        12.00         0.99        15.02        69.04 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 
       12.66        19.13        20.55        18.54        17.19        10.26 
TCGA-D7-6817 TCGA-D7-8573 TCGA-D7-A4YV TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A74A 
       12.79        19.50         5.92        15.65         8.38        19.96 
TCGA-EQ-5647 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-A4BF TCGA-FP-A9TM 
        0.62        11.38        14.07        22.29         5.52         6.21 
TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4GP 
        1.51        28.96        22.82        24.30        22.75         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H4 TCGA-HU-A4HD TCGA-IN-7808 
        6.51         6.58        20.25        23.84        33.40         3.45 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-AB1V TCGA-KB-A6F7 
        3.39        12.46        19.53         6.44        15.75        63.62 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-VQ-A8E0 TCGA-VQ-A8E2 
       74.53         6.08         5.13        16.67        18.48        43.36 
TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PS TCGA-VQ-A8PY 
        7.73        22.19        12.79         2.70        13.35        14.33 
TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A928 
       21.83        20.81         9.50         9.04         4.54         5.72 
TCGA-VQ-AA6K 
       12.43 

$`AMP PEAK 26(12Q15) WILD-TYPE`
TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 
       16.24        20.15         9.86        27.35        26.93        58.03 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4184 
       26.70        11.70        19.56        11.01         9.44         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        9.67         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 
       17.29        13.68        19.33        26.10         9.17        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 
       35.84        33.63        39.78        18.15        15.32         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8081 
        9.07        29.56        37.25        14.43         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 
        8.05         0.56        29.42         2.66        19.96        15.58 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 
        6.18        31.10        13.08        22.19        17.52        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 
        4.31        14.04        11.80        31.27        14.79        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        3.72         5.39         9.21        20.22         1.12        12.79 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A453 
       31.96        32.58         9.86        10.68        13.87         6.08 
TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
       34.98        27.55        28.57        12.89         8.98        14.17 
TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34        32.52        13.51         0.46        20.65        20.42 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 
       21.44        16.14         5.13        13.15        13.18        11.21 
TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.10        12.76        12.59         7.17        12.33        12.30 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 
       11.64        15.39        12.07        12.43         6.31        11.31 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 
        4.01        14.01        29.98        19.07         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 
        0.99         6.02       105.07        12.03        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6520 
        4.01        21.07         7.99        25.71        20.91        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 
       18.61        17.85        13.35        15.22        15.98        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 
       11.31        12.33        24.72        16.80        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 
       20.32        22.29         4.34         7.13         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8209 
       72.23        21.27         3.48        19.53        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        5.03        13.58         0.56        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       30.51        26.47         5.92        24.39        18.15        22.32 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       21.07         0.76         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
        3.25        25.81        11.77        21.37        29.98         0.10 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        29.00        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL 
       14.07        15.68        36.36        18.81        18.38        13.35 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X 
        6.74        12.59         6.51        10.62        11.70        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        37.64        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A804 TCGA-R5-A805 
       14.04        45.67        18.21         8.52         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
       11.05         8.61       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      116.38        71.38        57.44         8.94        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       13.02        21.73        37.41        38.14        37.22        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PK TCGA-VQ-A8PM 
       34.29        46.26        16.31         2.50        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ 
        9.27        23.41        15.65        29.59        64.57        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U 
       39.45        11.70        61.22        18.74        32.88         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 
       42.64        60.85         9.73        55.56         2.01        55.43 
TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
        6.58        66.81        21.04         2.66        42.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       18.41        43.66        28.41        38.93        32.94        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       54.12        26.04        16.14        27.55        17.26         0.79 

  AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE 
                        0.23                         0.00 
  AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE 
                       79.07                       122.30 
  AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE 
                       12.59                        16.14 
[1] "0.2 - 79.1 (12.6)"  "0.0 - 122.3 (16.1)"
[1] "hr=" "1.2"
D26V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 26(12Q15) MUTATED         0        3        8        7        13
  AMP PEAK 26(12Q15) WILD-TYPE       2       13       33       25        27
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 26(12Q15) MUTATED          14         1         21         13
  AMP PEAK 26(12Q15) WILD-TYPE        42         2         60         50
                              vv
clus                           STAGE IIIC STAGE IV
  AMP PEAK 26(12Q15) MUTATED            9       13
  AMP PEAK 26(12Q15) WILD-TYPE         30       31
D26V3, multiclass
            clus
vv           AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE
  STAGE I                             0                            2
  STAGE IA                            3                           13
  STAGE IB                            8                           33
  STAGE II                            7                           25
  STAGE IIA                          13                           27
  STAGE IIB                          14                           42
  STAGE III                           1                            2
  STAGE IIIA                         21                           60
  STAGE IIIB                         13                           50
  STAGE IIIC                          9                           30
  STAGE IV                           13                           31
[1] 11  2
[1] TRUE
[1] "dimension of 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(12Q15) MUTATED     7  20  50  30
  AMP PEAK 26(12Q15) WILD-TYPE  16  73 146  89
D26V4, multiclass
    clus
vv   AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE
  T1                          7                           16
  T2                         20                           73
  T3                         50                          146
  T4                         30                           89
[1] 4 2
[1] TRUE
[1] "dimension of 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(12Q15) MUTATED    28  34  26  18
  AMP PEAK 26(12Q15) WILD-TYPE 102  85  60  70
D26V5, multiclass
    clus
vv   AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE
  N0                         28                          102
  N1                         34                           85
  N2                         26                           60
  N3                         18                           70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                              cls
clus                             0   1
  AMP PEAK 26(12Q15) MUTATED    97   8
  AMP PEAK 26(12Q15) WILD-TYPE 292  22
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(12Q15) MUTATED     97    8
  AMP PEAK 26(12Q15) WILD-TYPE  292   22
   clus
vv  AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE
  0                         97                          292
  1                          8                           22
[1] 2 2
[1] FALSE
D26V7, binary
                              cls
clus                             0   1
  AMP PEAK 26(12Q15) MUTATED    36  73
  AMP PEAK 26(12Q15) WILD-TYPE 122 210
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(12Q15) MUTATED     36   73
  AMP PEAK 26(12Q15) WILD-TYPE  122  210
        clus
vv       AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE
  FEMALE                         36                          122
  MALE                           73                          210
[1] 2 2
[1] FALSE
D26V8, binary
                              cls
clus                             0   1
  AMP PEAK 26(12Q15) MUTATED    77  22
  AMP PEAK 26(12Q15) WILD-TYPE 245  54
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(12Q15) MUTATED     77   22
  AMP PEAK 26(12Q15) WILD-TYPE  245   54
     clus
vv    AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE
  NO                          77                          245
  YES                         22                           54
[1] 2 2
[1] FALSE
                              vv
clus                           STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK 26(12Q15) MUTATED                                          3
  AMP PEAK 26(12Q15) WILD-TYPE                                       10
                              vv
clus                           STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK 26(12Q15) MUTATED                                      22
  AMP PEAK 26(12Q15) WILD-TYPE                                    50
                              vv
clus                           STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 26(12Q15) MUTATED                                                       37
  AMP PEAK 26(12Q15) WILD-TYPE                                                    126
                              vv
clus                           STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK 26(12Q15) MUTATED                                                   3
  AMP PEAK 26(12Q15) WILD-TYPE                                                18
                              vv
clus                           STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 26(12Q15) MUTATED                                                                  14
  AMP PEAK 26(12Q15) WILD-TYPE                                                                68
                              vv
clus                           STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK 26(12Q15) MUTATED                                                    2
  AMP PEAK 26(12Q15) WILD-TYPE                                                  6
                              vv
clus                           STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK 26(12Q15) MUTATED                                                 26
  AMP PEAK 26(12Q15) WILD-TYPE                                               53
D26V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK 26(12Q15) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                   3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                     22
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                    37
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         14
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                         2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                          26
                                                                   clus
vv                                                                  AMP PEAK 26(12Q15) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       50
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     126
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            53
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 26(12Q15) MUTATED    84   5   7   5
  AMP PEAK 26(12Q15) WILD-TYPE 265  13  12  20
D26V10, multiclass
    clus
vv   AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE
  R0                         84                          265
  R1                          5                           13
  R2                          7                           12
  RX                          5                           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"
D26V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 26(12Q15) MUTATED      28                         2
  AMP PEAK 26(12Q15) WILD-TYPE    60                        10
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 26(12Q15) MUTATED                                           0    63
  AMP PEAK 26(12Q15) WILD-TYPE                                         1   215
D26V12, multiclass
                                           clus
vv                                          AMP PEAK 26(12Q15) MUTATED
  ASIAN                                                             28
  BLACK OR AFRICAN AMERICAN                                          2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          0
  WHITE                                                             63
                                           clus
vv                                          AMP PEAK 26(12Q15) WILD-TYPE
  ASIAN                                                               60
  BLACK OR AFRICAN AMERICAN                                           10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V13, binary
                              cls
clus                             0   1
  AMP PEAK 26(12Q15) MUTATED     2  79
  AMP PEAK 26(12Q15) WILD-TYPE   3 237
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(12Q15) MUTATED      2   79
  AMP PEAK 26(12Q15) WILD-TYPE    3  237
                        clus
vv                       AMP PEAK 26(12Q15) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         79
                        clus
vv                       AMP PEAK 26(12Q15) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          237
[1] 2 2
[1] FALSE

Clustering(27) Variable = AMP PEAK 27(13Q12.3) MUTATION ANALYSIS
D27V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 27(13Q12.3) MUTATED   100  60
  AMP PEAK 27(13Q12.3) WILD-TYPE 146 109
  AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE 
                           160                            255 
  AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE 
                            60                            109 
$`AMP PEAK 27(13Q12.3) MUTATED`
TCGA-CG-4444 TCGA-CG-5727 TCGA-MX-A663 TCGA-3M-AB46 TCGA-B7-5818 TCGA-B7-A5TJ 
       47.05        79.07         9.86        58.03        11.70        11.01 
TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4257 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.44         4.64         9.67         9.57         6.61        15.95 
TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6801 TCGA-BR-7197 
       39.12         9.17        32.78        25.61        40.21         9.21 
TCGA-BR-7704 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 
       35.24        18.15        28.73         3.45        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8362 TCGA-BR-8373 TCGA-BR-8382 
       29.59         9.60        29.42        13.08        14.79        25.05 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8682 TCGA-BR-8686 
        5.39         9.21        20.22        12.79        32.58        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4J2 
        8.22        10.68        13.87        34.98         0.72        14.17 
TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       28.34        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8527 
        5.13        13.02        13.15        12.10        12.59         7.17 
TCGA-CD-8528 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH 
       12.33        12.82         6.31        12.43         6.58        12.20 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       20.02         3.02        15.95         7.99         8.05        54.08 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5730 TCGA-CG-5732 
        7.07        12.00         1.02        12.03         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6524 
        7.99        25.71        12.66        19.13        18.54        17.85 
TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8573 
       17.19        15.98        12.79        12.36        11.31        19.50 
TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4Z0 TCGA-D7-A6EV 
       17.19        14.66        21.14        14.27        14.76        11.24 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
       22.29        15.65         8.38         0.62         7.99        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-A4BF TCGA-HF-7133 TCGA-HF-7134 
        3.48        19.53        17.06         5.52        63.06        52.21 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GD 
       18.15        28.96        22.82        24.26        22.68        22.75 
TCGA-HU-A4GF TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
       25.81         6.51         0.26        29.00        23.84        23.80 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NU 
       33.40         3.45        18.38         6.44        12.59        11.70 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        5.56        37.64        14.04        45.67        18.21         8.52 
TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 
        8.61       122.30        37.91       115.69        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       35.61         5.79        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       21.73        37.41         7.73        22.19         2.70        17.85 
TCGA-VQ-A8PP TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       23.41        14.33        39.45        20.81        32.88         1.71 
TCGA-VQ-A91V TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T 
       42.64        55.56         9.04        21.04        42.54        11.24 
TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       32.94        27.55        12.43         0.79 

$`AMP PEAK 27(13Q12.3) WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A8PU 
       21.99        22.98        16.24         0.23        20.15        27.35 
TCGA-VQ-A94U TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 
       26.93        26.70        19.56         9.47         6.61         6.97 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.18        34.68        13.87        17.29        13.68        19.33 
TCGA-BR-6564 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 
       26.10        18.05        19.89        12.16         8.98        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       31.20        44.94        21.90        36.16        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       39.78        15.32         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 
       14.43        32.25         8.05         0.56         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.20        15.58         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8484 
        3.32        11.80        31.27         7.36         3.72        25.18 
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-A44T TCGA-BR-A452 
       26.73        24.79        31.96         9.86        34.13         7.53 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 
        0.53         0.66        32.52        21.44        16.14        13.41 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8529 
       13.18        13.35        11.21        12.76        12.53        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 
       12.39        12.59        11.64        15.39        12.07        12.43 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 
       12.30        11.31        11.61        11.77        12.62        27.02 
TCGA-CG-4306 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
        1.02         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        0.00         9.01        18.97        30.97         6.97        36.00 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
       65.10        21.07        20.91        20.55        18.84        18.61 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       13.35        10.26        15.22        12.33        24.72        16.80 
TCGA-D7-8575 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       18.21        20.91        16.44         5.92        36.43        13.78 
TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74A 
       26.43        11.31        11.44        20.32         4.34        19.96 
TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 
        7.13        14.47        21.27        11.38        14.07        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 
       59.54         5.03        13.58         0.56         6.21        77.29 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 
       30.51        26.47         1.51         5.92        24.39        22.32 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G9 TCGA-HU-A4GC 
       21.07         0.76        24.30         5.59        24.20         3.25 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         0.10         6.58 
TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       20.25         2.10        12.95        21.17        14.07        15.68 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       36.36        18.81         3.39        12.46        13.35        19.53 
TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.74         6.51        10.62        15.75        13.51         2.53 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-R5-A7ZR 
       63.62        36.95         3.72        19.73        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N0 
        4.60         9.24        11.05         5.13        16.67        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8E0 
      116.38        71.38        16.87        19.04         0.92        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       43.36        38.14        37.22        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ 
       16.31         2.50        12.79         1.87         9.27        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E 
       13.35        29.59        64.57        73.41        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A923 
       61.22        18.74        60.85         9.50         9.73         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P 
       55.43         4.54         6.58         5.72        66.81         2.66 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-ZA-A8F6 
       26.04        16.14        17.26 

  AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE 
                          0.26                           0.00 
  AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE 
                        122.30                         116.38 
  AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE 
                         14.30                          15.39 
[1] "0.3 - 122.3 (14.3)" "0.0 - 116.4 (15.4)"
[1] "hr=" "1.2"
D27V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 27(13Q12.3) MUTATED         1        6       11       12        18
  AMP PEAK 27(13Q12.3) WILD-TYPE       1       10       30       20        22
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 27(13Q12.3) MUTATED          22         1         32         23
  AMP PEAK 27(13Q12.3) WILD-TYPE        34         2         49         40
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 27(13Q12.3) MUTATED           12       21
  AMP PEAK 27(13Q12.3) WILD-TYPE         27       23
D27V3, multiclass
            clus
vv           AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                              6                             10
  STAGE IB                             11                             30
  STAGE II                             12                             20
  STAGE IIA                            18                             22
  STAGE IIB                            22                             34
  STAGE III                             1                              2
  STAGE IIIA                           32                             49
  STAGE IIIB                           23                             40
  STAGE IIIC                           12                             27
  STAGE IV                             21                             23
[1] 11  2
[1] TRUE
[1] "dimension of 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(13Q12.3) MUTATED     7  41  74  43
  AMP PEAK 27(13Q12.3) WILD-TYPE  16  52 122  76
D27V4, multiclass
    clus
vv   AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE
  T1                            7                             16
  T2                           41                             52
  T3                           74                            122
  T4                           43                             76
[1] 4 2
[1] TRUE
[1] "dimension of 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(13Q12.3) MUTATED   47 43 34 37
  AMP PEAK 27(13Q12.3) WILD-TYPE 83 76 52 51
D27V5, multiclass
    clus
vv   AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE
  N0                           47                             83
  N1                           43                             76
  N2                           34                             52
  N3                           37                             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"
D27V6, binary
                                cls
clus                               0   1
  AMP PEAK 27(13Q12.3) MUTATED   151  12
  AMP PEAK 27(13Q12.3) WILD-TYPE 238  18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(13Q12.3) MUTATED    151   12
  AMP PEAK 27(13Q12.3) WILD-TYPE  238   18
   clus
vv  AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE
  0                          151                            238
  1                           12                             18
[1] 2 2
[1] FALSE
D27V7, binary
                                cls
clus                               0   1
  AMP PEAK 27(13Q12.3) MUTATED    56 114
  AMP PEAK 27(13Q12.3) WILD-TYPE 102 169
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(13Q12.3) MUTATED     56  114
  AMP PEAK 27(13Q12.3) WILD-TYPE  102  169
        clus
vv       AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE
  FEMALE                           56                            102
  MALE                            114                            169
[1] 2 2
[1] FALSE
D27V8, binary
                                cls
clus                               0   1
  AMP PEAK 27(13Q12.3) MUTATED   124  29
  AMP PEAK 27(13Q12.3) WILD-TYPE 198  47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(13Q12.3) MUTATED    124   29
  AMP PEAK 27(13Q12.3) WILD-TYPE  198   47
     clus
vv    AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE
  NO                           124                            198
  YES                           29                             47
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK 27(13Q12.3) MUTATED                                          3
  AMP PEAK 27(13Q12.3) WILD-TYPE                                       10
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK 27(13Q12.3) MUTATED                                      19
  AMP PEAK 27(13Q12.3) WILD-TYPE                                    53
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 27(13Q12.3) MUTATED                                                       65
  AMP PEAK 27(13Q12.3) WILD-TYPE                                                     98
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK 27(13Q12.3) MUTATED                                                  10
  AMP PEAK 27(13Q12.3) WILD-TYPE                                                11
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 27(13Q12.3) MUTATED                                                                  34
  AMP PEAK 27(13Q12.3) WILD-TYPE                                                                48
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK 27(13Q12.3) MUTATED                                                    4
  AMP PEAK 27(13Q12.3) WILD-TYPE                                                  4
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK 27(13Q12.3) MUTATED                                                 34
  AMP PEAK 27(13Q12.3) WILD-TYPE                                               45
D27V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK 27(13Q12.3) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       19
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      65
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           10
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           34
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            34
                                                                   clus
vv                                                                  AMP PEAK 27(13Q12.3) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         53
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                        98
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             11
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             48
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              45
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 27(13Q12.3) MUTATED   129   9   8   9
  AMP PEAK 27(13Q12.3) WILD-TYPE 220   9  11  16
D27V10, multiclass
    clus
vv   AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE
  R0                          129                            220
  R1                            9                              9
  R2                            8                             11
  RX                            9                             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"
D27V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 27(13Q12.3) MUTATED      33                         7
  AMP PEAK 27(13Q12.3) WILD-TYPE    55                         5
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 27(13Q12.3) MUTATED                                           1
  AMP PEAK 27(13Q12.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 27(13Q12.3) MUTATED     102
  AMP PEAK 27(13Q12.3) WILD-TYPE   176
D27V12, multiclass
                                           clus
vv                                          AMP PEAK 27(13Q12.3) MUTATED
  ASIAN                                                               33
  BLACK OR AFRICAN AMERICAN                                            7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              102
                                           clus
vv                                          AMP PEAK 27(13Q12.3) WILD-TYPE
  ASIAN                                                                 55
  BLACK OR AFRICAN AMERICAN                                              5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                176
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V13, binary
                                cls
clus                               0   1
  AMP PEAK 27(13Q12.3) MUTATED     2 122
  AMP PEAK 27(13Q12.3) WILD-TYPE   3 194
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(13Q12.3) MUTATED      2  122
  AMP PEAK 27(13Q12.3) WILD-TYPE    3  194
                        clus
vv                       AMP PEAK 27(13Q12.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          122
                        clus
vv                       AMP PEAK 27(13Q12.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            194
[1] 2 2
[1] FALSE

Clustering(28) Variable = AMP PEAK 28(13Q22.1) MUTATION ANALYSIS
D28V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 28(13Q22.1) MUTATED   107  64
  AMP PEAK 28(13Q22.1) WILD-TYPE 139 105
  AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE 
                           171                            244 
  AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE 
                            64                            105 
$`AMP PEAK 28(13Q22.1) MUTATED`
TCGA-MX-A663 TCGA-3M-AB46 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4187 
        9.86        58.03        11.70        11.01         9.44         4.64 
TCGA-BR-4188 TCGA-BR-4257 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6563 
        7.43         9.67         9.57         6.61        15.95        39.12 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 
        9.17        32.78        40.21         9.21        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8077 TCGA-BR-8078 
       39.78        18.15        28.73         3.45         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8362 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8483 
        9.60        13.08        14.79         7.36        25.05         5.39 
TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 
        9.21        12.79        24.79        32.58        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J2 
       10.68        13.87        34.98        12.89         0.72        14.17 
TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       28.34        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8525 TCGA-CD-8533 
        5.13        13.02        13.15        13.35        12.59        15.39 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 
       12.82         6.31        12.43         6.58        12.20        20.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 
       15.95         1.02         7.99        54.08         4.01        29.98 
TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5723 
       19.07         7.07        12.00        36.00         1.02       105.07 
TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       15.02         4.01        69.04         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 
       20.91        19.13        18.54        17.85        17.19        10.26 
TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8573 TCGA-D7-8574 
       15.98        12.36        11.31        12.33        19.50        17.19 
TCGA-D7-A4YT TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       14.27        14.76        11.24        22.29        15.65         8.38 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-8631 TCGA-FP-A4BF 
        0.62         7.99        72.23        19.53         0.56         5.52 
TCGA-HF-7134 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G6 TCGA-HU-A4G8 
       52.21        18.15        28.96        22.82        24.26        22.68 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H3 
       22.75        25.81         6.51         6.58         0.26        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL 
       23.84        23.80        33.40         3.39        18.38        13.35 
TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H 
        6.44         6.51        11.70         2.53         5.56        37.64 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-RD-A7BT TCGA-RD-A8MV 
       14.04        45.67        18.21         8.52         8.61       122.30 
TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB 
       37.91       115.69        57.44         8.94        35.61         5.79 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       48.79         5.46        13.25        13.02        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PP 
       37.41        22.19        12.79         2.70        17.85        23.41 
TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       13.35        14.33        61.22        20.81        32.88         1.71 
TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A92D 
       42.64         9.50        55.56         9.04         4.54        66.81 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6D 
       21.04        42.54        11.24        43.66        32.94        17.13 
TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K 
       26.04        27.55        12.43 

$`AMP PEAK 28(13Q22.1) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK 
       20.15        27.35        26.93        26.70        19.56         9.47 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        6.61         6.97        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.34         6.18        34.68        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       19.33        26.10        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
        8.98        30.90        31.20        44.94        21.90        36.16 
TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       35.84        15.32         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       14.43        11.44        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        19.96         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8384 
        4.31        14.04         3.32        11.80        31.27         3.72 
TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       25.18        20.22         1.12        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-A44T 
        6.28         7.53        26.73        31.96         9.86        34.13 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
        7.53         6.08         1.48        27.55        28.57         8.98 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 
        0.53         0.66        32.52        21.44        16.14        13.41 
TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 
       13.18        11.21        12.10        12.76        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 
       12.33        12.30        12.39        12.59        11.64        12.07 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        12.30        11.31        11.61        11.77        12.62 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4462 
        3.02        27.02         8.05        14.01        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 
        9.01        18.97        30.97         6.97         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-6519 
        0.99        12.03        28.96        65.10        21.07        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-8570 
       18.84        18.61        13.35        15.22        12.79        24.72 
TCGA-D7-8572 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU 
       16.80        18.21        14.66        21.14        20.91        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY 
        5.92        36.43        13.78        26.43        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 
       20.32         4.34        19.96         7.13        14.47        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       11.38         3.48        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB 
        5.03        13.58         6.21        77.29        63.06        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 
       26.47         1.51         5.92        24.39        22.32        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH 
        0.76        24.30         5.59        24.20         3.25        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4H0 
       21.37        29.98         8.98         0.10        20.25         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       12.95        21.17        14.07        15.68        36.36         3.45 
TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT 
       18.81        12.46        19.53         6.74        12.59        10.62 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
       15.75        13.51        63.62        36.95         3.72        19.73 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW 
       74.53         6.08         4.60         9.24        11.05         5.13 
TCGA-RD-A7C1 TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EA 
       16.67        40.64       116.38        71.38        16.87        19.04 
TCGA-VQ-A8DL TCGA-VQ-A8E0 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
        0.92        18.48        38.14        37.22         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO 
       34.29        46.26        16.31         2.50         1.87         9.27 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       15.65        29.59        64.57        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 
       21.83        18.74        60.85         9.73         2.01        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A 
        6.58         5.72         2.66        18.41        28.41        38.93 
TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       54.12        16.14        17.26         0.79 

  AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE 
                          0.26                           0.00 
  AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE 
                        122.30                         116.38 
  AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE 
                         14.33                          15.45 
[1] "0.3 - 122.3 (14.3)" "0.0 - 116.4 (15.4)"
[1] "hr=" "1.2"
D28V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 28(13Q22.1) MUTATED         1        5       13       14        18
  AMP PEAK 28(13Q22.1) WILD-TYPE       1       11       28       18        22
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 28(13Q22.1) MUTATED          26         1         36         24
  AMP PEAK 28(13Q22.1) WILD-TYPE        30         2         45         39
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 28(13Q22.1) MUTATED           12       21
  AMP PEAK 28(13Q22.1) WILD-TYPE         27       23
D28V3, multiclass
            clus
vv           AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                              5                             11
  STAGE IB                             13                             28
  STAGE II                             14                             18
  STAGE IIA                            18                             22
  STAGE IIB                            26                             30
  STAGE III                             1                              2
  STAGE IIIA                           36                             45
  STAGE IIIB                           24                             39
  STAGE IIIC                           12                             27
  STAGE IV                             21                             23
[1] 11  2
[1] TRUE
[1] "dimension of 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(13Q22.1) MUTATED     6  43  83  43
  AMP PEAK 28(13Q22.1) WILD-TYPE  17  50 113  76
D28V4, multiclass
    clus
vv   AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE
  T1                            6                             17
  T2                           43                             50
  T3                           83                            113
  T4                           43                             76
[1] 4 2
[1] TRUE
[1] "dimension of 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(13Q22.1) MUTATED   48 52 40 33
  AMP PEAK 28(13Q22.1) WILD-TYPE 82 67 46 55
D28V5, multiclass
    clus
vv   AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE
  N0                           48                             82
  N1                           52                             67
  N2                           40                             46
  N3                           33                             55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                                cls
clus                               0   1
  AMP PEAK 28(13Q22.1) MUTATED   163  12
  AMP PEAK 28(13Q22.1) WILD-TYPE 226  18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(13Q22.1) MUTATED    163   12
  AMP PEAK 28(13Q22.1) WILD-TYPE  226   18
   clus
vv  AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE
  0                          163                            226
  1                           12                             18
[1] 2 2
[1] FALSE
D28V7, binary
                                cls
clus                               0   1
  AMP PEAK 28(13Q22.1) MUTATED    54 127
  AMP PEAK 28(13Q22.1) WILD-TYPE 104 156
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(13Q22.1) MUTATED     54  127
  AMP PEAK 28(13Q22.1) WILD-TYPE  104  156
        clus
vv       AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE
  FEMALE                           54                            104
  MALE                            127                            156
[1] 2 2
[1] FALSE
D28V8, binary
                                cls
clus                               0   1
  AMP PEAK 28(13Q22.1) MUTATED   130  30
  AMP PEAK 28(13Q22.1) WILD-TYPE 192  46
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(13Q22.1) MUTATED    130   30
  AMP PEAK 28(13Q22.1) WILD-TYPE  192   46
     clus
vv    AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE
  NO                           130                            192
  YES                           30                             46
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK 28(13Q22.1) MUTATED                                          3
  AMP PEAK 28(13Q22.1) WILD-TYPE                                       10
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK 28(13Q22.1) MUTATED                                      17
  AMP PEAK 28(13Q22.1) WILD-TYPE                                    55
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 28(13Q22.1) MUTATED                                                       69
  AMP PEAK 28(13Q22.1) WILD-TYPE                                                     94
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK 28(13Q22.1) MUTATED                                                  10
  AMP PEAK 28(13Q22.1) WILD-TYPE                                                11
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 28(13Q22.1) MUTATED                                                                  38
  AMP PEAK 28(13Q22.1) WILD-TYPE                                                                44
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK 28(13Q22.1) MUTATED                                                    5
  AMP PEAK 28(13Q22.1) WILD-TYPE                                                  3
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK 28(13Q22.1) MUTATED                                                 38
  AMP PEAK 28(13Q22.1) WILD-TYPE                                               41
D28V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK 28(13Q22.1) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       17
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      69
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           10
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           38
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            38
                                                                   clus
vv                                                                  AMP PEAK 28(13Q22.1) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         55
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                        94
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             11
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             44
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              41
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 28(13Q22.1) MUTATED   137  10   9  10
  AMP PEAK 28(13Q22.1) WILD-TYPE 212   8  10  15
D28V10, multiclass
    clus
vv   AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE
  R0                          137                            212
  R1                           10                              8
  R2                            9                             10
  RX                           10                             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"
D28V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 28(13Q22.1) MUTATED      35                         6
  AMP PEAK 28(13Q22.1) WILD-TYPE    53                         6
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 28(13Q22.1) MUTATED                                           1
  AMP PEAK 28(13Q22.1) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 28(13Q22.1) MUTATED     110
  AMP PEAK 28(13Q22.1) WILD-TYPE   168
D28V12, multiclass
                                           clus
vv                                          AMP PEAK 28(13Q22.1) MUTATED
  ASIAN                                                               35
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              110
                                           clus
vv                                          AMP PEAK 28(13Q22.1) WILD-TYPE
  ASIAN                                                                 53
  BLACK OR AFRICAN AMERICAN                                              6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                168
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V13, binary
                                cls
clus                               0   1
  AMP PEAK 28(13Q22.1) MUTATED     2 124
  AMP PEAK 28(13Q22.1) WILD-TYPE   3 192
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(13Q22.1) MUTATED      2  124
  AMP PEAK 28(13Q22.1) WILD-TYPE    3  192
                        clus
vv                       AMP PEAK 28(13Q22.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          124
                        clus
vv                       AMP PEAK 28(13Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            192
[1] 2 2
[1] FALSE

Clustering(29) Variable = AMP PEAK 29(14Q21.3) MUTATION ANALYSIS
D29V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 29(14Q21.3) MUTATED    26  24
  AMP PEAK 29(14Q21.3) WILD-TYPE 220 145
  AMP PEAK 29(14Q21.3) MUTATED AMP PEAK 29(14Q21.3) WILD-TYPE 
                            50                            365 
  AMP PEAK 29(14Q21.3) MUTATED AMP PEAK 29(14Q21.3) WILD-TYPE 
                            24                            145 
$`AMP PEAK 29(14Q21.3) MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-3M-AB46 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-6705 
       47.05        21.99        58.03         6.61         4.64        25.61 
TCGA-BR-6709 TCGA-BR-7717 TCGA-BR-8060 TCGA-BR-8295 TCGA-BR-8486 TCGA-BR-A4CQ 
       12.16        18.15        11.44         2.20        20.22        34.98 
TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-A48A TCGA-CG-4436 TCGA-CG-5724 
       13.51        20.42        21.44        12.43         7.99        12.03 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-FP-8211 TCGA-HF-7133 
       20.91        19.13        15.65         0.62        13.58        63.06 
TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-A4GF TCGA-HU-A4GT TCGA-IN-8462 TCGA-IN-A6RI 
        5.92        28.96        25.81         6.51        18.81        18.38 
TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF 
        6.74         6.51        10.62        14.04        45.67         8.52 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-VQ-A8E0 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PY 
        9.24        11.05        18.48        22.19        17.85        14.33 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-AA68 
        1.71        42.64         9.04         4.54        66.81        43.66 
TCGA-VQ-AA6D TCGA-VQ-AA6I 
       17.13        16.14 

$`AMP PEAK 29(14Q21.3) WILD-TYPE`
TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       22.98        79.07        16.24         0.23        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       27.35        26.93        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.47         9.44         6.97         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6706 
       19.33        39.12        26.10         9.17        32.78        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       19.89         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       39.78        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       33.21        37.25        14.43         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 
        3.72         5.39        25.18         9.21         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS 
       10.68        34.13        13.87         7.53         6.08         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52         0.46        20.65 
TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 
       13.18        13.35        11.21        12.10        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03         0.00         9.01        18.97         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6519 
       69.04        21.07         7.99        25.71        12.66        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.44        20.32        22.29         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 
        5.03         0.56         5.52         6.21        77.29        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       30.51        26.47         1.51        24.39        18.15        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ 
       22.68        24.20         3.25        22.75        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 
       14.07        15.68        33.40        36.36         3.45         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NU 
       12.46        13.35        19.53         6.44        12.59        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
       15.75        13.51         2.53         5.56        63.62        37.64 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A7ZR 
       36.95         3.72        19.73        18.21        74.53         6.08 
TCGA-R5-A804 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
        4.60         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       35.61        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        5.46        13.25        13.02        43.36        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       38.14        37.22         7.73        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO 
       16.31         2.50        12.79         2.70         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ 
       23.41        15.65        13.35        29.59        64.57        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       39.45        11.70        21.83        61.22        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 
       32.88        60.85         9.50         9.73        55.56         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
       55.43         6.58         5.72        21.04         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       11.24        18.41        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        27.55        12.43        17.26         0.79 

  AMP PEAK 29(14Q21.3) MUTATED AMP PEAK 29(14Q21.3) WILD-TYPE 
                          0.62                           0.00 
  AMP PEAK 29(14Q21.3) MUTATED AMP PEAK 29(14Q21.3) WILD-TYPE 
                         66.81                         122.30 
  AMP PEAK 29(14Q21.3) MUTATED AMP PEAK 29(14Q21.3) WILD-TYPE 
                        15.895                         14.760 
[1] "0.6 - 66.8 (15.9)"  "0.0 - 122.3 (14.8)"
[1] "hr=" "1.2"
D29V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 29(14Q21.3) MUTATED         1        2        5        0         6
  AMP PEAK 29(14Q21.3) WILD-TYPE       1       14       36       32        34
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 29(14Q21.3) MUTATED           5         0         13          8
  AMP PEAK 29(14Q21.3) WILD-TYPE        51         3         68         55
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 29(14Q21.3) MUTATED            3        9
  AMP PEAK 29(14Q21.3) WILD-TYPE         36       35
D29V3, multiclass
            clus
vv           AMP PEAK 29(14Q21.3) MUTATED AMP PEAK 29(14Q21.3) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                              2                             14
  STAGE IB                              5                             36
  STAGE II                              0                             32
  STAGE IIA                             6                             34
  STAGE IIB                             5                             51
  STAGE III                             0                              3
  STAGE IIIA                           13                             68
  STAGE IIIB                            8                             55
  STAGE IIIC                            3                             36
  STAGE IV                              9                             35
[1] 11  2
[1] TRUE
[1] "dimension of 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(14Q21.3) MUTATED     3  11  27  11
  AMP PEAK 29(14Q21.3) WILD-TYPE  20  82 169 108
D29V4, multiclass
    clus
vv   AMP PEAK 29(14Q21.3) MUTATED AMP PEAK 29(14Q21.3) WILD-TYPE
  T1                            3                             20
  T2                           11                             82
  T3                           27                            169
  T4                           11                            108
[1] 4 2
[1] TRUE
[1] "dimension of 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(14Q21.3) MUTATED    14  14   9  14
  AMP PEAK 29(14Q21.3) WILD-TYPE 116 105  77  74
D29V5, multiclass
    clus
vv   AMP PEAK 29(14Q21.3) MUTATED AMP PEAK 29(14Q21.3) WILD-TYPE
  N0                           14                            116
  N1                           14                            105
  N2                            9                             77
  N3                           14                             74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                                cls
clus                               0   1
  AMP PEAK 29(14Q21.3) MUTATED    45   6
  AMP PEAK 29(14Q21.3) WILD-TYPE 344  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(14Q21.3) MUTATED     45    6
  AMP PEAK 29(14Q21.3) WILD-TYPE  344   24
   clus
vv  AMP PEAK 29(14Q21.3) MUTATED AMP PEAK 29(14Q21.3) WILD-TYPE
  0                           45                            344
  1                            6                             24
[1] 2 2
[1] FALSE
D29V7, binary
                                cls
clus                               0   1
  AMP PEAK 29(14Q21.3) MUTATED    20  34
  AMP PEAK 29(14Q21.3) WILD-TYPE 138 249
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(14Q21.3) MUTATED     20   34
  AMP PEAK 29(14Q21.3) WILD-TYPE  138  249
        clus
vv       AMP PEAK 29(14Q21.3) MUTATED AMP PEAK 29(14Q21.3) WILD-TYPE
  FEMALE                           20                            138
  MALE                             34                            249
[1] 2 2
[1] FALSE
D29V8, binary
                                cls
clus                               0   1
  AMP PEAK 29(14Q21.3) MUTATED    39  12
  AMP PEAK 29(14Q21.3) WILD-TYPE 283  64
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(14Q21.3) MUTATED     39   12
  AMP PEAK 29(14Q21.3) WILD-TYPE  283   64
     clus
vv    AMP PEAK 29(14Q21.3) MUTATED AMP PEAK 29(14Q21.3) WILD-TYPE
  NO                            39                            283
  YES                           12                             64
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK 29(14Q21.3) MUTATED                                          0
  AMP PEAK 29(14Q21.3) WILD-TYPE                                       13
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK 29(14Q21.3) MUTATED                                       4
  AMP PEAK 29(14Q21.3) WILD-TYPE                                    68
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 29(14Q21.3) MUTATED                                                       26
  AMP PEAK 29(14Q21.3) WILD-TYPE                                                    137
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK 29(14Q21.3) MUTATED                                                   2
  AMP PEAK 29(14Q21.3) WILD-TYPE                                                19
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 29(14Q21.3) MUTATED                                                                   7
  AMP PEAK 29(14Q21.3) WILD-TYPE                                                                75
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK 29(14Q21.3) MUTATED                                                    0
  AMP PEAK 29(14Q21.3) WILD-TYPE                                                  8
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK 29(14Q21.3) MUTATED                                                 15
  AMP PEAK 29(14Q21.3) WILD-TYPE                                               64
D29V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK 29(14Q21.3) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      26
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            7
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            15
                                                                   clus
vv                                                                  AMP PEAK 29(14Q21.3) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      13
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       137
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             75
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             8
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              64
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 29(14Q21.3) MUTATED    36   5   4   3
  AMP PEAK 29(14Q21.3) WILD-TYPE 313  13  15  22
D29V10, multiclass
    clus
vv   AMP PEAK 29(14Q21.3) MUTATED AMP PEAK 29(14Q21.3) WILD-TYPE
  R0                           36                            313
  R1                            5                             13
  R2                            4                             15
  RX                            3                             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"
D29V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 29(14Q21.3) MUTATED       7                         2
  AMP PEAK 29(14Q21.3) WILD-TYPE    81                        10
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 29(14Q21.3) MUTATED                                           0
  AMP PEAK 29(14Q21.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 29(14Q21.3) MUTATED      37
  AMP PEAK 29(14Q21.3) WILD-TYPE   241
D29V12, multiclass
                                           clus
vv                                          AMP PEAK 29(14Q21.3) MUTATED
  ASIAN                                                                7
  BLACK OR AFRICAN AMERICAN                                            2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               37
                                           clus
vv                                          AMP PEAK 29(14Q21.3) WILD-TYPE
  ASIAN                                                                 81
  BLACK OR AFRICAN AMERICAN                                             10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V13, binary
                                cls
clus                               0   1
  AMP PEAK 29(14Q21.3) MUTATED     2  35
  AMP PEAK 29(14Q21.3) WILD-TYPE   3 281
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(14Q21.3) MUTATED      2   35
  AMP PEAK 29(14Q21.3) WILD-TYPE    3  281
                        clus
vv                       AMP PEAK 29(14Q21.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           35
                        clus
vv                       AMP PEAK 29(14Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            281
[1] 2 2
[1] FALSE

Clustering(30) Variable = AMP PEAK 30(15Q26.1) MUTATION ANALYSIS
D30V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 30(15Q26.1) MUTATED    61  45
  AMP PEAK 30(15Q26.1) WILD-TYPE 185 124
  AMP PEAK 30(15Q26.1) MUTATED AMP PEAK 30(15Q26.1) WILD-TYPE 
                           106                            309 
  AMP PEAK 30(15Q26.1) MUTATED AMP PEAK 30(15Q26.1) WILD-TYPE 
                            45                            124 
$`AMP PEAK 30(15Q26.1) MUTATED`
TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-VQ-A8PU TCGA-BR-4183 TCGA-BR-4191 
       47.05        22.98        79.07        27.35         6.61        18.35 
TCGA-BR-4267 TCGA-BR-6458 TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7717 
        6.18        19.33        12.16         9.21        33.63        18.15 
TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8683 
       33.21        11.44         0.69        31.10        22.19         9.86 
TCGA-BR-8687 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4J4 TCGA-BR-A4PF TCGA-BR-A4QI 
        8.22         7.53        34.98         0.53         1.15        21.44 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       13.02        13.15        12.59         7.17        12.33        12.30 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-A486 TCGA-CD-A4MG TCGA-CG-4449 TCGA-CG-4477 
       15.39        12.07         6.31         6.58        19.07        30.97 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5579 
        6.97         1.02        12.03         4.01        69.04        20.91 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 
       20.55        18.84        13.35        15.22        15.98        12.36 
TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A4YT TCGA-D7-A4YY TCGA-D7-A6F2 TCGA-EQ-5647 
       12.33        18.21        14.27        13.78        15.65         0.62 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 
       72.23        11.38        19.53        17.06        13.58         0.56 
TCGA-FP-A9TM TCGA-HF-7133 TCGA-HU-A4G8 TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GY 
        6.21        63.06        22.68        25.81        11.77         0.26 
TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       23.80        33.40         3.45        18.81         3.39        18.38 
TCGA-IN-A6RN TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A666 TCGA-R5-A7O7 
       19.53         5.56        63.62        37.64        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8N6 
       18.21         6.08         9.24         8.61       122.30         8.94 
TCGA-VQ-A8DL TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PC 
        0.92        13.02        18.48        37.22         7.73        46.26 
TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A91K TCGA-VQ-A91Q 
       22.19        12.79         2.70        17.85        61.22        20.81 
TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
        9.50         9.04         4.54        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       43.66        32.94        17.13        54.12 

$`AMP PEAK 30(15Q26.1) WILD-TYPE`
TCGA-CG-4460 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A94U 
       21.99        16.24         0.23        20.15         9.86        26.93 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       58.03        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 
        9.44         6.97         4.64         7.43        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         9.67         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.87        17.29        13.68        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
       40.21        30.90        31.20        44.94        21.90        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       35.24        35.84        39.78        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 
        9.07        29.56        37.25        14.43        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 
        2.20        15.58         7.40         6.18        13.08         0.26 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T 
       24.79        31.96        32.58        20.88        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       13.87         6.08         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM 
       13.51         0.46        20.65        20.42        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 
       13.41        13.18        13.35        11.21        12.10        12.76 
TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
       12.53        12.39        12.59        11.64        12.82        12.43 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03         0.00         9.01        18.97         7.07        12.00 
TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 
       36.00         0.99         6.02         0.99       105.07        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       28.96        65.10        21.07         7.99        25.71        12.66 
TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 
       19.13        18.54        18.61        17.85        17.19        10.26 
TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       12.79        11.31        24.72        16.80        19.50        17.19 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       14.66        21.14        20.91        16.44         5.92        36.43 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 
       22.29         8.38         4.34        19.96         7.13         7.99 
TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
       14.47        21.27         3.48        14.07        22.29        59.54 
TCGA-FP-8210 TCGA-FP-A4BF TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.03         5.52        77.29        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        1.51         5.92        24.39        18.15        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       24.20         3.25        22.75        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.58        20.25         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       29.00        23.84        21.17        14.07        15.68        36.36 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       12.46        13.35         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A93J 
       10.62        11.70        15.75        13.51         2.53        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS 
        3.72        19.73         8.52        74.53         4.60        11.05 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        5.13        16.67        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44        35.61        16.87        19.04         5.79 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       48.79         5.46        13.25        43.36        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PM 
       38.14        30.97        34.29        16.31         2.50         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91N 
       14.33        73.41        39.45        11.70        21.83        18.74 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z 
       32.88         1.71        42.64        60.85         9.73        55.56 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P 
        2.01        55.43         6.58         5.72        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       42.54        28.41        38.93        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        17.26         0.79 

  AMP PEAK 30(15Q26.1) MUTATED AMP PEAK 30(15Q26.1) WILD-TYPE 
                          0.26                           0.00 
  AMP PEAK 30(15Q26.1) MUTATED AMP PEAK 30(15Q26.1) WILD-TYPE 
                        122.30                         116.38 
  AMP PEAK 30(15Q26.1) MUTATED AMP PEAK 30(15Q26.1) WILD-TYPE 
                        14.745                         14.790 
[1] "0.3 - 122.3 (14.7)" "0.0 - 116.4 (14.8)"
[1] "hr=" "1.1"
D30V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 30(15Q26.1) MUTATED         2        3        8        9        12
  AMP PEAK 30(15Q26.1) WILD-TYPE       0       13       33       23        28
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 30(15Q26.1) MUTATED          11         1         26         15
  AMP PEAK 30(15Q26.1) WILD-TYPE        45         2         55         48
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 30(15Q26.1) MUTATED            5       15
  AMP PEAK 30(15Q26.1) WILD-TYPE         34       29
D30V3, multiclass
            clus
vv           AMP PEAK 30(15Q26.1) MUTATED AMP PEAK 30(15Q26.1) WILD-TYPE
  STAGE I                               2                              0
  STAGE IA                              3                             13
  STAGE IB                              8                             33
  STAGE II                              9                             23
  STAGE IIA                            12                             28
  STAGE IIB                            11                             45
  STAGE III                             1                              2
  STAGE IIIA                           26                             55
  STAGE IIIB                           15                             48
  STAGE IIIC                            5                             34
  STAGE IV                             15                             29
[1] 11  2
[1] TRUE
[1] "dimension of 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(15Q26.1) MUTATED     7  27  52  25
  AMP PEAK 30(15Q26.1) WILD-TYPE  16  66 144  94
D30V4, multiclass
    clus
vv   AMP PEAK 30(15Q26.1) MUTATED AMP PEAK 30(15Q26.1) WILD-TYPE
  T1                            7                             16
  T2                           27                             66
  T3                           52                            144
  T4                           25                             94
[1] 4 2
[1] TRUE
[1] "dimension of 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(15Q26.1) MUTATED    29  33  30  17
  AMP PEAK 30(15Q26.1) WILD-TYPE 101  86  56  71
D30V5, multiclass
    clus
vv   AMP PEAK 30(15Q26.1) MUTATED AMP PEAK 30(15Q26.1) WILD-TYPE
  N0                           29                            101
  N1                           33                             86
  N2                           30                             56
  N3                           17                             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                                cls
clus                               0   1
  AMP PEAK 30(15Q26.1) MUTATED    97  10
  AMP PEAK 30(15Q26.1) WILD-TYPE 292  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 30(15Q26.1) MUTATED     97   10
  AMP PEAK 30(15Q26.1) WILD-TYPE  292   20
   clus
vv  AMP PEAK 30(15Q26.1) MUTATED AMP PEAK 30(15Q26.1) WILD-TYPE
  0                           97                            292
  1                           10                             20
[1] 2 2
[1] FALSE
D30V7, binary
                                cls
clus                               0   1
  AMP PEAK 30(15Q26.1) MUTATED    34  79
  AMP PEAK 30(15Q26.1) WILD-TYPE 124 204
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 30(15Q26.1) MUTATED     34   79
  AMP PEAK 30(15Q26.1) WILD-TYPE  124  204
        clus
vv       AMP PEAK 30(15Q26.1) MUTATED AMP PEAK 30(15Q26.1) WILD-TYPE
  FEMALE                           34                            124
  MALE                             79                            204
[1] 2 2
[1] FALSE
D30V8, binary
                                cls
clus                               0   1
  AMP PEAK 30(15Q26.1) MUTATED    75  27
  AMP PEAK 30(15Q26.1) WILD-TYPE 247  49
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 30(15Q26.1) MUTATED     75   27
  AMP PEAK 30(15Q26.1) WILD-TYPE  247   49
     clus
vv    AMP PEAK 30(15Q26.1) MUTATED AMP PEAK 30(15Q26.1) WILD-TYPE
  NO                            75                            247
  YES                           27                             49
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK 30(15Q26.1) MUTATED                                          2
  AMP PEAK 30(15Q26.1) WILD-TYPE                                       11
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK 30(15Q26.1) MUTATED                                      14
  AMP PEAK 30(15Q26.1) WILD-TYPE                                    58
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 30(15Q26.1) MUTATED                                                       35
  AMP PEAK 30(15Q26.1) WILD-TYPE                                                    128
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK 30(15Q26.1) MUTATED                                                   7
  AMP PEAK 30(15Q26.1) WILD-TYPE                                                14
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 30(15Q26.1) MUTATED                                                                  24
  AMP PEAK 30(15Q26.1) WILD-TYPE                                                                58
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK 30(15Q26.1) MUTATED                                                    2
  AMP PEAK 30(15Q26.1) WILD-TYPE                                                  6
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK 30(15Q26.1) MUTATED                                                 28
  AMP PEAK 30(15Q26.1) WILD-TYPE                                               51
D30V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK 30(15Q26.1) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       14
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      35
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            7
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           24
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            28
                                                                   clus
vv                                                                  AMP PEAK 30(15Q26.1) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         58
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       128
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             14
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             58
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              51
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 30(15Q26.1) MUTATED    84   6   8   5
  AMP PEAK 30(15Q26.1) WILD-TYPE 265  12  11  20
D30V10, multiclass
    clus
vv   AMP PEAK 30(15Q26.1) MUTATED AMP PEAK 30(15Q26.1) WILD-TYPE
  R0                           84                            265
  R1                            6                             12
  R2                            8                             11
  RX                            5                             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"
D30V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 30(15Q26.1) MUTATED      22                         5
  AMP PEAK 30(15Q26.1) WILD-TYPE    66                         7
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 30(15Q26.1) MUTATED                                           1
  AMP PEAK 30(15Q26.1) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 30(15Q26.1) MUTATED      65
  AMP PEAK 30(15Q26.1) WILD-TYPE   213
D30V12, multiclass
                                           clus
vv                                          AMP PEAK 30(15Q26.1) MUTATED
  ASIAN                                                               22
  BLACK OR AFRICAN AMERICAN                                            5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               65
                                           clus
vv                                          AMP PEAK 30(15Q26.1) WILD-TYPE
  ASIAN                                                                 66
  BLACK OR AFRICAN AMERICAN                                              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V13, binary
                                cls
clus                               0   1
  AMP PEAK 30(15Q26.1) MUTATED     1  73
  AMP PEAK 30(15Q26.1) WILD-TYPE   4 243
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 30(15Q26.1) MUTATED      1   73
  AMP PEAK 30(15Q26.1) WILD-TYPE    4  243
                        clus
vv                       AMP PEAK 30(15Q26.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           73
                        clus
vv                       AMP PEAK 30(15Q26.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            243
[1] 2 2
[1] FALSE

Clustering(31) Variable = AMP PEAK 31(17Q12) MUTATION ANALYSIS
D31V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 31(17Q12) MUTATED    81  59
  AMP PEAK 31(17Q12) WILD-TYPE 165 110
  AMP PEAK 31(17Q12) MUTATED AMP PEAK 31(17Q12) WILD-TYPE 
                         140                          275 
  AMP PEAK 31(17Q12) MUTATED AMP PEAK 31(17Q12) WILD-TYPE 
                          59                          110 
$`AMP PEAK 31(17Q12) MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-3M-AB46 
       47.05        21.99        22.98        16.24         0.23        58.03 
TCGA-B7-5818 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7959 
       11.70         9.17         9.21        33.63        18.15        33.21 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 
       14.43        11.44         0.69        29.42         2.66        15.58 
TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-8590 TCGA-BR-8682 
       14.04        14.79         5.39        20.22         9.34        32.58 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY 
       20.88        10.68        13.87        34.98         1.48        12.89 
TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 
        0.72         0.53        20.42        21.44        13.02        13.15 
TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8529 TCGA-CD-A486 TCGA-CD-A489 TCGA-CG-4300 
       12.10        12.59        12.30         6.31        11.31        20.02 
TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 
        3.02         7.99         4.01        19.07        12.03        18.97 
TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5730 TCGA-CG-5732 
       30.97         1.02         0.99        12.03         4.01        69.04 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
       18.54        13.35        17.19        10.26        15.98        12.79 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8573 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT 
       11.31        12.33        19.50        14.66        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 
       16.44        36.43        11.24        11.44        22.29        15.65 
TCGA-D7-A748 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 
        4.34         0.62         7.99        72.23         3.48        14.07 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 
        0.56        26.47         1.51         5.92        18.15        22.82 
TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4H0 TCGA-HU-A4H2 
       24.26        22.75        25.81        11.77         2.10        12.95 
TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
       33.40        18.81        18.38        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 
        6.74        12.59        10.62        11.70        15.75         2.53 
TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A8N6 
       14.04        18.21         6.08         9.24         8.61         8.94 
TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E7 
        0.92         5.46        13.25        13.02        18.48        37.41 
TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
        7.73        46.26        22.19        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V 
        1.87        29.59        73.41        20.81        32.88        42.64 
TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O 
        9.50         9.04         2.01         4.54        66.81        21.04 
TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       42.54        43.66        32.94        17.13        54.12        26.04 
TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       27.55         0.79 

$`AMP PEAK 31(17Q12) WILD-TYPE`
TCGA-CG-5727 TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-B7-5816 
       79.07        20.15         9.86        27.35        26.93        26.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       36.16        35.24        35.84        39.78        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8078 TCGA-BR-8080 
        3.45         9.07        29.56        37.25        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
       32.25         8.05         0.56        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        31.10        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33         4.31         3.32        11.80        31.27 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 
        7.36        25.05         3.72        25.18         9.21         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A452 
       24.79        31.96         9.86         8.22        34.13         7.53 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 
        6.08        27.55        28.57         8.98        14.17        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF 
        0.66        32.52        13.51         0.46        20.65         1.15 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       16.14         5.13        13.41        13.18        13.35        11.21 
TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 
       12.76        12.53         7.17        12.33        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 
       11.64        15.39        12.07        12.82        12.43        12.30 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 
       27.02        15.95         1.02         8.05        54.08        14.01 
TCGA-CG-4443 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 
       29.98         0.00         9.01         7.07        12.00         6.97 
TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 
       36.00         0.99         6.02       105.07        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       65.10        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6528 
       19.13        20.55        18.84        18.61        17.85        15.22 
TCGA-D7-6818 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 
       12.36        24.72        16.80        17.19        18.21        21.14 
TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EZ 
        5.92        13.78        14.76        26.43        11.31        20.32 
TCGA-D7-A747 TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        8.38        19.96         7.13        14.47        21.27        11.38 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       19.53        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.32        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GN 
        5.59        22.68        24.20         3.25        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A7NR TCGA-IN-AB1X 
       36.36         3.45         3.39        12.46         6.51        13.51 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        63.62        37.64        36.95         3.72        19.73 
TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BW 
       45.67         8.52        74.53         4.60        11.05         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44        35.61        16.87        19.04         5.79 
TCGA-VQ-A8DT TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       48.79        43.36        21.73        38.14        37.22        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       34.29        16.31         2.50         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       13.35        64.57        14.33        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z 
       61.22        18.74         1.71        60.85         9.73        55.56 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 
       55.43         6.58         5.72         2.66        11.24        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       28.41        38.93        16.14        12.43        17.26 

  AMP PEAK 31(17Q12) MUTATED AMP PEAK 31(17Q12) WILD-TYPE 
                        0.23                         0.00 
  AMP PEAK 31(17Q12) MUTATED AMP PEAK 31(17Q12) WILD-TYPE 
                       73.41                       122.30 
  AMP PEAK 31(17Q12) MUTATED AMP PEAK 31(17Q12) WILD-TYPE 
                       13.61                        15.95 
[1] "0.2 - 73.4 (13.6)"  "0.0 - 122.3 (15.9)"
[1] "hr=" "1.2"
D31V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 31(17Q12) MUTATED         1        7       14        8        14
  AMP PEAK 31(17Q12) WILD-TYPE       1        9       27       24        26
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 31(17Q12) MUTATED          15         2         24         23
  AMP PEAK 31(17Q12) WILD-TYPE        41         1         57         40
                              vv
clus                           STAGE IIIC STAGE IV
  AMP PEAK 31(17Q12) MUTATED           11       21
  AMP PEAK 31(17Q12) WILD-TYPE         28       23
D31V3, multiclass
            clus
vv           AMP PEAK 31(17Q12) MUTATED AMP PEAK 31(17Q12) WILD-TYPE
  STAGE I                             1                            1
  STAGE IA                            7                            9
  STAGE IB                           14                           27
  STAGE II                            8                           24
  STAGE IIA                          14                           26
  STAGE IIB                          15                           41
  STAGE III                           2                            1
  STAGE IIIA                         24                           57
  STAGE IIIB                         23                           40
  STAGE IIIC                         11                           28
  STAGE IV                           21                           23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK 31(17Q12) MUTATED     9  35  61  40
  AMP PEAK 31(17Q12) WILD-TYPE  14  58 135  79
D31V4, multiclass
    clus
vv   AMP PEAK 31(17Q12) MUTATED AMP PEAK 31(17Q12) WILD-TYPE
  T1                          9                           14
  T2                         35                           58
  T3                         61                          135
  T4                         40                           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"
                              vv
clus                           N0 N1 N2 N3
  AMP PEAK 31(17Q12) MUTATED   44 34 32 32
  AMP PEAK 31(17Q12) WILD-TYPE 86 85 54 56
D31V5, multiclass
    clus
vv   AMP PEAK 31(17Q12) MUTATED AMP PEAK 31(17Q12) WILD-TYPE
  N0                         44                           86
  N1                         34                           85
  N2                         32                           54
  N3                         32                           56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
                              cls
clus                             0   1
  AMP PEAK 31(17Q12) MUTATED   119  15
  AMP PEAK 31(17Q12) WILD-TYPE 270  15
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 31(17Q12) MUTATED    119   15
  AMP PEAK 31(17Q12) WILD-TYPE  270   15
   clus
vv  AMP PEAK 31(17Q12) MUTATED AMP PEAK 31(17Q12) WILD-TYPE
  0                        119                          270
  1                         15                           15
[1] 2 2
[1] FALSE
D31V7, binary
                              cls
clus                             0   1
  AMP PEAK 31(17Q12) MUTATED    43 104
  AMP PEAK 31(17Q12) WILD-TYPE 115 179
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 31(17Q12) MUTATED     43  104
  AMP PEAK 31(17Q12) WILD-TYPE  115  179
        clus
vv       AMP PEAK 31(17Q12) MUTATED AMP PEAK 31(17Q12) WILD-TYPE
  FEMALE                         43                          115
  MALE                          104                          179
[1] 2 2
[1] FALSE
D31V8, binary
                              cls
clus                             0   1
  AMP PEAK 31(17Q12) MUTATED   102  27
  AMP PEAK 31(17Q12) WILD-TYPE 220  49
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 31(17Q12) MUTATED    102   27
  AMP PEAK 31(17Q12) WILD-TYPE  220   49
     clus
vv    AMP PEAK 31(17Q12) MUTATED AMP PEAK 31(17Q12) WILD-TYPE
  NO                         102                          220
  YES                         27                           49
[1] 2 2
[1] FALSE
                              vv
clus                           STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK 31(17Q12) MUTATED                                          6
  AMP PEAK 31(17Q12) WILD-TYPE                                        7
                              vv
clus                           STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK 31(17Q12) MUTATED                                       9
  AMP PEAK 31(17Q12) WILD-TYPE                                    63
                              vv
clus                           STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 31(17Q12) MUTATED                                                       47
  AMP PEAK 31(17Q12) WILD-TYPE                                                    116
                              vv
clus                           STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK 31(17Q12) MUTATED                                                   6
  AMP PEAK 31(17Q12) WILD-TYPE                                                15
                              vv
clus                           STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 31(17Q12) MUTATED                                                                  35
  AMP PEAK 31(17Q12) WILD-TYPE                                                                47
                              vv
clus                           STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK 31(17Q12) MUTATED                                                    4
  AMP PEAK 31(17Q12) WILD-TYPE                                                  4
                              vv
clus                           STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK 31(17Q12) MUTATED                                                 38
  AMP PEAK 31(17Q12) WILD-TYPE                                               41
D31V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK 31(17Q12) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                   6
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                      9
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                    47
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                          6
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         35
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                          38
                                                                   clus
vv                                                                  AMP PEAK 31(17Q12) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       63
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     116
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           15
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           47
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            41
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 31(17Q12) MUTATED   121   1  12   3
  AMP PEAK 31(17Q12) WILD-TYPE 228  17   7  22
D31V10, multiclass
    clus
vv   AMP PEAK 31(17Q12) MUTATED AMP PEAK 31(17Q12) WILD-TYPE
  R0                        121                          228
  R1                          1                           17
  R2                         12                            7
  RX                          3                           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"
D31V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 31(17Q12) MUTATED      25                         8
  AMP PEAK 31(17Q12) WILD-TYPE    63                         4
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 31(17Q12) MUTATED                                           1    90
  AMP PEAK 31(17Q12) WILD-TYPE                                         0   188
D31V12, multiclass
                                           clus
vv                                          AMP PEAK 31(17Q12) MUTATED
  ASIAN                                                             25
  BLACK OR AFRICAN AMERICAN                                          8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                             90
                                           clus
vv                                          AMP PEAK 31(17Q12) WILD-TYPE
  ASIAN                                                               63
  BLACK OR AFRICAN AMERICAN                                            4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              188
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V13, binary
                              cls
clus                             0   1
  AMP PEAK 31(17Q12) MUTATED     1  97
  AMP PEAK 31(17Q12) WILD-TYPE   4 219
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 31(17Q12) MUTATED      1   97
  AMP PEAK 31(17Q12) WILD-TYPE    4  219
                        clus
vv                       AMP PEAK 31(17Q12) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         97
                        clus
vv                       AMP PEAK 31(17Q12) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          219
[1] 2 2
[1] FALSE

Clustering(32) Variable = AMP PEAK 32(18Q11.2) MUTATION ANALYSIS
D32V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 32(18Q11.2) MUTATED    76  54
  AMP PEAK 32(18Q11.2) WILD-TYPE 170 115
  AMP PEAK 32(18Q11.2) MUTATED AMP PEAK 32(18Q11.2) WILD-TYPE 
                           130                            285 
  AMP PEAK 32(18Q11.2) MUTATED AMP PEAK 32(18Q11.2) WILD-TYPE 
                            54                            115 
$`AMP PEAK 32(18Q11.2) MUTATED`
TCGA-CG-4460 TCGA-FP-A8CX TCGA-MX-A663 TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-A5TN 
       21.99         0.23         9.86        26.93        58.03         9.44 
TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4257 TCGA-BR-6564 TCGA-BR-6565 
        6.97         7.43        18.35         9.67        26.10         9.17 
TCGA-BR-7715 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8077 TCGA-BR-8080 
       33.63        15.32        28.73         3.45         0.69         9.60 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8362 
        8.05        29.42         2.20        15.58         7.40        13.08 
TCGA-BR-8370 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 
        3.32        14.79         3.72        25.18        20.22         1.12 
TCGA-BR-8589 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44U 
       27.12        26.73        24.79        20.88         8.22        13.87 
TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD 
       34.98        12.89         0.72         0.66        13.51        20.65 
TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5804 TCGA-CD-8526 
        1.15        13.41        13.02        13.15        12.10        12.53 
TCGA-CD-8529 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 
       12.30         6.31        12.43        12.20        20.02         3.02 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5724 
        4.01        14.01        19.07         7.07        12.00        12.03 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       20.91        19.13        18.54        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-8576 TCGA-D7-A4YY TCGA-D7-A6EV TCGA-D7-A6EX 
       15.22        12.79        14.66        13.78        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-5647 TCGA-F1-6875 TCGA-F1-A72C 
       11.44        22.29        19.96         0.62        72.23        11.38 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8243 
        0.56         5.52         6.21        63.06        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4H4 TCGA-HU-A4H5 
       18.15         0.76        22.75         8.98        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN 
       21.17        33.40        18.81        18.38        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-KB-A6F7 TCGA-KB-A93H 
        6.44         6.74        11.70        15.75        63.62        37.64 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BW 
       14.04        45.67        74.53         6.08         9.24         5.13 
TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU 
       16.67       115.69        35.61         5.79         0.92         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PZ 
       13.02        18.48         2.70         1.87         9.27        73.41 
TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A922 TCGA-VQ-A92D 
       21.83        18.74         1.71        42.64         9.04        66.81 
TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-ZQ-A9CR 
       42.54        43.66        38.93         0.79 

$`AMP PEAK 32(18Q11.2) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-VQ-A8PU 
       47.05        22.98        79.07        16.24        20.15        27.35 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 
       26.70        11.70        19.56        11.01         9.47         6.61 
TCGA-BR-4187 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 
        4.64        30.90         4.08         4.08         9.34         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.68        19.33        39.12        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       39.78        18.15         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8289 
       14.43        11.44        29.59        32.25         0.56         2.66 
TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       19.96         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33         4.31        14.04        11.80        31.27 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8590 
        7.36        25.05         5.39         9.21        12.79         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
       28.14         6.28         7.53        31.96        32.58         9.86 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       10.68        34.13         7.53         6.08         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 
       28.57         8.98        14.17         0.53        28.34        32.52 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5801 
        0.46        20.42        21.44        16.14         5.13        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 
       13.35        11.21        12.76        12.59         7.17        12.33 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI 
       12.43        12.30        11.31        11.61         6.58        11.77 
TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       12.62        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       54.08        29.98        12.03         0.00         9.01        18.97 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6519 
       69.04        21.07         7.99        25.71        12.66        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 
       18.84        18.61        17.85        15.98        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       14.76        26.43        20.32        15.65         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        7.13         7.99        14.47        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 
       77.29        52.21        30.51         1.51        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.32        22.82        21.07        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       22.68        24.20         3.25        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
        2.10        12.95        29.00        14.07        15.68        36.36 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
        3.45         3.39        12.46        12.59         6.51        10.62 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
       13.51         2.53         5.56        36.95         3.72        19.73 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A8MV 
       18.21         8.52         4.60        11.05         8.61       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       37.91        40.64       116.38        71.38        57.44         8.94 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       16.87        19.04        48.79        13.25        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK 
       46.26        16.31        22.19         2.50        12.79        17.85 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY 
       23.41        15.65        13.35        29.59        64.57        14.33 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91W 
       39.45        11.70        61.22        20.81        32.88        60.85 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.50         9.73        55.56         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 
        6.58         5.72        21.04         2.66        11.24        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        32.94        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  AMP PEAK 32(18Q11.2) MUTATED AMP PEAK 32(18Q11.2) WILD-TYPE 
                          0.23                           0.00 
  AMP PEAK 32(18Q11.2) MUTATED AMP PEAK 32(18Q11.2) WILD-TYPE 
                        115.69                         122.30 
  AMP PEAK 32(18Q11.2) MUTATED AMP PEAK 32(18Q11.2) WILD-TYPE 
                         13.35                          16.14 
[1] "0.2 - 115.7 (13.3)" "0.0 - 122.3 (16.1)"
[1] "hr=" "1.2"
D32V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 32(18Q11.2) MUTATED         1        5       11        8        14
  AMP PEAK 32(18Q11.2) WILD-TYPE       1       11       30       24        26
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 32(18Q11.2) MUTATED          14         1         27         17
  AMP PEAK 32(18Q11.2) WILD-TYPE        42         2         54         46
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 32(18Q11.2) MUTATED           14       17
  AMP PEAK 32(18Q11.2) WILD-TYPE         25       27
D32V3, multiclass
            clus
vv           AMP PEAK 32(18Q11.2) MUTATED AMP PEAK 32(18Q11.2) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                              5                             11
  STAGE IB                             11                             30
  STAGE II                              8                             24
  STAGE IIA                            14                             26
  STAGE IIB                            14                             42
  STAGE III                             1                              2
  STAGE IIIA                           27                             54
  STAGE IIIB                           17                             46
  STAGE IIIC                           14                             25
  STAGE IV                             17                             27
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 32(18Q11.2) MUTATED     9  27  56  42
  AMP PEAK 32(18Q11.2) WILD-TYPE  14  66 140  77
D32V4, multiclass
    clus
vv   AMP PEAK 32(18Q11.2) MUTATED AMP PEAK 32(18Q11.2) WILD-TYPE
  T1                            9                             14
  T2                           27                             66
  T3                           56                            140
  T4                           42                             77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 32(18Q11.2) MUTATED   39 35 29 30
  AMP PEAK 32(18Q11.2) WILD-TYPE 91 84 57 58
D32V5, multiclass
    clus
vv   AMP PEAK 32(18Q11.2) MUTATED AMP PEAK 32(18Q11.2) WILD-TYPE
  N0                           39                             91
  N1                           35                             84
  N2                           29                             57
  N3                           30                             58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
                                cls
clus                               0   1
  AMP PEAK 32(18Q11.2) MUTATED   120  11
  AMP PEAK 32(18Q11.2) WILD-TYPE 269  19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 32(18Q11.2) MUTATED    120   11
  AMP PEAK 32(18Q11.2) WILD-TYPE  269   19
   clus
vv  AMP PEAK 32(18Q11.2) MUTATED AMP PEAK 32(18Q11.2) WILD-TYPE
  0                          120                            269
  1                           11                             19
[1] 2 2
[1] FALSE
D32V7, binary
                                cls
clus                               0   1
  AMP PEAK 32(18Q11.2) MUTATED    51  89
  AMP PEAK 32(18Q11.2) WILD-TYPE 107 194
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 32(18Q11.2) MUTATED     51   89
  AMP PEAK 32(18Q11.2) WILD-TYPE  107  194
        clus
vv       AMP PEAK 32(18Q11.2) MUTATED AMP PEAK 32(18Q11.2) WILD-TYPE
  FEMALE                           51                            107
  MALE                             89                            194
[1] 2 2
[1] FALSE
D32V8, binary
                                cls
clus                               0   1
  AMP PEAK 32(18Q11.2) MUTATED    98  25
  AMP PEAK 32(18Q11.2) WILD-TYPE 224  51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 32(18Q11.2) MUTATED     98   25
  AMP PEAK 32(18Q11.2) WILD-TYPE  224   51
     clus
vv    AMP PEAK 32(18Q11.2) MUTATED AMP PEAK 32(18Q11.2) WILD-TYPE
  NO                            98                            224
  YES                           25                             51
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK 32(18Q11.2) MUTATED                                          8
  AMP PEAK 32(18Q11.2) WILD-TYPE                                        5
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK 32(18Q11.2) MUTATED                                      15
  AMP PEAK 32(18Q11.2) WILD-TYPE                                    57
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 32(18Q11.2) MUTATED                                                       59
  AMP PEAK 32(18Q11.2) WILD-TYPE                                                    104
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK 32(18Q11.2) MUTATED                                                   7
  AMP PEAK 32(18Q11.2) WILD-TYPE                                                14
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 32(18Q11.2) MUTATED                                                                  19
  AMP PEAK 32(18Q11.2) WILD-TYPE                                                                63
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK 32(18Q11.2) MUTATED                                                    4
  AMP PEAK 32(18Q11.2) WILD-TYPE                                                  4
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK 32(18Q11.2) MUTATED                                                 27
  AMP PEAK 32(18Q11.2) WILD-TYPE                                               52
D32V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK 32(18Q11.2) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       15
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      59
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            7
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           19
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            27
                                                                   clus
vv                                                                  AMP PEAK 32(18Q11.2) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                       5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         57
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       104
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             14
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              52
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 32(18Q11.2) MUTATED   105   8   8   8
  AMP PEAK 32(18Q11.2) WILD-TYPE 244  10  11  17
D32V10, multiclass
    clus
vv   AMP PEAK 32(18Q11.2) MUTATED AMP PEAK 32(18Q11.2) WILD-TYPE
  R0                          105                            244
  R1                            8                             10
  R2                            8                             11
  RX                            8                             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"
D32V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 32(18Q11.2) MUTATED      26                         4
  AMP PEAK 32(18Q11.2) WILD-TYPE    62                         8
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 32(18Q11.2) MUTATED                                           0
  AMP PEAK 32(18Q11.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 32(18Q11.2) MUTATED      91
  AMP PEAK 32(18Q11.2) WILD-TYPE   187
D32V12, multiclass
                                           clus
vv                                          AMP PEAK 32(18Q11.2) MUTATED
  ASIAN                                                               26
  BLACK OR AFRICAN AMERICAN                                            4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               91
                                           clus
vv                                          AMP PEAK 32(18Q11.2) WILD-TYPE
  ASIAN                                                                 62
  BLACK OR AFRICAN AMERICAN                                              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                187
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V13, binary
                                cls
clus                               0   1
  AMP PEAK 32(18Q11.2) MUTATED     3 103
  AMP PEAK 32(18Q11.2) WILD-TYPE   2 213
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 32(18Q11.2) MUTATED      3  103
  AMP PEAK 32(18Q11.2) WILD-TYPE    2  213
                        clus
vv                       AMP PEAK 32(18Q11.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          103
                        clus
vv                       AMP PEAK 32(18Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            213
[1] 2 2
[1] FALSE

Clustering(33) Variable = AMP PEAK 33(19Q12) MUTATION ANALYSIS
D33V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 33(19Q12) MUTATED    72  47
  AMP PEAK 33(19Q12) WILD-TYPE 174 122
  AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE 
                         119                          296 
  AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE 
                          47                          122 
$`AMP PEAK 33(19Q12) MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-B7-A5TK TCGA-BR-4253 
       47.05        21.99        22.98        16.24         9.47         4.08 
TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 
       17.29        19.33         9.21        33.63        39.78        28.73 
TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8289 
        3.45        33.21        11.44         0.69        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8370 TCGA-BR-8373 TCGA-BR-8485 TCGA-BR-8487 
       19.96         2.20         3.32        14.79         9.21         1.12 
TCGA-BR-8590 TCGA-BR-8678 TCGA-BR-8690 TCGA-BR-A453 TCGA-BR-A4J1 TCGA-BR-A4J8 
        9.34        24.79        10.68         6.08         0.72        13.51 
TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 
       20.65        21.44        13.15        13.18        13.35        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
       12.59        12.53        12.39        12.82         6.31        12.30 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-5722 
       12.43        11.61        12.20        54.08        19.07         0.99 
TCGA-CG-5730 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
        4.01        25.71        20.91        19.13        18.84        18.54 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8578 
       17.19        10.26        15.22        12.36        12.33        21.14 
TCGA-D7-A4YU TCGA-D7-A4YY TCGA-D7-A6F0 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
       16.44        13.78        22.29         7.13         0.62         7.99 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-7133 
       72.23         3.48        14.07         0.56         5.52        63.06 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4GD 
       24.39        18.15        28.96        22.82        24.30        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4HD 
       25.81        11.77         2.10        12.95        23.80        33.40 
TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RP TCGA-KB-A6F5 TCGA-KB-A6F7 
        3.45        18.38        13.35         6.44         5.56        63.62 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A7BW 
       14.04        45.67        18.21         6.08         8.61         5.13 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E2 
       35.61         5.79        48.79         5.46        13.25        43.36 
TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A91A TCGA-VQ-A91N 
        7.73        22.19        17.85         1.87        39.45        18.74 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A923 
       32.88         1.71        42.64         9.50         9.04         2.01 
TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6K 
        4.54        21.04        17.13        54.12        12.43 

$`AMP PEAK 33(19Q12) WILD-TYPE`
TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U 
       79.07         0.23        20.15         9.86        27.35        26.93 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN 
       58.03        26.70        11.70        19.56        11.01         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
       34.68        15.95        13.87        13.68        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7957 
       36.16        35.24        35.84        18.15        15.32         9.07 
TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       29.56        37.25        14.43        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        8.05         0.56        15.58         7.40         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
        4.31        14.04        11.80        31.27         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        3.72         5.39        25.18        20.22        12.79        27.12 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
        9.86        20.88         8.22        34.13        13.87         7.53 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 
       14.17         0.53        28.34         0.66        32.52         0.46 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        16.14         5.13        13.41        13.02 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 
       11.21        12.10         7.17        12.33        12.30        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A4MG 
       11.64        15.39        12.07        12.43        11.31         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02         7.99         8.05         4.01        14.01        29.98 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03         0.00         9.01        18.97         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 
      105.07        12.03        15.02        28.96        65.10        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 
       21.07         7.99        12.66        20.55        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 
       13.35        15.98        12.79        11.31        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19        18.21        14.66        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
        5.92        36.43        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.44        20.32        15.65         8.38         4.34        19.96 
TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 
       14.47        21.27        11.38        19.53        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 
       59.54         5.03        13.58         6.21        77.29        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8602 TCGA-HU-8608 
       30.51        26.47         1.51         5.92        22.32        21.07 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
       20.25         0.26        29.00        23.84        21.17        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN 
       15.68        36.36        18.81         3.39        12.46        19.53 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
       13.51         2.53        37.64        36.95         3.72        19.73 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7C1 
        8.52        74.53         4.60         9.24        11.05        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DZ 
       57.44         8.94        16.87        19.04         0.92        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       18.48        21.73        37.41        38.14        37.22        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       34.29        46.26        16.31         2.50        12.79         2.70 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q 
       14.33        73.41        11.70        21.83        61.22        20.81 
TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
       60.85         9.73        55.56        55.43         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       66.81         2.66        42.54        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       28.41        38.93        32.94        26.04        16.14        27.55 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

  AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE 
                        0.56                         0.00 
  AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE 
                       72.23                       122.30 
  AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE 
                       13.35                        15.65 
[1] "0.6 - 72.2 (13.3)"  "0.0 - 122.3 (15.7)"
[1] "hr=" "1.1"
D33V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 33(19Q12) MUTATED         1        4       11        9        12
  AMP PEAK 33(19Q12) WILD-TYPE       1       12       30       23        28
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 33(19Q12) MUTATED          15         1         31         17
  AMP PEAK 33(19Q12) WILD-TYPE        41         2         50         46
                              vv
clus                           STAGE IIIC STAGE IV
  AMP PEAK 33(19Q12) MUTATED            8       14
  AMP PEAK 33(19Q12) WILD-TYPE         31       30
D33V3, multiclass
            clus
vv           AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE
  STAGE I                             1                            1
  STAGE IA                            4                           12
  STAGE IB                           11                           30
  STAGE II                            9                           23
  STAGE IIA                          12                           28
  STAGE IIB                          15                           41
  STAGE III                           1                            2
  STAGE IIIA                         31                           50
  STAGE IIIB                         17                           46
  STAGE IIIC                          8                           31
  STAGE IV                           14                           30
[1] 11  2
[1] TRUE
[1] "dimension of 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 33(19Q12) MUTATED     6  26  69  26
  AMP PEAK 33(19Q12) WILD-TYPE  17  67 127  93
D33V4, multiclass
    clus
vv   AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE
  T1                          6                           17
  T2                         26                           67
  T3                         69                          127
  T4                         26                           93
[1] 4 2
[1] TRUE
[1] "dimension of 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 33(19Q12) MUTATED   34 37 22 30
  AMP PEAK 33(19Q12) WILD-TYPE 96 82 64 58
D33V5, multiclass
    clus
vv   AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE
  N0                         34                           96
  N1                         37                           82
  N2                         22                           64
  N3                         30                           58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                              cls
clus                             0   1
  AMP PEAK 33(19Q12) MUTATED   113   9
  AMP PEAK 33(19Q12) WILD-TYPE 276  21
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 33(19Q12) MUTATED    113    9
  AMP PEAK 33(19Q12) WILD-TYPE  276   21
   clus
vv  AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE
  0                        113                          276
  1                          9                           21
[1] 2 2
[1] FALSE
D33V7, binary
                              cls
clus                             0   1
  AMP PEAK 33(19Q12) MUTATED    45  85
  AMP PEAK 33(19Q12) WILD-TYPE 113 198
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 33(19Q12) MUTATED     45   85
  AMP PEAK 33(19Q12) WILD-TYPE  113  198
        clus
vv       AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE
  FEMALE                         45                          113
  MALE                           85                          198
[1] 2 2
[1] FALSE
D33V8, binary
                              cls
clus                             0   1
  AMP PEAK 33(19Q12) MUTATED    89  28
  AMP PEAK 33(19Q12) WILD-TYPE 233  48
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 33(19Q12) MUTATED     89   28
  AMP PEAK 33(19Q12) WILD-TYPE  233   48
     clus
vv    AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE
  NO                          89                          233
  YES                         28                           48
[1] 2 2
[1] FALSE
                              vv
clus                           STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK 33(19Q12) MUTATED                                          4
  AMP PEAK 33(19Q12) WILD-TYPE                                        9
                              vv
clus                           STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK 33(19Q12) MUTATED                                      16
  AMP PEAK 33(19Q12) WILD-TYPE                                    56
                              vv
clus                           STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 33(19Q12) MUTATED                                                       46
  AMP PEAK 33(19Q12) WILD-TYPE                                                    117
                              vv
clus                           STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK 33(19Q12) MUTATED                                                   7
  AMP PEAK 33(19Q12) WILD-TYPE                                                14
                              vv
clus                           STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 33(19Q12) MUTATED                                                                  24
  AMP PEAK 33(19Q12) WILD-TYPE                                                                58
                              vv
clus                           STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK 33(19Q12) MUTATED                                                    4
  AMP PEAK 33(19Q12) WILD-TYPE                                                  4
                              vv
clus                           STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK 33(19Q12) MUTATED                                                 27
  AMP PEAK 33(19Q12) WILD-TYPE                                               52
D33V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK 33(19Q12) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                   4
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                     16
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                    46
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                          7
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         24
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                          27
                                                                   clus
vv                                                                  AMP PEAK 33(19Q12) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     9
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       56
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     117
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           14
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           58
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            52
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 33(19Q12) MUTATED    98   6   7   6
  AMP PEAK 33(19Q12) WILD-TYPE 251  12  12  19
D33V10, multiclass
    clus
vv   AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE
  R0                         98                          251
  R1                          6                           12
  R2                          7                           12
  RX                          6                           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"
D33V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 33(19Q12) MUTATED      32                         5
  AMP PEAK 33(19Q12) WILD-TYPE    56                         7
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 33(19Q12) MUTATED                                           1    74
  AMP PEAK 33(19Q12) WILD-TYPE                                         0   204
D33V12, multiclass
                                           clus
vv                                          AMP PEAK 33(19Q12) MUTATED
  ASIAN                                                             32
  BLACK OR AFRICAN AMERICAN                                          5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                             74
                                           clus
vv                                          AMP PEAK 33(19Q12) WILD-TYPE
  ASIAN                                                               56
  BLACK OR AFRICAN AMERICAN                                            7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              204
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V13, binary
                              cls
clus                             0   1
  AMP PEAK 33(19Q12) MUTATED     1  95
  AMP PEAK 33(19Q12) WILD-TYPE   4 221
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 33(19Q12) MUTATED      1   95
  AMP PEAK 33(19Q12) WILD-TYPE    4  221
                        clus
vv                       AMP PEAK 33(19Q12) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         95
                        clus
vv                       AMP PEAK 33(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          221
[1] 2 2
[1] FALSE

Clustering(34) Variable = AMP PEAK 34(19Q13.32) MUTATION ANALYSIS
D34V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 34(19Q13.32) MUTATED    63  40
  AMP PEAK 34(19Q13.32) WILD-TYPE 183 129
  AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE 
                            103                             312 
  AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE 
                             40                             129 
$`AMP PEAK 34(19Q13.32) MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-B7-A5TK 
       47.05        21.99        22.98        16.24         0.23         9.47 
TCGA-BR-4183 TCGA-BR-4253 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7716 
        6.61         4.08        19.33         9.17         9.21        39.78 
TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8286 
        3.45        29.56        33.21         0.69        29.59        29.42 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8370 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8690 
       19.96         2.20         3.32         9.21         1.12        10.68 
TCGA-BR-A453 TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-5801 
        6.08         0.72        13.51        20.65        21.44        13.18 
TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-A487 
       12.10        12.76        12.59        12.53        12.33        12.30 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4472 TCGA-CG-5722 
       12.43        11.61        54.08         4.01        12.00         0.99 
TCGA-CG-5730 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6526 
        4.01        25.71        20.91        19.13        18.54        17.19 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8578 TCGA-D7-A4YU TCGA-EQ-8122 
       12.36        12.33        24.72        21.14        16.44         7.99 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 
       72.23         3.48        14.07         5.52         6.21        63.06 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4GD 
       24.39        18.15        28.96        22.82        24.30        22.75 
TCGA-HU-A4GH TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-7808 
       11.77         2.10        12.95        23.80        21.17         3.45 
TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-AB1V TCGA-KB-A6F7 TCGA-MX-A666 TCGA-R5-A7ZR 
       13.35         6.44        15.75        63.62        14.04         6.08 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU 
       11.05         8.61        35.61         5.79        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PH 
       13.25        43.36        37.22         7.73        22.19        12.79 
TCGA-VQ-A8PM TCGA-VQ-A91A TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A922 
        1.87        39.45         1.71        42.64         9.50         9.04 
TCGA-VQ-A923 TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA6F TCGA-VQ-AA6I 
        2.01        66.81        42.54        11.24        54.12        16.14 
TCGA-VQ-AA6K 
       12.43 

$`AMP PEAK 34(19Q13.32) WILD-TYPE`
TCGA-CG-5727 TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 
       79.07        20.15         9.86        27.35        26.93        58.03 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4184 
       26.70        11.70        19.56        11.01         9.44         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35        30.90         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       13.87        17.29        13.68        39.12        26.10        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 
       30.90        31.20        44.94        21.90        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 
       35.84        33.63        18.15        15.32        28.73         9.07 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       37.25        14.43        11.44         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        0.56         2.66        15.58         7.40         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8588 
       25.05         3.72         5.39        25.18        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       34.13        13.87         7.53        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57        12.89         8.98        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL 
        0.66        32.52         0.46        20.42         1.15        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13        13.41        13.02        13.15        13.35        11.21 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        7.17        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A4MG 
       12.07        12.82        12.43         6.31        11.31         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 
       15.95         1.02         7.99         8.05        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 
      105.07        12.03        15.02        28.96        65.10        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
       21.07         7.99        12.66        20.55        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        10.26        15.22        15.98        12.79 
TCGA-D7-6820 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       11.31        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 
       14.47        21.27        11.38        19.53        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-7132 TCGA-HF-7134 
       59.54         5.03        13.58         0.56        77.29        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8602 TCGA-HU-8608 
       30.51        26.47         1.51         5.92        22.32        21.07 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H8 
        6.58        20.25         0.26        29.00        23.84        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       15.68        33.40        36.36        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       12.46        19.53         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J 
       11.70        13.51         2.53         5.56        37.64        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        19.73        45.67        18.21         8.52        74.53 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
        4.60         9.24         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E3 
       16.87        19.04         0.92        13.02        18.48        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       37.41        38.14        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.50         2.70        17.85         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D 
       13.35        29.59        64.57        14.33        73.41        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91W 
       21.83        61.22        18.74        20.81        32.88        60.85 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        9.73        55.56        55.43         4.54         6.58         5.72 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       21.04         2.66        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       32.94        17.13        26.04        27.55        17.26         0.79 

  AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE 
                           0.23                            0.00 
  AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE 
                          72.23                          122.30 
  AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE 
                          12.95                           15.65 
[1] "0.2 - 72.2 (12.9)"  "0.0 - 122.3 (15.7)"
[1] "hr=" "1"  
D34V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 34(19Q13.32) MUTATED         0        4        8        4         7
  AMP PEAK 34(19Q13.32) WILD-TYPE       2       12       33       28        33
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 34(19Q13.32) MUTATED          15         1         27         17
  AMP PEAK 34(19Q13.32) WILD-TYPE        41         2         54         46
                                 vv
clus                              STAGE IIIC STAGE IV
  AMP PEAK 34(19Q13.32) MUTATED            7       12
  AMP PEAK 34(19Q13.32) WILD-TYPE         32       32
D34V3, multiclass
            clus
vv           AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE
  STAGE I                                0                               2
  STAGE IA                               4                              12
  STAGE IB                               8                              33
  STAGE II                               4                              28
  STAGE IIA                              7                              33
  STAGE IIB                             15                              41
  STAGE III                              1                               2
  STAGE IIIA                            27                              54
  STAGE IIIB                            17                              46
  STAGE IIIC                             7                              32
  STAGE IV                              12                              32
[1] 11  2
[1] TRUE
[1] "dimension of 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 34(19Q13.32) MUTATED     6  19  58  26
  AMP PEAK 34(19Q13.32) WILD-TYPE  17  74 138  93
D34V4, multiclass
    clus
vv   AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE
  T1                             6                              17
  T2                            19                              74
  T3                            58                             138
  T4                            26                              93
[1] 4 2
[1] TRUE
[1] "dimension of 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 34(19Q13.32) MUTATED    26  35  17  27
  AMP PEAK 34(19Q13.32) WILD-TYPE 104  84  69  61
D34V5, multiclass
    clus
vv   AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE
  N0                            26                             104
  N1                            35                              84
  N2                            17                              69
  N3                            27                              61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                                 cls
clus                                0   1
  AMP PEAK 34(19Q13.32) MUTATED    96   7
  AMP PEAK 34(19Q13.32) WILD-TYPE 293  23
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 34(19Q13.32) MUTATED     96    7
  AMP PEAK 34(19Q13.32) WILD-TYPE  293   23
   clus
vv  AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE
  0                            96                             293
  1                             7                              23
[1] 2 2
[1] FALSE
D34V7, binary
                                 cls
clus                                0   1
  AMP PEAK 34(19Q13.32) MUTATED    37  74
  AMP PEAK 34(19Q13.32) WILD-TYPE 121 209
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 34(19Q13.32) MUTATED     37   74
  AMP PEAK 34(19Q13.32) WILD-TYPE  121  209
        clus
vv       AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE
  FEMALE                            37                             121
  MALE                              74                             209
[1] 2 2
[1] FALSE
D34V8, binary
                                 cls
clus                                0   1
  AMP PEAK 34(19Q13.32) MUTATED    74  25
  AMP PEAK 34(19Q13.32) WILD-TYPE 248  51
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 34(19Q13.32) MUTATED     74   25
  AMP PEAK 34(19Q13.32) WILD-TYPE  248   51
     clus
vv    AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE
  NO                             74                             248
  YES                            25                              51
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK 34(19Q13.32) MUTATED                                          5
  AMP PEAK 34(19Q13.32) WILD-TYPE                                        8
                                 vv
clus                              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK 34(19Q13.32) MUTATED                                      15
  AMP PEAK 34(19Q13.32) WILD-TYPE                                    57
                                 vv
clus                              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 34(19Q13.32) MUTATED                                                       38
  AMP PEAK 34(19Q13.32) WILD-TYPE                                                    125
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK 34(19Q13.32) MUTATED                                                   6
  AMP PEAK 34(19Q13.32) WILD-TYPE                                                15
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 34(19Q13.32) MUTATED                                                                  20
  AMP PEAK 34(19Q13.32) WILD-TYPE                                                                62
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK 34(19Q13.32) MUTATED                                                    2
  AMP PEAK 34(19Q13.32) WILD-TYPE                                                  6
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK 34(19Q13.32) MUTATED                                                 22
  AMP PEAK 34(19Q13.32) WILD-TYPE                                               57
D34V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK 34(19Q13.32) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        15
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       38
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             6
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            20
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             22
                                                                   clus
vv                                                                  AMP PEAK 34(19Q13.32) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                          57
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                        125
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                              15
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                              62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                              6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 34(19Q13.32) MUTATED    84   7   6   6
  AMP PEAK 34(19Q13.32) WILD-TYPE 265  11  13  19
D34V10, multiclass
    clus
vv   AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE
  R0                            84                             265
  R1                             7                              11
  R2                             6                              13
  RX                             6                              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"
D34V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 34(19Q13.32) MUTATED      26                         3
  AMP PEAK 34(19Q13.32) WILD-TYPE    62                         9
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 34(19Q13.32) MUTATED                                           1
  AMP PEAK 34(19Q13.32) WILD-TYPE                                         0
                                 vv
clus                              WHITE
  AMP PEAK 34(19Q13.32) MUTATED      64
  AMP PEAK 34(19Q13.32) WILD-TYPE   214
D34V12, multiclass
                                           clus
vv                                          AMP PEAK 34(19Q13.32) MUTATED
  ASIAN                                                                26
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                64
                                           clus
vv                                          AMP PEAK 34(19Q13.32) WILD-TYPE
  ASIAN                                                                  62
  BLACK OR AFRICAN AMERICAN                                               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               0
  WHITE                                                                 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"
D34V13, binary
                                 cls
clus                                0   1
  AMP PEAK 34(19Q13.32) MUTATED     0  77
  AMP PEAK 34(19Q13.32) WILD-TYPE   5 239
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 34(19Q13.32) MUTATED      0   77
  AMP PEAK 34(19Q13.32) WILD-TYPE    5  239
                        clus
vv                       AMP PEAK 34(19Q13.32) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            77
                        clus
vv                       AMP PEAK 34(19Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             239
[1] 2 2
[1] FALSE

Clustering(35) Variable = AMP PEAK 35(20Q13.2) MUTATION ANALYSIS
D35V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 35(20Q13.2) MUTATED   165 116
  AMP PEAK 35(20Q13.2) WILD-TYPE  81  53
  AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE 
                           281                            134 
  AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE 
                           116                             53 
$`AMP PEAK 35(20Q13.2) MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-3M-AB46 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        27.35        58.03        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         6.97         4.64        18.35        30.90 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        4.08         9.67         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6706 
       13.68        19.33        39.12        26.10         9.17        18.05 
TCGA-BR-6707 TCGA-BR-6801 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 
       19.89        40.21        44.94        21.90         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       29.56        33.21        14.43        11.44         0.69         9.60 
TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.56         2.66        19.96         2.20        15.58         7.40 
TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.04        14.79         7.36         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       20.22        27.12         9.34         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U 
       32.58         9.86        20.88         8.22        10.68        13.87 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J4 
        7.53        34.98         1.48        12.89         0.72         0.53 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       13.51         0.46        20.65        20.42         1.15        21.44 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 
       13.02        13.15        13.18        12.10        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 
       12.53         7.17        12.33        12.30        12.39        11.64 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C 
       15.39        12.82         6.31        12.30        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        11.77        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       29.98        19.07        12.03        18.97         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
       30.97        36.00         1.02         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       28.96         4.01        69.04         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 
       20.91        19.13        20.55        18.84        18.54        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 
       17.19        10.26        15.22        15.98        12.79        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8576 TCGA-D7-8578 
       12.33        24.72        16.80        19.50        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A6ET 
       20.91        14.27        16.44         5.92        36.43        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
       19.96         0.62         7.99        14.47        72.23        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8631 
        3.48        19.53        14.07        22.29        17.06         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        5.52         6.21        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        18.15        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        0.76        24.30        24.26         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       11.77         8.98         0.10         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB 
        2.10        12.95        23.84        23.80        21.17        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL 
       33.40        36.36         3.45         3.39        18.38        13.35 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 
        6.74        12.59        10.62        11.70        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
        5.56        63.62        37.64        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MW 
        8.52        74.53         6.08         8.61        16.67        37.91 
TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL 
      115.69        57.44         8.94        35.61         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
       48.79         5.46        13.25        13.02        18.48        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       21.73        46.26        22.19         2.50        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       17.85         1.87        15.65        64.57        14.33        73.41 
TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       39.45        21.83        18.74        32.88         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
       60.85         9.50         9.73        55.56         9.04         2.01 
TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T 
        4.54         5.72        66.81        21.04        42.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       18.41        43.66        38.93        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        27.55        12.43        17.26         0.79 

$`AMP PEAK 35(20Q13.2) WILD-TYPE`
TCGA-VQ-A94U TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-BR-4188 TCGA-BR-4253 
       26.93        26.70        11.70        19.56         7.43         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6705 
        9.34         6.18         9.57        34.68        32.78        25.61 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7703 TCGA-BR-7707 
       12.16         8.98        30.90        31.20        36.16        35.84 
TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
        9.07        37.25        29.59        32.25         8.05        29.42 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        31.10        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33         4.31         3.32        11.80        31.27 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8591 TCGA-BR-8592 
       25.05         3.72         1.12        12.79        28.14         6.28 
TCGA-BR-8680 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
       31.96        34.13         6.08        27.55        28.57         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4QL TCGA-BR-A4QM 
       14.17        28.34         0.66        32.52        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8531 TCGA-CD-8534 TCGA-CD-8536 
       13.41        13.35        11.21        12.59        12.07        12.43 
TCGA-CD-A489 TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-5717 
       11.31        12.62         1.02         0.00         9.01         6.97 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-6522 
        0.99         6.02       105.07        65.10        21.07        18.61 
TCGA-D7-6524 TCGA-D7-6818 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-A4YY TCGA-D7-A4Z0 
       17.85        12.36        17.19        18.21        13.78        14.76 
TCGA-D7-A6EY TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-A448 TCGA-FP-8209 TCGA-FP-8210 
       11.44         4.34         7.13        21.27        59.54         5.03 
TCGA-FP-8211 TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4G3 TCGA-HU-A4G8 
       13.58        77.29        30.51        22.32         5.59        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-HU-A4H8 
       24.20        21.37        29.98         6.51        29.00        14.07 
TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-AB1V 
       18.81        12.46        19.53         6.44         6.51        15.75 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       36.95         3.72        19.73         4.60         9.24        11.05 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB 
        5.13       122.30        40.64       116.38        71.38        16.87 
TCGA-SW-A7EA TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       19.04        37.41        38.14        37.22         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PS TCGA-VQ-A8PT 
       34.29        16.31         9.27        23.41        13.35        29.59 
TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A94P 
       11.70        61.22        20.81        55.43         6.58         2.66 
TCGA-VQ-AA69 TCGA-VQ-AA6I 
       28.41        16.14 

  AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE 
                           0.1                            0.0 
  AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE 
                        115.69                         122.30 
  AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE 
                         14.47                          16.14 
[1] "0.1 - 115.7 (14.5)" "0.0 - 122.3 (16.1)"
[1] "hr=" "1.1"
D35V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 35(20Q13.2) MUTATED         1       12       25       18        26
  AMP PEAK 35(20Q13.2) WILD-TYPE       1        4       16       14        14
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 35(20Q13.2) MUTATED          40         3         59         42
  AMP PEAK 35(20Q13.2) WILD-TYPE        16         0         22         21
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 35(20Q13.2) MUTATED           22       28
  AMP PEAK 35(20Q13.2) WILD-TYPE         17       16
D35V3, multiclass
            clus
vv           AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                             12                              4
  STAGE IB                             25                             16
  STAGE II                             18                             14
  STAGE IIA                            26                             14
  STAGE IIB                            40                             16
  STAGE III                             3                              0
  STAGE IIIA                           59                             22
  STAGE IIIB                           42                             21
  STAGE IIIC                           22                             17
  STAGE IV                             28                             16
[1] 11  2
[1] TRUE
[1] "dimension of 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 35(20Q13.2) MUTATED    14  65 136  72
  AMP PEAK 35(20Q13.2) WILD-TYPE   9  28  60  47
D35V4, multiclass
    clus
vv   AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE
  T1                           14                              9
  T2                           65                             28
  T3                          136                             60
  T4                           72                             47
[1] 4 2
[1] TRUE
[1] "dimension of 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 35(20Q13.2) MUTATED   79 87 60 54
  AMP PEAK 35(20Q13.2) WILD-TYPE 51 32 26 34
D35V5, multiclass
    clus
vv   AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE
  N0                           79                             51
  N1                           87                             32
  N2                           60                             26
  N3                           54                             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"
D35V6, binary
                                cls
clus                               0   1
  AMP PEAK 35(20Q13.2) MUTATED   258  18
  AMP PEAK 35(20Q13.2) WILD-TYPE 131  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 35(20Q13.2) MUTATED    258   18
  AMP PEAK 35(20Q13.2) WILD-TYPE  131   12
   clus
vv  AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE
  0                          258                            131
  1                           18                             12
[1] 2 2
[1] FALSE
D35V7, binary
                                cls
clus                               0   1
  AMP PEAK 35(20Q13.2) MUTATED    93 200
  AMP PEAK 35(20Q13.2) WILD-TYPE  65  83
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 35(20Q13.2) MUTATED     93  200
  AMP PEAK 35(20Q13.2) WILD-TYPE   65   83
        clus
vv       AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE
  FEMALE                           93                             65
  MALE                            200                             83
[1] 2 2
[1] FALSE
D35V8, binary
                                cls
clus                               0   1
  AMP PEAK 35(20Q13.2) MUTATED   219  47
  AMP PEAK 35(20Q13.2) WILD-TYPE 103  29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 35(20Q13.2) MUTATED    219   47
  AMP PEAK 35(20Q13.2) WILD-TYPE  103   29
     clus
vv    AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE
  NO                           219                            103
  YES                           47                             29
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK 35(20Q13.2) MUTATED                                          9
  AMP PEAK 35(20Q13.2) WILD-TYPE                                        4
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK 35(20Q13.2) MUTATED                                      32
  AMP PEAK 35(20Q13.2) WILD-TYPE                                    40
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 35(20Q13.2) MUTATED                                                      101
  AMP PEAK 35(20Q13.2) WILD-TYPE                                                     62
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK 35(20Q13.2) MUTATED                                                  13
  AMP PEAK 35(20Q13.2) WILD-TYPE                                                 8
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 35(20Q13.2) MUTATED                                                                  64
  AMP PEAK 35(20Q13.2) WILD-TYPE                                                                18
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK 35(20Q13.2) MUTATED                                                    6
  AMP PEAK 35(20Q13.2) WILD-TYPE                                                  2
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK 35(20Q13.2) MUTATED                                                 65
  AMP PEAK 35(20Q13.2) WILD-TYPE                                               14
D35V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK 35(20Q13.2) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     9
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       32
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     101
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           13
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            65
                                                                   clus
vv                                                                  AMP PEAK 35(20Q13.2) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                       4
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         40
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                        62
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                              8
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             18
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              14
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 35(20Q13.2) MUTATED   237  10  13  14
  AMP PEAK 35(20Q13.2) WILD-TYPE 112   8   6  11
D35V10, multiclass
    clus
vv   AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE
  R0                          237                            112
  R1                           10                              8
  R2                           13                              6
  RX                           14                             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"
D35V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 35(20Q13.2) MUTATED      61                         9
  AMP PEAK 35(20Q13.2) WILD-TYPE    27                         3
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 35(20Q13.2) MUTATED                                           1
  AMP PEAK 35(20Q13.2) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 35(20Q13.2) MUTATED     177
  AMP PEAK 35(20Q13.2) WILD-TYPE   101
D35V12, multiclass
                                           clus
vv                                          AMP PEAK 35(20Q13.2) MUTATED
  ASIAN                                                               61
  BLACK OR AFRICAN AMERICAN                                            9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              177
                                           clus
vv                                          AMP PEAK 35(20Q13.2) WILD-TYPE
  ASIAN                                                                 27
  BLACK OR AFRICAN AMERICAN                                              3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V13, binary
                                cls
clus                               0   1
  AMP PEAK 35(20Q13.2) MUTATED     4 204
  AMP PEAK 35(20Q13.2) WILD-TYPE   1 112
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 35(20Q13.2) MUTATED      4  204
  AMP PEAK 35(20Q13.2) WILD-TYPE    1  112
                        clus
vv                       AMP PEAK 35(20Q13.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          204
                        clus
vv                       AMP PEAK 35(20Q13.2) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            112
[1] 2 2
[1] FALSE

Clustering(36) Variable = AMP PEAK 36(XQ27.3) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 36(XQ27.3) MUTATED    48  30
  AMP PEAK 36(XQ27.3) WILD-TYPE 198 139
  AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE 
                           78                           337 
  AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE 
                           30                           139 
$`AMP PEAK 36(XQ27.3) MUTATED`
TCGA-CG-4460 TCGA-CG-5727 TCGA-VQ-A8PU TCGA-3M-AB46 TCGA-B7-5818 TCGA-B7-A5TJ 
       21.99        79.07        27.35        58.03        11.70        11.01 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-6458 TCGA-BR-6801 TCGA-BR-7717 
        9.44         6.61        18.35        19.33        40.21        18.15 
TCGA-BR-8059 TCGA-BR-8362 TCGA-BR-8370 TCGA-BR-8486 TCGA-BR-8677 TCGA-BR-8680 
       14.43        13.08         3.32        20.22        26.73        31.96 
TCGA-BR-8683 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J2 TCGA-BR-A4QI 
        9.86        13.87        34.98        12.89        14.17        21.44 
TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-A4MG TCGA-CG-4300 TCGA-CG-4437 
       12.10        12.76         7.17         6.58        20.02         8.05 
TCGA-CG-4438 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5720 TCGA-CG-5734 TCGA-D7-5579 
       54.08         7.07        12.00         0.99         7.99        20.91 
TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6822 TCGA-D7-A4YX 
       18.54        17.19        15.22        15.98        12.33        36.43 
TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 
       11.24        20.32        15.65        19.96         0.62         7.99 
TCGA-F1-6875 TCGA-FP-7735 TCGA-HF-7133 TCGA-HF-7134 TCGA-HU-8244 TCGA-HU-8604 
       72.23         3.48        63.06        52.21        24.39        22.82 
TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4H5 
       24.30        24.26        24.20        22.75        25.81        23.80 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RP TCGA-R5-A7O7 TCGA-VQ-A8E2 
        3.45         3.39        13.35         6.44        45.67        43.36 
TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91E TCGA-VQ-A91Q 
        7.73        46.26        14.33        73.41        21.83        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91Z TCGA-VQ-A92D TCGA-VQ-AA68 TCGA-VQ-AA6A 
       32.88         1.71        55.56        66.81        43.66        38.93 

$`AMP PEAK 36(XQ27.3) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       47.05        22.98        16.24         0.23        20.15         9.86 
TCGA-VQ-A94U TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 
       26.93        26.70        19.56         9.47         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       17.29        13.68        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 
       25.61        18.05        19.89        12.16         8.98        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       35.84        33.63        39.78        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 
        9.07        29.56        33.21        37.25        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        19.96         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 
       25.05         3.72         5.39        25.18         9.21         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       24.79        32.58        20.88         8.22        10.68        34.13 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
        7.53         6.08         1.48        27.55        28.57         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM 
        0.46        20.65        20.42         1.15        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.59        12.53        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       12.62         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        9.01        18.97        30.97         6.97        36.00         1.02 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        69.04        21.07        25.71        12.66 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        20.55        18.84        18.61        17.85        13.35 
TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 
       10.26        12.79        12.36        11.31        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44         5.92        13.78        14.76        26.43 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       11.31        11.44        22.29         8.38         4.34         7.13 
TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       14.47        21.27        11.38        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        6.21        77.29        30.51        26.47         1.51         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 
       18.15        28.96        22.32        21.07         0.76         5.59 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.68         3.25        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        29.00        23.84        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
       33.40        36.36        18.81        18.38        12.46        19.53 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J 
       13.51         2.53         5.56        63.62        37.64        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        19.73        14.04        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
       71.38        57.44         8.94        35.61        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       18.48        21.73        37.41        38.14        37.22        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       34.29        16.31        22.19         2.50        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       17.85         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N 
       29.59        64.57        39.45        11.70        61.22        18.74 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 
       42.64        60.85         9.50         9.73         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P 
       55.43         4.54         6.58         5.72        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D 
       42.54        11.24        18.41        28.41        32.94        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 
TCGA-ZQ-A9CR 
        0.79 

  AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE 
                         0.62                          0.00 
  AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE 
                        79.07                        122.30 
  AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE 
                       18.935                        14.040 
[1] "0.6 - 79.1 (18.9)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.3"
D36V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 36(XQ27.3) MUTATED         0        6       10        5         6
  AMP PEAK 36(XQ27.3) WILD-TYPE       2       10       31       27        34
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 36(XQ27.3) MUTATED          12         1         12         10
  AMP PEAK 36(XQ27.3) WILD-TYPE        44         2         69         53
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 36(XQ27.3) MUTATED            4       11
  AMP PEAK 36(XQ27.3) WILD-TYPE         35       33
D36V3, multiclass
            clus
vv           AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             6                            10
  STAGE IB                            10                            31
  STAGE II                             5                            27
  STAGE IIA                            6                            34
  STAGE IIB                           12                            44
  STAGE III                            1                             2
  STAGE IIIA                          12                            69
  STAGE IIIB                          10                            53
  STAGE IIIC                           4                            35
  STAGE IV                            11                            33
[1] 11  2
[1] TRUE
[1] "dimension of 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 36(XQ27.3) MUTATED     6  20  35  20
  AMP PEAK 36(XQ27.3) WILD-TYPE  17  73 161  99
D36V4, multiclass
    clus
vv   AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE
  T1                           6                            17
  T2                          20                            73
  T3                          35                           161
  T4                          20                            99
[1] 4 2
[1] TRUE
[1] "dimension of 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 36(XQ27.3) MUTATED    28  24  16  12
  AMP PEAK 36(XQ27.3) WILD-TYPE 102  95  70  76
D36V5, multiclass
    clus
vv   AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE
  N0                          28                           102
  N1                          24                            95
  N2                          16                            70
  N3                          12                            76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                               cls
clus                              0   1
  AMP PEAK 36(XQ27.3) MUTATED    74   5
  AMP PEAK 36(XQ27.3) WILD-TYPE 315  25
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 36(XQ27.3) MUTATED     74    5
  AMP PEAK 36(XQ27.3) WILD-TYPE  315   25
   clus
vv  AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE
  0                          74                           315
  1                           5                            25
[1] 2 2
[1] FALSE
D36V7, binary
                               cls
clus                              0   1
  AMP PEAK 36(XQ27.3) MUTATED    29  54
  AMP PEAK 36(XQ27.3) WILD-TYPE 129 229
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 36(XQ27.3) MUTATED     29   54
  AMP PEAK 36(XQ27.3) WILD-TYPE  129  229
        clus
vv       AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE
  FEMALE                          29                           129
  MALE                            54                           229
[1] 2 2
[1] FALSE
D36V8, binary
                               cls
clus                              0   1
  AMP PEAK 36(XQ27.3) MUTATED    60  15
  AMP PEAK 36(XQ27.3) WILD-TYPE 262  61
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 36(XQ27.3) MUTATED     60   15
  AMP PEAK 36(XQ27.3) WILD-TYPE  262   61
     clus
vv    AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE
  NO                           60                           262
  YES                          15                            61
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMP PEAK 36(XQ27.3) MUTATED                                          2
  AMP PEAK 36(XQ27.3) WILD-TYPE                                       11
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMP PEAK 36(XQ27.3) MUTATED                                       7
  AMP PEAK 36(XQ27.3) WILD-TYPE                                    65
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 36(XQ27.3) MUTATED                                                       30
  AMP PEAK 36(XQ27.3) WILD-TYPE                                                    133
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMP PEAK 36(XQ27.3) MUTATED                                                   2
  AMP PEAK 36(XQ27.3) WILD-TYPE                                                19
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 36(XQ27.3) MUTATED                                                                  16
  AMP PEAK 36(XQ27.3) WILD-TYPE                                                                66
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMP PEAK 36(XQ27.3) MUTATED                                                    2
  AMP PEAK 36(XQ27.3) WILD-TYPE                                                  6
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMP PEAK 36(XQ27.3) MUTATED                                                 23
  AMP PEAK 36(XQ27.3) WILD-TYPE                                               56
D36V9, multiclass
                                                                   clus
vv                                                                  AMP PEAK 36(XQ27.3) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       7
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     30
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          16
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           23
                                                                   clus
vv                                                                  AMP PEAK 36(XQ27.3) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      133
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 36(XQ27.3) MUTATED    65   3   2   5
  AMP PEAK 36(XQ27.3) WILD-TYPE 284  15  17  20
D36V10, multiclass
    clus
vv   AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE
  R0                          65                           284
  R1                           3                            15
  R2                           2                            17
  RX                           5                            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"
D36V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 36(XQ27.3) MUTATED      18                         3
  AMP PEAK 36(XQ27.3) WILD-TYPE    70                         9
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 36(XQ27.3) MUTATED                                           0    50
  AMP PEAK 36(XQ27.3) WILD-TYPE                                         1   228
D36V12, multiclass
                                           clus
vv                                          AMP PEAK 36(XQ27.3) MUTATED
  ASIAN                                                              18
  BLACK OR AFRICAN AMERICAN                                           3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              50
                                           clus
vv                                          AMP PEAK 36(XQ27.3) WILD-TYPE
  ASIAN                                                                70
  BLACK OR AFRICAN AMERICAN                                             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               228
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V13, binary
                               cls
clus                              0   1
  AMP PEAK 36(XQ27.3) MUTATED     2  56
  AMP PEAK 36(XQ27.3) WILD-TYPE   3 260
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 36(XQ27.3) MUTATED      2   56
  AMP PEAK 36(XQ27.3) WILD-TYPE    3  260
                        clus
vv                       AMP PEAK 36(XQ27.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          56
                        clus
vv                       AMP PEAK 36(XQ27.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           260
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK  1(1P36.11) MUTATION ANALYSIS
D37V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.11) MUTATED    72  57
  DEL PEAK  1(1P36.11) WILD-TYPE 174 112
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           129                            286 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            57                            112 
$`DEL PEAK  1(1P36.11) MUTATED`
TCGA-CG-4444 TCGA-EQ-A4SO TCGA-MX-A663 TCGA-VQ-A8PU TCGA-3M-AB46 TCGA-B7-5816 
       47.05        16.24         9.86        27.35        58.03        26.70 
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4191 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 
       11.01         9.44        18.35         4.08         9.67         6.18 
TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7704 TCGA-BR-7959 
        9.57        17.29        19.33         9.17        35.24        33.21 
TCGA-BR-8060 TCGA-BR-8289 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8677 
       11.44         2.66         5.39        25.18         9.21        26.73 
TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4PD 
       24.79         9.86        10.68         7.53        34.98        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-8525 TCGA-CD-8527 
       20.42         1.15        21.44        13.02        12.59         7.17 
TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 
       12.30        11.64        15.39        12.07        12.82         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 
       12.30        11.31        11.61        12.20        20.02         3.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        7.99         8.05        54.08        14.01        29.98        19.07 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 
        7.07        30.97         1.02        12.03        15.02         4.01 
TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 
       20.91        20.55        17.19        10.26        15.22        12.79 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-A4YY TCGA-D7-A6EX 
       12.33        24.72        19.50        18.21        13.78        11.31 
TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-A72C TCGA-FP-8099 
       22.29        19.96         0.62         7.99        11.38        17.06 
TCGA-FP-8211 TCGA-FP-A4BF TCGA-HF-7133 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8249 
       13.58         5.52        63.06         1.51         5.92        28.96 
TCGA-HU-8604 TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       22.82        25.81         8.98        12.95        23.84        23.80 
TCGA-HU-A4HD TCGA-IN-AB1V TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-R5-A7ZE 
       33.40        15.75        63.62        37.64        36.95        18.21 
TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N9 
        6.08         9.24         8.61        16.67       122.30        35.61 
TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8P5 TCGA-VQ-A8PC 
        0.92        13.25        13.02        18.48         7.73        46.26 
TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PS 
       22.19        12.79         2.70        17.85         1.87        13.35 
TCGA-VQ-A91A TCGA-VQ-A91Q TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-A92D 
       39.45        20.81         9.73        55.56         4.54        66.81 
TCGA-VQ-A94O TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       21.04        11.24        18.41        43.66        38.93        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       17.13        12.43         0.79 

$`DEL PEAK  1(1P36.11) WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A94U 
       21.99        22.98        79.07         0.23        20.15        26.93 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.70        19.56         9.47         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4280 TCGA-BR-6452 
        7.43        30.90         4.08         9.34         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       15.95        13.87        13.68        39.12        26.10        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        3.45         9.07        29.56        37.25        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       19.96         2.20        15.58         7.40         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        7.36        25.05         3.72        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 
       27.12         9.34        28.14         6.28         7.53        31.96 
TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 
       32.58        20.88         8.22        34.13        13.87         6.08 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 
        0.46        16.14         5.13        13.41        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8528 
       13.35        11.21        12.10        12.76        12.53        12.33 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI 
       12.39        12.59        12.43        12.43         6.58        11.77 
TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4440 TCGA-CG-4455 
       12.62        27.02        15.95         1.02         4.01        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 
        0.00         9.01        18.97        12.00         6.97        36.00 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 
        0.99         6.02         0.99       105.07        28.96        65.10 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 
       69.04        21.07         7.99        25.71        12.66        19.13 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 
       18.84        18.54        18.61        17.85        13.35        15.98 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 
       12.36        11.31        16.80        17.19        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 
       20.91        14.27        16.44         5.92        36.43        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 
       26.43        11.24        11.44        20.32        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        4.34         7.13        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 
       19.53        14.07        22.29        59.54         5.03         0.56 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 
        6.21        77.29        52.21        30.51        26.47        24.39 
TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       18.15        22.32        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH 
       24.26        22.68        24.20         3.25        22.75        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
        0.26         2.10        29.00        21.17        14.07        15.68 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-MX-A5UG 
       10.62        11.70        13.51         2.53         5.56         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
       19.73        14.04        45.67         8.52        74.53         4.60 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       11.05         5.13        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        16.87        19.04         5.79 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       48.79         5.46        43.36        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PO 
       37.22        30.97        34.29        16.31         2.50         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       23.41        15.65        29.59        64.57        14.33        73.41 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U 
       11.70        21.83        61.22        18.74        32.88         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
       42.64        60.85         9.50         9.04         2.01        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA69 TCGA-VQ-AA6F 
        6.58         5.72         2.66        42.54        28.41        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       26.04        16.14        27.55        17.26 

  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                          0.62                           0.00 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                        122.30                         116.38 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                         13.78                          15.45 
[1] "0.6 - 122.3 (13.8)" "0.0 - 116.4 (15.4)"
[1] "hr=" "1.2"
D37V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  1(1P36.11) MUTATED         0        2       15       12        14
  DEL PEAK  1(1P36.11) WILD-TYPE       2       14       26       20        26
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  1(1P36.11) MUTATED          14         1         28         18
  DEL PEAK  1(1P36.11) WILD-TYPE        42         2         53         45
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK  1(1P36.11) MUTATED            8       15
  DEL PEAK  1(1P36.11) WILD-TYPE         31       29
D37V3, multiclass
            clus
vv           DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              2                             14
  STAGE IB                             15                             26
  STAGE II                             12                             20
  STAGE IIA                            14                             26
  STAGE IIB                            14                             42
  STAGE III                             1                              2
  STAGE IIIA                           28                             53
  STAGE IIIB                           18                             45
  STAGE IIIC                            8                             31
  STAGE IV                             15                             29
[1] 11  2
[1] TRUE
[1] "dimension of 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     3  32  65  31
  DEL PEAK  1(1P36.11) WILD-TYPE  20  61 131  88
D37V4, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  T1                            3                             20
  T2                           32                             61
  T3                           65                            131
  T4                           31                             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"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK  1(1P36.11) MUTATED   38 35 27 27
  DEL PEAK  1(1P36.11) WILD-TYPE 92 84 59 61
D37V5, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  N0                           38                             92
  N1                           35                             84
  N2                           27                             59
  N3                           27                             61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED   119   9
  DEL PEAK  1(1P36.11) WILD-TYPE 270  21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    119    9
  DEL PEAK  1(1P36.11) WILD-TYPE  270   21
   clus
vv  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  0                          119                            270
  1                            9                             21
[1] 2 2
[1] FALSE
D37V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED    45  90
  DEL PEAK  1(1P36.11) WILD-TYPE 113 193
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     45   90
  DEL PEAK  1(1P36.11) WILD-TYPE  113  193
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  FEMALE                           45                            113
  MALE                             90                            193
[1] 2 2
[1] FALSE
D37V8, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED    90  31
  DEL PEAK  1(1P36.11) WILD-TYPE 232  45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     90   31
  DEL PEAK  1(1P36.11) WILD-TYPE  232   45
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  NO                            90                            232
  YES                           31                             45
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK  1(1P36.11) MUTATED                                          5
  DEL PEAK  1(1P36.11) WILD-TYPE                                        8
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK  1(1P36.11) MUTATED                                      12
  DEL PEAK  1(1P36.11) WILD-TYPE                                    60
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  1(1P36.11) MUTATED                                                       41
  DEL PEAK  1(1P36.11) WILD-TYPE                                                    122
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK  1(1P36.11) MUTATED                                                   7
  DEL PEAK  1(1P36.11) WILD-TYPE                                                14
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  1(1P36.11) MUTATED                                                                  31
  DEL PEAK  1(1P36.11) WILD-TYPE                                                                51
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK  1(1P36.11) MUTATED                                                    2
  DEL PEAK  1(1P36.11) WILD-TYPE                                                  6
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK  1(1P36.11) MUTATED                                                 36
  DEL PEAK  1(1P36.11) WILD-TYPE                                               43
D37V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK  1(1P36.11) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       12
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      41
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            7
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           31
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            36
                                                                   clus
vv                                                                  DEL PEAK  1(1P36.11) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         60
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       122
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             14
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             51
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              43
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  1(1P36.11) MUTATED    97   8   9   9
  DEL PEAK  1(1P36.11) WILD-TYPE 252  10  10  16
D37V10, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  R0                           97                            252
  R1                            8                             10
  R2                            9                             10
  RX                            9                             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"
D37V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  1(1P36.11) MUTATED      28                         4
  DEL PEAK  1(1P36.11) WILD-TYPE    60                         8
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK  1(1P36.11) MUTATED                                           1
  DEL PEAK  1(1P36.11) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK  1(1P36.11) MUTATED      80
  DEL PEAK  1(1P36.11) WILD-TYPE   198
D37V12, multiclass
                                           clus
vv                                          DEL PEAK  1(1P36.11) MUTATED
  ASIAN                                                               28
  BLACK OR AFRICAN AMERICAN                                            4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               80
                                           clus
vv                                          DEL PEAK  1(1P36.11) WILD-TYPE
  ASIAN                                                                 60
  BLACK OR AFRICAN AMERICAN                                              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                198
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V13, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED     1  87
  DEL PEAK  1(1P36.11) WILD-TYPE   4 229
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      1   87
  DEL PEAK  1(1P36.11) WILD-TYPE    4  229
                        clus
vv                       DEL PEAK  1(1P36.11) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           87
                        clus
vv                       DEL PEAK  1(1P36.11) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            229
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK  2(1P13.2) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P13.2) MUTATED    52  37
  DEL PEAK  2(1P13.2) WILD-TYPE 194 132
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           89                           326 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           37                           132 
$`DEL PEAK  2(1P13.2) MUTATED`
TCGA-CG-4475 TCGA-EQ-A4SO TCGA-MX-A663 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4257 
       22.98        16.24         9.86        11.01         9.44         9.67 
TCGA-BR-6456 TCGA-BR-7704 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8289 TCGA-BR-8295 
       17.29        35.24         3.45        33.21         2.66         2.20 
TCGA-BR-8369 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8687 
       14.04         5.39         9.21        24.79         9.86         8.22 
TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 
       34.98        12.89        20.42         1.15        21.44        13.02 
TCGA-CD-5802 TCGA-CD-8527 TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       13.35         7.17        12.59        15.39        12.07        12.82 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4438 
        6.31        11.31        12.20         3.02         7.99        54.08 
TCGA-CG-4443 TCGA-CG-4466 TCGA-CG-5724 TCGA-CG-5730 TCGA-D7-5579 TCGA-D7-6519 
       29.98        18.97        12.03         4.01        20.91        20.55 
TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-8570 
       18.54        17.19        10.26        15.22        12.79        24.72 
TCGA-D7-8573 TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 
       19.50        11.31        20.32        15.65        19.96         0.62 
TCGA-EQ-8122 TCGA-FP-7829 TCGA-FP-A4BF TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8604 
        7.99        19.53         5.52         1.51        28.96        22.82 
TCGA-HU-A4GD TCGA-HU-A4HD TCGA-IN-A6RL TCGA-IP-7968 TCGA-KB-A93H TCGA-R5-A7ZE 
       22.75        33.40        13.35         2.53        37.64        18.21 
TCGA-R5-A805 TCGA-RD-A7BT TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
        9.24         8.61         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PO 
       13.02         7.73        22.19         2.70        17.85         9.27 
TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91V TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-A94O 
       39.45        18.74        42.64        55.56         4.54        21.04 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6K 
       11.24        18.41        38.93        32.94        12.43 

$`DEL PEAK  2(1P13.2) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A8PU 
       47.05        21.99        79.07         0.23        20.15        27.35 
TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
       26.93        58.03        26.70        11.70        19.56         9.47 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       34.68        15.95        13.87        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
       18.15        15.32        28.73         9.07        29.56        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 
        8.05         0.56        29.42        19.96        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        31.10        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33         4.31         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8486 
       14.79         7.36        25.05         3.72        25.18        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8690 
        7.53        26.73        31.96        32.58        20.88        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       34.13        13.87         7.53         6.08         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4QL 
        0.66        32.52        13.51         0.46        20.65        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 
        5.13        13.41        13.15        13.18        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.76        12.59        12.53        12.33        12.30        12.39 
TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
       11.64        12.43        12.30        12.43        11.61         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        12.62        20.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        8.05         4.01        14.01        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01         7.07        12.00        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 
        1.02         0.99         6.02         0.99       105.07        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       12.66        19.13        18.84        18.61        17.85        13.35 
TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8574 
       15.98        12.36        11.31        12.33        16.80        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6874 
       11.44        22.29         8.38         4.34         7.13        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27        11.38         3.48        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A9TM 
       17.06        59.54         5.03        13.58         0.56         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 
       77.29        63.06        52.21        30.51        26.47         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        18.15        22.32        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
        5.59        24.26        22.68        24.20         3.25        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       23.84        23.80        21.17        14.07        15.68        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
        3.45        18.81         3.39        18.38        12.46        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       15.75        13.51         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       19.73        14.04        45.67         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
        4.60        11.05         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8E0 TCGA-VQ-A8E2 
       35.61        16.87        19.04         5.79        18.48        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        37.41        38.14        37.22        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PP 
       46.26        16.31         2.50        12.79         1.87        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        13.35        29.59        64.57        14.33        73.41 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       11.70        21.83        61.22        20.81        32.88         1.71 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
       60.85         9.50         9.73         9.04         2.01        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA68 
        6.58         5.72        66.81         2.66        42.54        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       28.41        17.13        54.12        26.04        16.14        27.55 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                         0.62                          0.00 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                        55.56                        122.30 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                       13.250                        15.615 
[1] "0.6 - 55.6 (13.2)"  "0.0 - 122.3 (15.6)"
[1] "hr=" "1.2"
D38V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  2(1P13.2) MUTATED         0        2        7        7        10
  DEL PEAK  2(1P13.2) WILD-TYPE       2       14       34       25        30
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  2(1P13.2) MUTATED          12         0         20         14
  DEL PEAK  2(1P13.2) WILD-TYPE        44         3         61         49
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  2(1P13.2) MUTATED            5       10
  DEL PEAK  2(1P13.2) WILD-TYPE         34       34
D38V3, multiclass
            clus
vv           DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             2                            14
  STAGE IB                             7                            34
  STAGE II                             7                            25
  STAGE IIA                           10                            30
  STAGE IIB                           12                            44
  STAGE III                            0                             3
  STAGE IIIA                          20                            61
  STAGE IIIB                          14                            49
  STAGE IIIC                           5                            34
  STAGE IV                            10                            34
[1] 11  2
[1] TRUE
[1] "dimension of 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(1P13.2) MUTATED     2  16  51  22
  DEL PEAK  2(1P13.2) WILD-TYPE  21  77 145  97
D38V4, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  T1                           2                            21
  T2                          16                            77
  T3                          51                           145
  T4                          22                            97
[1] 4 2
[1] TRUE
[1] "dimension of 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(1P13.2) MUTATED    26  20  25  17
  DEL PEAK  2(1P13.2) WILD-TYPE 104  99  61  71
D38V5, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  N0                          26                           104
  N1                          20                            99
  N2                          25                            61
  N3                          17                            71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED    83   7
  DEL PEAK  2(1P13.2) WILD-TYPE 306  23
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     83    7
  DEL PEAK  2(1P13.2) WILD-TYPE  306   23
   clus
vv  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  0                          83                           306
  1                           7                            23
[1] 2 2
[1] FALSE
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED    28  65
  DEL PEAK  2(1P13.2) WILD-TYPE 130 218
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     28   65
  DEL PEAK  2(1P13.2) WILD-TYPE  130  218
        clus
vv       DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  FEMALE                          28                           130
  MALE                            65                           218
[1] 2 2
[1] FALSE
D38V8, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED    66  18
  DEL PEAK  2(1P13.2) WILD-TYPE 256  58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     66   18
  DEL PEAK  2(1P13.2) WILD-TYPE  256   58
     clus
vv    DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  NO                           66                           256
  YES                          18                            58
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK  2(1P13.2) MUTATED                                          4
  DEL PEAK  2(1P13.2) WILD-TYPE                                        9
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK  2(1P13.2) MUTATED                                       7
  DEL PEAK  2(1P13.2) WILD-TYPE                                    65
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  2(1P13.2) MUTATED                                                       27
  DEL PEAK  2(1P13.2) WILD-TYPE                                                    136
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK  2(1P13.2) MUTATED                                                   4
  DEL PEAK  2(1P13.2) WILD-TYPE                                                17
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  2(1P13.2) MUTATED                                                                  23
  DEL PEAK  2(1P13.2) WILD-TYPE                                                                59
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK  2(1P13.2) MUTATED                                                    1
  DEL PEAK  2(1P13.2) WILD-TYPE                                                  7
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK  2(1P13.2) MUTATED                                                 25
  DEL PEAK  2(1P13.2) WILD-TYPE                                               54
D38V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK  2(1P13.2) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    4
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       7
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     27
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          23
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           25
                                                                   clus
vv                                                                  DEL PEAK  2(1P13.2) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      9
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      136
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            17
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            59
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             54
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  2(1P13.2) MUTATED    68   4   8   3
  DEL PEAK  2(1P13.2) WILD-TYPE 281  14  11  22
D38V10, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  R0                          68                           281
  R1                           4                            14
  R2                           8                            11
  RX                           3                            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"
D38V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  2(1P13.2) MUTATED      19                         2
  DEL PEAK  2(1P13.2) WILD-TYPE    69                        10
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  2(1P13.2) MUTATED                                           1    58
  DEL PEAK  2(1P13.2) WILD-TYPE                                         0   220
D38V12, multiclass
                                           clus
vv                                          DEL PEAK  2(1P13.2) MUTATED
  ASIAN                                                              19
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              58
                                           clus
vv                                          DEL PEAK  2(1P13.2) WILD-TYPE
  ASIAN                                                                69
  BLACK OR AFRICAN AMERICAN                                            10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               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"
D38V13, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED     0  63
  DEL PEAK  2(1P13.2) WILD-TYPE   5 253
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      0   63
  DEL PEAK  2(1P13.2) WILD-TYPE    5  253
                        clus
vv                       DEL PEAK  2(1P13.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          63
                        clus
vv                       DEL PEAK  2(1P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           253
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK  3(1Q44) MUTATION ANALYSIS
D39V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  3(1Q44) MUTATED    14  10
  DEL PEAK  3(1Q44) WILD-TYPE 232 159
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         24                         391 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         10                         159 
$`DEL PEAK  3(1Q44) MUTATED`
TCGA-B7-A5TN TCGA-BR-6456 TCGA-BR-7704 TCGA-BR-8362 TCGA-BR-A4PD TCGA-CD-A486 
        9.44        17.29        35.24        13.08        20.65         6.31 
TCGA-CD-A48A TCGA-CG-4441 TCGA-CG-4465 TCGA-CG-5724 TCGA-D7-6519 TCGA-D7-8576 
       12.43        14.01         9.01        12.03        20.55        14.66 
TCGA-D7-A6F2 TCGA-HU-8604 TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-IN-8663 TCGA-IP-7968 
       15.65        22.82         8.98         2.10         3.39         2.53 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-R5-A7ZE TCGA-VQ-A91V TCGA-VQ-A91Z TCGA-VQ-A928 
        5.56        37.64        18.21        42.64        55.56         5.72 

$`DEL PEAK  3(1Q44) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 
       20.15         9.86        27.35        26.93        58.03        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 
       11.70        19.56        11.01         9.47         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.87        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.20        15.58         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51         0.46        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       11.21        12.10        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C 
       12.07        12.82        12.43        12.30        11.31        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 
        4.01        29.98        19.07        12.03         0.00        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.66        20.91        19.13        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19        18.21        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 
       11.24        11.31        11.44        20.32        22.29         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
       26.47         1.51         5.92        24.39        18.15        28.96 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.32        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       16.87        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       13.25        13.02        18.48        43.36        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       38.14        37.22         7.73        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       16.31        22.19         2.50        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        73.41        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W 
       61.22        18.74        20.81        32.88         1.71        60.85 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.50         9.73         9.04         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
        6.58        66.81        21.04         2.66        42.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       18.41        43.66        28.41        38.93        32.94        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 
TCGA-ZQ-A9CR 
        0.79 

  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                        2.1                         0.0 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                      55.56                      122.30 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                     13.545                      15.220 
[1] "2.1 - 55.6 (13.5)"  "0.0 - 122.3 (15.2)"
[1] "hr=" "1.2"
D39V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  3(1Q44) MUTATED         0        0        1        1         4
  DEL PEAK  3(1Q44) WILD-TYPE       2       16       40       31        36
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  3(1Q44) MUTATED           5         0          5          2
  DEL PEAK  3(1Q44) WILD-TYPE        51         3         76         61
                             vv
clus                          STAGE IIIC STAGE IV
  DEL PEAK  3(1Q44) MUTATED            3        3
  DEL PEAK  3(1Q44) WILD-TYPE         36       41
D39V3, multiclass
            clus
vv           DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  STAGE I                            0                           2
  STAGE IA                           0                          16
  STAGE IB                           1                          40
  STAGE II                           1                          31
  STAGE IIA                          4                          36
  STAGE IIB                          5                          51
  STAGE III                          0                           3
  STAGE IIIA                         5                          76
  STAGE IIIB                         2                          61
  STAGE IIIC                         3                          36
  STAGE IV                           3                          41
[1] 11  2
[1] TRUE
[1] "dimension of 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(1Q44) MUTATED     0   5  14   6
  DEL PEAK  3(1Q44) WILD-TYPE  23  88 182 113
D39V4, multiclass
    clus
vv   DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  T1                         0                          23
  T2                         5                          88
  T3                        14                         182
  T4                         6                         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"
                             vv
clus                           N0  N1  N2  N3
  DEL PEAK  3(1Q44) MUTATED     6   5   6   7
  DEL PEAK  3(1Q44) WILD-TYPE 124 114  80  81
D39V5, multiclass
    clus
vv   DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  N0                         6                         124
  N1                         5                         114
  N2                         6                          80
  N3                         7                          81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED    22   2
  DEL PEAK  3(1Q44) WILD-TYPE 367  28
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED     22    2
  DEL PEAK  3(1Q44) WILD-TYPE  367   28
   clus
vv  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  0                        22                         367
  1                         2                          28
[1] 2 2
[1] FALSE
D39V7, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED    12  13
  DEL PEAK  3(1Q44) WILD-TYPE 146 270
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED     12   13
  DEL PEAK  3(1Q44) WILD-TYPE  146  270
        clus
vv       DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  FEMALE                        12                         146
  MALE                          13                         270
[1] 2 2
[1] FALSE
D39V8, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED    19   3
  DEL PEAK  3(1Q44) WILD-TYPE 303  73
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED     19    3
  DEL PEAK  3(1Q44) WILD-TYPE  303   73
     clus
vv    DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  NO                         19                         303
  YES                         3                          73
[1] 2 2
[1] FALSE
                             vv
clus                          STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK  3(1Q44) MUTATED                                          0
  DEL PEAK  3(1Q44) WILD-TYPE                                       13
                             vv
clus                          STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK  3(1Q44) MUTATED                                       5
  DEL PEAK  3(1Q44) WILD-TYPE                                    67
                             vv
clus                          STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  3(1Q44) MUTATED                                                        9
  DEL PEAK  3(1Q44) WILD-TYPE                                                    154
                             vv
clus                          STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK  3(1Q44) MUTATED                                                   0
  DEL PEAK  3(1Q44) WILD-TYPE                                                21
                             vv
clus                          STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  3(1Q44) MUTATED                                                                   3
  DEL PEAK  3(1Q44) WILD-TYPE                                                                79
                             vv
clus                          STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK  3(1Q44) MUTATED                                                    1
  DEL PEAK  3(1Q44) WILD-TYPE                                                  7
                             vv
clus                          STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK  3(1Q44) MUTATED                                                  7
  DEL PEAK  3(1Q44) WILD-TYPE                                               72
D39V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK  3(1Q44) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                  0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                     5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                    9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                         0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                        1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                          7
                                                                   clus
vv                                                                  DEL PEAK  3(1Q44) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                   13
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                      67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                    154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                          21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          79
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           72
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  3(1Q44) MUTATED    19   0   2   0
  DEL PEAK  3(1Q44) WILD-TYPE 330  18  17  25
D39V10, multiclass
    clus
vv   DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  R0                        19                         330
  R1                         0                          18
  R2                         2                          17
  RX                         0                          25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  3(1Q44) MUTATED       6                         0
  DEL PEAK  3(1Q44) WILD-TYPE    82                        12
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  3(1Q44) MUTATED                                           0    14
  DEL PEAK  3(1Q44) WILD-TYPE                                         1   264
D39V12, multiclass
                                           clus
vv                                          DEL PEAK  3(1Q44) MUTATED
  ASIAN                                                             6
  BLACK OR AFRICAN AMERICAN                                         0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         0
  WHITE                                                            14
                                           clus
vv                                          DEL PEAK  3(1Q44) WILD-TYPE
  ASIAN                                                              82
  BLACK OR AFRICAN AMERICAN                                          12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             264
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V13, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED     0  17
  DEL PEAK  3(1Q44) WILD-TYPE   5 299
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED      0   17
  DEL PEAK  3(1Q44) WILD-TYPE    5  299
                        clus
vv                       DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  HISPANIC OR LATINO                             0                           5
  NOT HISPANIC OR LATINO                        17                         299
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK  4(2Q32.1) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(2Q32.1) MUTATED    32  29
  DEL PEAK  4(2Q32.1) WILD-TYPE 214 140
  DEL PEAK  4(2Q32.1) MUTATED DEL PEAK  4(2Q32.1) WILD-TYPE 
                           61                           354 
  DEL PEAK  4(2Q32.1) MUTATED DEL PEAK  4(2Q32.1) WILD-TYPE 
                           29                           140 
$`DEL PEAK  4(2Q32.1) MUTATED`
TCGA-CG-4444 TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-BR-4188 TCGA-BR-6456 
       47.05         9.86        27.35        26.93         7.43        17.29 
TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 
       19.33         9.17        37.25         0.69         9.60        29.42 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8676 TCGA-BR-8682 
       26.33         4.31        14.04         3.32         7.53        32.58 
TCGA-BR-8687 TCGA-BR-A4PD TCGA-CD-8525 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 
        8.22        20.65        12.59        11.64        12.07        12.82 
TCGA-CD-A486 TCGA-CG-4300 TCGA-CG-4462 TCGA-CG-4472 TCGA-CG-5720 TCGA-CG-5724 
        6.31        20.02         0.00        12.00         0.99        12.03 
TCGA-CG-5725 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-8575 TCGA-D7-8576 
       15.02        12.66        20.91        17.19        18.21        14.66 
TCGA-D7-A6F0 TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-A4G3 TCGA-HU-A4GD 
       22.29        63.06        26.47         5.92         5.59        22.75 
TCGA-HU-A4GU TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-AB1V TCGA-KB-A93J TCGA-MX-A666 
        6.58        33.40        18.38        15.75        36.95        14.04 
TCGA-R5-A7ZE TCGA-RD-A7C1 TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8P3 
       18.21        16.67         0.92        13.25        13.02        37.22 
TCGA-VQ-A8PK TCGA-VQ-A8PY TCGA-VQ-A91Y TCGA-VQ-A94O TCGA-VQ-AA68 TCGA-VQ-AA6A 
       17.85        14.33         9.73        21.04        43.66        38.93 
TCGA-ZA-A8F6 
       17.26 

$`DEL PEAK  4(2Q32.1) WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       21.99        22.98        79.07        16.24         0.23        20.15 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       58.03        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         6.97         4.64        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        6.61        34.68        15.95        13.87        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       33.21        14.43        11.44        29.59        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.56         2.66        19.96         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        31.10        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        0.95        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8677 
       12.79        27.12         9.34        28.14         6.28        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T 
       24.79        31.96         9.86        20.88        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51         0.46        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 
       13.15        13.18        13.35        11.21        12.10        12.76 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       15.39        12.43        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        11.77        12.62         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 
       14.01        29.98        19.07        12.03         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5721 
        7.07        30.97         6.97        36.00         1.02         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
        0.99       105.07        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       21.07         7.99        25.71        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 
       18.54        18.61        17.85        13.35        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       16.80        19.50        17.19        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        11.44        20.32        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 
        5.52         6.21        77.29        52.21        30.51         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       24.39        18.15        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30        24.26        22.68        24.20         3.25 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       23.84        23.80        21.17        14.07        15.68        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45        18.81         3.39        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        37.64         3.72 
TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       19.73        45.67         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
        9.24        11.05         8.61         5.13       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        16.87        19.04         5.79        48.79         5.46 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P5 
       18.48        43.36        21.73        37.41        38.14         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       30.97        34.29        46.26        16.31        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       12.79         2.70         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       13.35        29.59        64.57        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       21.83        61.22        18.74        20.81        32.88         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
       42.64        60.85         9.50        55.56         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P 
       55.43         4.54         6.58         5.72        66.81         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D 
       42.54        11.24        18.41        28.41        32.94        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       54.12        26.04        16.14        27.55        12.43         0.79 

  DEL PEAK  4(2Q32.1) MUTATED DEL PEAK  4(2Q32.1) WILD-TYPE 
                          0.0                           0.1 
  DEL PEAK  4(2Q32.1) MUTATED DEL PEAK  4(2Q32.1) WILD-TYPE 
                        63.06                        122.30 
  DEL PEAK  4(2Q32.1) MUTATED DEL PEAK  4(2Q32.1) WILD-TYPE 
                       15.020                        14.775 
[1] "0.0 - 63.1 (15.0)"  "0.1 - 122.3 (14.8)"
[1] "hr=" "1.3"
D40V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  4(2Q32.1) MUTATED         1        1        8        4         4
  DEL PEAK  4(2Q32.1) WILD-TYPE       1       15       33       28        36
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  4(2Q32.1) MUTATED           9         0         11         10
  DEL PEAK  4(2Q32.1) WILD-TYPE        47         3         70         53
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  4(2Q32.1) MUTATED            8        5
  DEL PEAK  4(2Q32.1) WILD-TYPE         31       39
D40V3, multiclass
            clus
vv           DEL PEAK  4(2Q32.1) MUTATED DEL PEAK  4(2Q32.1) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             1                            15
  STAGE IB                             8                            33
  STAGE II                             4                            28
  STAGE IIA                            4                            36
  STAGE IIB                            9                            47
  STAGE III                            0                             3
  STAGE IIIA                          11                            70
  STAGE IIIB                          10                            53
  STAGE IIIC                           8                            31
  STAGE IV                             5                            39
[1] 11  2
[1] TRUE
[1] "dimension of 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(2Q32.1) MUTATED     2  13  29  18
  DEL PEAK  4(2Q32.1) WILD-TYPE  21  80 167 101
D40V4, multiclass
    clus
vv   DEL PEAK  4(2Q32.1) MUTATED DEL PEAK  4(2Q32.1) WILD-TYPE
  T1                           2                            21
  T2                          13                            80
  T3                          29                           167
  T4                          18                           101
[1] 4 2
[1] TRUE
[1] "dimension of 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(2Q32.1) MUTATED    20  12  12  17
  DEL PEAK  4(2Q32.1) WILD-TYPE 110 107  74  71
D40V5, multiclass
    clus
vv   DEL PEAK  4(2Q32.1) MUTATED DEL PEAK  4(2Q32.1) WILD-TYPE
  N0                          20                           110
  N1                          12                           107
  N2                          12                            74
  N3                          17                            71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q32.1) MUTATED    57   3
  DEL PEAK  4(2Q32.1) WILD-TYPE 332  27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q32.1) MUTATED     57    3
  DEL PEAK  4(2Q32.1) WILD-TYPE  332   27
   clus
vv  DEL PEAK  4(2Q32.1) MUTATED DEL PEAK  4(2Q32.1) WILD-TYPE
  0                          57                           332
  1                           3                            27
[1] 2 2
[1] FALSE
D40V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q32.1) MUTATED    22  42
  DEL PEAK  4(2Q32.1) WILD-TYPE 136 241
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q32.1) MUTATED     22   42
  DEL PEAK  4(2Q32.1) WILD-TYPE  136  241
        clus
vv       DEL PEAK  4(2Q32.1) MUTATED DEL PEAK  4(2Q32.1) WILD-TYPE
  FEMALE                          22                           136
  MALE                            42                           241
[1] 2 2
[1] FALSE
D40V8, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q32.1) MUTATED    47  10
  DEL PEAK  4(2Q32.1) WILD-TYPE 275  66
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q32.1) MUTATED     47   10
  DEL PEAK  4(2Q32.1) WILD-TYPE  275   66
     clus
vv    DEL PEAK  4(2Q32.1) MUTATED DEL PEAK  4(2Q32.1) WILD-TYPE
  NO                           47                           275
  YES                          10                            66
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK  4(2Q32.1) MUTATED                                          3
  DEL PEAK  4(2Q32.1) WILD-TYPE                                       10
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK  4(2Q32.1) MUTATED                                       9
  DEL PEAK  4(2Q32.1) WILD-TYPE                                    63
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  4(2Q32.1) MUTATED                                                       23
  DEL PEAK  4(2Q32.1) WILD-TYPE                                                    140
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK  4(2Q32.1) MUTATED                                                   5
  DEL PEAK  4(2Q32.1) WILD-TYPE                                                16
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  4(2Q32.1) MUTATED                                                                   8
  DEL PEAK  4(2Q32.1) WILD-TYPE                                                                74
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK  4(2Q32.1) MUTATED                                                    0
  DEL PEAK  4(2Q32.1) WILD-TYPE                                                  8
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK  4(2Q32.1) MUTATED                                                 15
  DEL PEAK  4(2Q32.1) WILD-TYPE                                               64
D40V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK  4(2Q32.1) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       9
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     23
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           5
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           8
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           15
                                                                   clus
vv                                                                  DEL PEAK  4(2Q32.1) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        63
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      140
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            16
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            74
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            8
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             64
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  4(2Q32.1) MUTATED    51   3   4   3
  DEL PEAK  4(2Q32.1) WILD-TYPE 298  15  15  22
D40V10, multiclass
    clus
vv   DEL PEAK  4(2Q32.1) MUTATED DEL PEAK  4(2Q32.1) WILD-TYPE
  R0                          51                           298
  R1                           3                            15
  R2                           4                            15
  RX                           3                            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"
D40V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  4(2Q32.1) MUTATED      11                         2
  DEL PEAK  4(2Q32.1) WILD-TYPE    77                        10
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  4(2Q32.1) MUTATED                                           0    42
  DEL PEAK  4(2Q32.1) WILD-TYPE                                         1   236
D40V12, multiclass
                                           clus
vv                                          DEL PEAK  4(2Q32.1) MUTATED
  ASIAN                                                              11
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              42
                                           clus
vv                                          DEL PEAK  4(2Q32.1) WILD-TYPE
  ASIAN                                                                77
  BLACK OR AFRICAN AMERICAN                                            10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V13, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q32.1) MUTATED     0  42
  DEL PEAK  4(2Q32.1) WILD-TYPE   5 274
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q32.1) MUTATED      0   42
  DEL PEAK  4(2Q32.1) WILD-TYPE    5  274
                        clus
vv                       DEL PEAK  4(2Q32.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          42
                        clus
vv                       DEL PEAK  4(2Q32.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           274
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK  5(2Q33.3) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(2Q33.3) MUTATED    25  21
  DEL PEAK  5(2Q33.3) WILD-TYPE 221 148
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                           46                           369 
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                           21                           148 
$`DEL PEAK  5(2Q33.3) MUTATED`
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7901 
       27.35        26.93        19.33         9.17        12.16         3.45 
TCGA-BR-8058 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8369 TCGA-BR-8687 TCGA-CD-8525 
       37.25         9.60        29.42        14.04         8.22        12.59 
TCGA-CD-8526 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CG-4300 TCGA-CG-4462 
       12.53        12.07        12.82         6.31        20.02         0.00 
TCGA-CG-5720 TCGA-CG-5724 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6528 
        0.99        12.03        12.66        20.91        17.19        15.22 
TCGA-D7-8573 TCGA-D7-8576 TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-A4G8 
       19.50        14.66        63.06        26.47         5.92        22.68 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4HD TCGA-IN-A6RI 
       22.75        25.81         6.58         2.10        33.40        18.38 
TCGA-IN-AB1V TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8PC TCGA-VQ-A8PK 
       15.75         5.46        13.25        13.02        46.26        17.85 
TCGA-VQ-A8PY TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6J 
       14.33        43.66        38.93        27.55 

$`DEL PEAK  5(2Q33.3) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
       20.15         9.86        58.03        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       13.87        17.29        13.68        39.12        26.10        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        9.07        29.56        33.21        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 
       29.59        32.25         8.05         0.56         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        2.20        15.58         7.40         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
        0.46        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       11.21        12.10        12.76         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A487 
       12.39        12.59        11.64        15.39        12.43        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       12.62         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
       12.03         9.01        18.97         7.07        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         6.02         0.99       105.07 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
        7.99        25.71        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
       18.61        17.85        13.35        10.26        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 
       12.36        11.31        12.33        24.72        16.80        17.19 
TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       18.21        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 
        6.21        77.29        52.21        30.51         1.51        24.39 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       18.15        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH 
       24.30         5.59        24.26        24.20         3.25        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       14.07        15.68        36.36         3.45        18.81         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        6.51        10.62        11.70        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
       63.62        37.64        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
        8.94        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       48.79        18.48        43.36        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE 
       37.22         7.73        30.97        34.29        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
        2.50        12.79         2.70         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        13.35        29.59        64.57        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       11.70        21.83        61.22        18.74        20.81        32.88 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
        1.71        42.64        60.85         9.50         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        9.04         2.01        55.43         4.54         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
       66.81        21.04         2.66        42.54        11.24        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        32.94        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        17.26         0.79 

  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                          0.0                           0.1 
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                        63.06                        122.30 
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                        14.94                         14.79 
[1] "0.0 - 63.1 (14.9)"  "0.1 - 122.3 (14.8)"
[1] "hr=" "1.1"
D41V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  5(2Q33.3) MUTATED         1        2        5        2         3
  DEL PEAK  5(2Q33.3) WILD-TYPE       1       14       36       30        37
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  5(2Q33.3) MUTATED           7         0         10          8
  DEL PEAK  5(2Q33.3) WILD-TYPE        49         3         71         55
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  5(2Q33.3) MUTATED            7        4
  DEL PEAK  5(2Q33.3) WILD-TYPE         32       40
D41V3, multiclass
            clus
vv           DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             2                            14
  STAGE IB                             5                            36
  STAGE II                             2                            30
  STAGE IIA                            3                            37
  STAGE IIB                            7                            49
  STAGE III                            0                             3
  STAGE IIIA                          10                            71
  STAGE IIIB                           8                            55
  STAGE IIIC                           7                            32
  STAGE IV                             4                            40
[1] 11  2
[1] TRUE
[1] "dimension of 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(2Q33.3) MUTATED     3   6  27  13
  DEL PEAK  5(2Q33.3) WILD-TYPE  20  87 169 106
D41V4, multiclass
    clus
vv   DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  T1                           3                            20
  T2                           6                            87
  T3                          27                           169
  T4                          13                           106
[1] 4 2
[1] TRUE
[1] "dimension of 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(2Q33.3) MUTATED    15  10  10  14
  DEL PEAK  5(2Q33.3) WILD-TYPE 115 109  76  74
D41V5, multiclass
    clus
vv   DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  N0                          15                           115
  N1                          10                           109
  N2                          10                            76
  N3                          14                            74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q33.3) MUTATED    44   3
  DEL PEAK  5(2Q33.3) WILD-TYPE 345  27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q33.3) MUTATED     44    3
  DEL PEAK  5(2Q33.3) WILD-TYPE  345   27
   clus
vv  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  0                          44                           345
  1                           3                            27
[1] 2 2
[1] FALSE
D41V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q33.3) MUTATED    19  30
  DEL PEAK  5(2Q33.3) WILD-TYPE 139 253
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q33.3) MUTATED     19   30
  DEL PEAK  5(2Q33.3) WILD-TYPE  139  253
        clus
vv       DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  FEMALE                          19                           139
  MALE                            30                           253
[1] 2 2
[1] FALSE
D41V8, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q33.3) MUTATED    36   9
  DEL PEAK  5(2Q33.3) WILD-TYPE 286  67
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q33.3) MUTATED     36    9
  DEL PEAK  5(2Q33.3) WILD-TYPE  286   67
     clus
vv    DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  NO                           36                           286
  YES                           9                            67
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK  5(2Q33.3) MUTATED                                          4
  DEL PEAK  5(2Q33.3) WILD-TYPE                                        9
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK  5(2Q33.3) MUTATED                                       7
  DEL PEAK  5(2Q33.3) WILD-TYPE                                    65
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  5(2Q33.3) MUTATED                                                       16
  DEL PEAK  5(2Q33.3) WILD-TYPE                                                    147
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK  5(2Q33.3) MUTATED                                                   4
  DEL PEAK  5(2Q33.3) WILD-TYPE                                                17
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  5(2Q33.3) MUTATED                                                                   5
  DEL PEAK  5(2Q33.3) WILD-TYPE                                                                77
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK  5(2Q33.3) MUTATED                                                    0
  DEL PEAK  5(2Q33.3) WILD-TYPE                                                  8
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK  5(2Q33.3) MUTATED                                                 13
  DEL PEAK  5(2Q33.3) WILD-TYPE                                               66
D41V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK  5(2Q33.3) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    4
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       7
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     16
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           13
                                                                   clus
vv                                                                  DEL PEAK  5(2Q33.3) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      9
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            17
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            77
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            8
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             66
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  5(2Q33.3) MUTATED    40   4   3   0
  DEL PEAK  5(2Q33.3) WILD-TYPE 309  14  16  25
D41V10, multiclass
    clus
vv   DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  R0                          40                           309
  R1                           4                            14
  R2                           3                            16
  RX                           0                            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  5(2Q33.3) MUTATED      13                         2
  DEL PEAK  5(2Q33.3) WILD-TYPE    75                        10
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  5(2Q33.3) MUTATED                                           0    27
  DEL PEAK  5(2Q33.3) WILD-TYPE                                         1   251
D41V12, multiclass
                                           clus
vv                                          DEL PEAK  5(2Q33.3) MUTATED
  ASIAN                                                              13
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              27
                                           clus
vv                                          DEL PEAK  5(2Q33.3) WILD-TYPE
  ASIAN                                                                75
  BLACK OR AFRICAN AMERICAN                                            10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               251
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V13, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q33.3) MUTATED     0  31
  DEL PEAK  5(2Q33.3) WILD-TYPE   5 285
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q33.3) MUTATED      0   31
  DEL PEAK  5(2Q33.3) WILD-TYPE    5  285
                        clus
vv                       DEL PEAK  5(2Q33.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          31
                        clus
vv                       DEL PEAK  5(2Q33.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           285
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK  6(2Q37.2) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(2Q37.2) MUTATED    39  30
  DEL PEAK  6(2Q37.2) WILD-TYPE 207 139
  DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE 
                           69                           346 
  DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE 
                           30                           139 
$`DEL PEAK  6(2Q37.2) MUTATED`
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7704 TCGA-BR-7901 
       27.35        26.93         9.17        12.16        35.24         3.45 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8361 
       37.25        14.43        11.44         9.60        29.42        31.10 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8677 TCGA-BR-8687 
       14.79         7.36        25.18         9.21        26.73         8.22 
TCGA-BR-A4PD TCGA-CD-5800 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8533 TCGA-CD-8534 
       20.65        13.15        12.59        12.53        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 TCGA-CG-4300 TCGA-CG-4437 TCGA-CG-4441 
       12.82         6.31        11.31        20.02         8.05        14.01 
TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-5719 TCGA-D7-5578 TCGA-D7-6519 
       19.07        18.97        12.00         1.02        12.66        20.55 
TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-8576 TCGA-D7-A6EV 
       17.19        15.22        15.98        12.36        14.66        11.24 
TCGA-D7-A6F0 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-A4GD TCGA-HU-A4GP 
       22.29        52.21        26.47         5.92        22.75         8.98 
TCGA-HU-A4H2 TCGA-HU-A4HD TCGA-IN-A6RR TCGA-IN-AB1V TCGA-R5-A7ZE TCGA-VQ-A8DV 
       12.95        33.40         6.74        15.75        18.21        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8PE TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91N TCGA-VQ-A91Q 
       13.02        22.19        64.57        14.33        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-AA64 TCGA-VQ-AA68 
       32.88         9.04         4.54         5.72        18.41        43.66 
TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6I 
       38.93        54.12        16.14 

$`DEL PEAK  6(2Q37.2) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
       20.15         9.86        58.03        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 
        9.07        29.56        33.21         0.69        29.59        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56         2.66        19.96         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-8487 
       31.27        25.05         3.72         5.39        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 
       24.79        31.96        32.58         9.86        20.88        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.53        28.34         0.66        32.52        13.51         0.46 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 
       13.02        13.18        13.35        11.21        12.10        12.76 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.43        12.30        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        12.62         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4462 
        7.99        54.08         4.01        29.98        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 
        9.01         7.07        30.97         6.97        36.00         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       20.91        19.13        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       13.35        10.26        12.79        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19        18.21        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 
       26.43        11.31        11.44        20.32        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB TCGA-HU-8238 
        5.52         6.21        77.29        63.06        30.51         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       24.39        18.15        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
        3.25        25.81        11.77        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 
        6.51         6.58        20.25         0.26         2.10        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       23.84        23.80        21.17        14.07        15.68        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
       19.53         6.44        12.59         6.51        10.62        11.70 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J 
       13.51         2.53         5.56        63.62        37.64        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        19.73        14.04        45.67         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
       71.38        57.44         8.94        35.61        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8E2 
        5.79         0.92        48.79         5.46        18.48        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        37.41        38.14        37.22         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       34.29        46.26        16.31         2.50        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       17.85         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       29.59        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
        1.71        42.64        60.85         9.50         9.73        55.56 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P 
        2.01        55.43         6.58        66.81        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G 
       42.54        11.24        28.41        32.94        17.13        26.04 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       27.55        12.43        17.26         0.79 

  DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE 
                         1.02                          0.00 
  DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE 
                        64.57                        122.30 
  DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE 
                        14.79                         14.89 
[1] "1.0 - 64.6 (14.8)"  "0.0 - 122.3 (14.9)"
[1] "hr=" "1.1"
D42V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  6(2Q37.2) MUTATED         0        4        6        7         3
  DEL PEAK  6(2Q37.2) WILD-TYPE       2       12       35       25        37
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  6(2Q37.2) MUTATED          10         1         14         11
  DEL PEAK  6(2Q37.2) WILD-TYPE        46         2         67         52
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  6(2Q37.2) MUTATED            8        7
  DEL PEAK  6(2Q37.2) WILD-TYPE         31       37
D42V3, multiclass
            clus
vv           DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             4                            12
  STAGE IB                             6                            35
  STAGE II                             7                            25
  STAGE IIA                            3                            37
  STAGE IIB                           10                            46
  STAGE III                            1                             2
  STAGE IIIA                          14                            67
  STAGE IIIB                          11                            52
  STAGE IIIC                           8                            31
  STAGE IV                             7                            37
[1] 11  2
[1] TRUE
[1] "dimension of 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(2Q37.2) MUTATED     4  15  31  22
  DEL PEAK  6(2Q37.2) WILD-TYPE  19  78 165  97
D42V4, multiclass
    clus
vv   DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE
  T1                           4                            19
  T2                          15                            78
  T3                          31                           165
  T4                          22                            97
[1] 4 2
[1] TRUE
[1] "dimension of 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(2Q37.2) MUTATED    21  19  15  17
  DEL PEAK  6(2Q37.2) WILD-TYPE 109 100  71  71
D42V5, multiclass
    clus
vv   DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE
  N0                          21                           109
  N1                          19                           100
  N2                          15                            71
  N3                          17                            71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V6, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q37.2) MUTATED    68   2
  DEL PEAK  6(2Q37.2) WILD-TYPE 321  28
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q37.2) MUTATED     68    2
  DEL PEAK  6(2Q37.2) WILD-TYPE  321   28
   clus
vv  DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE
  0                          68                           321
  1                           2                            28
[1] 2 2
[1] FALSE
D42V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q37.2) MUTATED    32  40
  DEL PEAK  6(2Q37.2) WILD-TYPE 126 243
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q37.2) MUTATED     32   40
  DEL PEAK  6(2Q37.2) WILD-TYPE  126  243
        clus
vv       DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE
  FEMALE                          32                           126
  MALE                            40                           243
[1] 2 2
[1] FALSE
D42V8, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q37.2) MUTATED    54  14
  DEL PEAK  6(2Q37.2) WILD-TYPE 268  62
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q37.2) MUTATED     54   14
  DEL PEAK  6(2Q37.2) WILD-TYPE  268   62
     clus
vv    DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE
  NO                           54                           268
  YES                          14                            62
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK  6(2Q37.2) MUTATED                                          3
  DEL PEAK  6(2Q37.2) WILD-TYPE                                       10
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK  6(2Q37.2) MUTATED                                       6
  DEL PEAK  6(2Q37.2) WILD-TYPE                                    66
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  6(2Q37.2) MUTATED                                                       22
  DEL PEAK  6(2Q37.2) WILD-TYPE                                                    141
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK  6(2Q37.2) MUTATED                                                   3
  DEL PEAK  6(2Q37.2) WILD-TYPE                                                18
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  6(2Q37.2) MUTATED                                                                  16
  DEL PEAK  6(2Q37.2) WILD-TYPE                                                                66
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK  6(2Q37.2) MUTATED                                                    2
  DEL PEAK  6(2Q37.2) WILD-TYPE                                                  6
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK  6(2Q37.2) MUTATED                                                 19
  DEL PEAK  6(2Q37.2) WILD-TYPE                                               60
D42V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK  6(2Q37.2) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     22
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          16
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           19
                                                                   clus
vv                                                                  DEL PEAK  6(2Q37.2) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      141
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  6(2Q37.2) MUTATED    65   2   2   0
  DEL PEAK  6(2Q37.2) WILD-TYPE 284  16  17  25
D42V10, multiclass
    clus
vv   DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE
  R0                          65                           284
  R1                           2                            16
  R2                           2                            17
  RX                           0                            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  6(2Q37.2) MUTATED      14                         2
  DEL PEAK  6(2Q37.2) WILD-TYPE    74                        10
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  6(2Q37.2) MUTATED                                           0    42
  DEL PEAK  6(2Q37.2) WILD-TYPE                                         1   236
D42V12, multiclass
                                           clus
vv                                          DEL PEAK  6(2Q37.2) MUTATED
  ASIAN                                                              14
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              42
                                           clus
vv                                          DEL PEAK  6(2Q37.2) WILD-TYPE
  ASIAN                                                                74
  BLACK OR AFRICAN AMERICAN                                            10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V13, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q37.2) MUTATED     0  44
  DEL PEAK  6(2Q37.2) WILD-TYPE   5 272
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q37.2) MUTATED      0   44
  DEL PEAK  6(2Q37.2) WILD-TYPE    5  272
                        clus
vv                       DEL PEAK  6(2Q37.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          44
                        clus
vv                       DEL PEAK  6(2Q37.2) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           272
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK  7(3P26.1) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(3P26.1) MUTATED    80  56
  DEL PEAK  7(3P26.1) WILD-TYPE 166 113
  DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE 
                          136                           279 
  DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE 
                           56                           113 
$`DEL PEAK  7(3P26.1) MUTATED`
TCGA-CG-4444 TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-B7-A5TJ TCGA-B7-A5TN 
       47.05         9.86        27.35        26.93        11.01         9.44 
TCGA-BR-4191 TCGA-BR-4255 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6803 
       18.35         4.08        19.33         9.17        25.61        31.20 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 
       35.24        33.63        39.78         9.07        33.21        37.25 
TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8483 
        0.69         2.66        19.96         7.40        13.08         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 
       25.18         9.21        20.22        24.79        31.96        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY 
        8.22        10.68         7.53        34.98         1.48        12.89 
TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.72         0.53        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8526 TCGA-CD-8527 
       21.44        13.02        13.18        12.10        12.53         7.17 
TCGA-CD-8533 TCGA-CD-A487 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4437 
       15.39        12.30        20.02         3.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-5718 
       54.08         4.01        14.01        12.03        18.97        36.00 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5730 TCGA-D7-5578 TCGA-D7-6521 TCGA-D7-6525 
      105.07        15.02         4.01        12.66        18.54        13.35 
TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
       17.19        15.22        12.79        11.31        20.32        22.29 
TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 
       15.65         0.62         7.99        19.53        14.07        17.06 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4G6 
        0.56         5.52         6.21        18.15        28.96        24.26 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H5 
        3.25        22.75         6.58         2.10        23.84        23.80 
TCGA-IN-7806 TCGA-IN-A6RI TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       36.36        18.38         6.44        12.59         6.51        10.62 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        63.62        37.64        36.95        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 
       18.21         8.52         8.61        16.67        37.91       115.69 
TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E0 
        8.94         5.79         0.92         5.46        13.25        18.48 
TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       37.41         7.73        22.19        12.79         2.70        17.85 
TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A923 
       14.33        39.45        42.64         9.50         9.73         2.01 
TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B 
        4.54        21.04        42.54        18.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       54.12        27.55        12.43         0.79 

$`DEL PEAK  7(3P26.1) WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       21.99        22.98        79.07        16.24         0.23        20.15 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 
       58.03        26.70        11.70        19.56         9.47         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 
        6.97         4.64         7.43        30.90         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       13.87        17.29        13.68        39.12        26.10        32.78 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 
       44.94        21.90         9.21        36.16        35.84        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 
       15.32        28.73         3.45        29.56        14.43        11.44 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20        15.58         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-A44T TCGA-BR-A44U 
        7.53        26.73        32.58         9.86        34.13        13.87 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 
        6.08        27.55        28.57         8.98        14.17        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.66        32.52         0.46        16.14         5.13        13.41 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8528 
       13.15        13.35        11.21        12.76        12.59        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 
       12.30        12.39        12.59        11.64        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
       12.43         6.31        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.20        11.77        12.62        27.02        15.95         1.02 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 
       29.98        19.07         0.00         9.01         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       30.97         6.97         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       12.03        28.96        65.10        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
       25.71        20.91        19.13        20.55        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       17.85        10.26        15.98        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A747 
       13.78        14.76        26.43        11.24        11.44         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        4.34        19.96         7.13        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       11.38         3.48        22.29        59.54         5.03        13.58 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GF TCGA-HU-A4GH 
       24.30         5.59        22.68        24.20        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
        0.26        12.95        29.00        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL 
       33.40         3.45        18.81         3.39        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
       19.53         6.74        11.70        15.75        13.51         2.53 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
        3.72        19.73        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
       11.05         5.13       122.30        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DT TCGA-VQ-A8DZ 
       57.44        35.61        16.87        19.04        48.79        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       43.36        21.73        38.14        37.22        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       46.26        16.31         2.50         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91D 
       15.65        13.35        29.59        64.57        73.41        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       21.83        61.22        18.74        20.81        32.88         1.71 
TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
       60.85        55.56         9.04        55.43         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D 
       66.81         2.66        11.24        43.66        28.41        17.13 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-ZA-A8F6 
       26.04        16.14        17.26 

  DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE 
                         0.53                          0.00 
  DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE 
                       115.69                        122.30 
  DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE 
                       14.055                        15.580 
[1] "0.5 - 115.7 (14.1)" "0.0 - 122.3 (15.6)"
[1] "hr=" "1.1"
D43V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  7(3P26.1) MUTATED         1        4       14        9         9
  DEL PEAK  7(3P26.1) WILD-TYPE       1       12       27       23        31
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  7(3P26.1) MUTATED          19         0         30         21
  DEL PEAK  7(3P26.1) WILD-TYPE        37         3         51         42
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  7(3P26.1) MUTATED           14       14
  DEL PEAK  7(3P26.1) WILD-TYPE         25       30
D43V3, multiclass
            clus
vv           DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             4                            12
  STAGE IB                            14                            27
  STAGE II                             9                            23
  STAGE IIA                            9                            31
  STAGE IIB                           19                            37
  STAGE III                            0                             3
  STAGE IIIA                          30                            51
  STAGE IIIB                          21                            42
  STAGE IIIC                          14                            25
  STAGE IV                            14                            30
[1] 11  2
[1] TRUE
[1] "dimension of 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(3P26.1) MUTATED     8  29  63  40
  DEL PEAK  7(3P26.1) WILD-TYPE  15  64 133  79
D43V4, multiclass
    clus
vv   DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE
  T1                           8                            15
  T2                          29                            64
  T3                          63                           133
  T4                          40                            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"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK  7(3P26.1) MUTATED   32 40 38 27
  DEL PEAK  7(3P26.1) WILD-TYPE 98 79 48 61
D43V5, multiclass
    clus
vv   DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE
  N0                          32                            98
  N1                          40                            79
  N2                          38                            48
  N3                          27                            61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P26.1) MUTATED   123  12
  DEL PEAK  7(3P26.1) WILD-TYPE 266  18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P26.1) MUTATED    123   12
  DEL PEAK  7(3P26.1) WILD-TYPE  266   18
   clus
vv  DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE
  0                         123                           266
  1                          12                            18
[1] 2 2
[1] FALSE
D43V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P26.1) MUTATED    45  98
  DEL PEAK  7(3P26.1) WILD-TYPE 113 185
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P26.1) MUTATED     45   98
  DEL PEAK  7(3P26.1) WILD-TYPE  113  185
        clus
vv       DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE
  FEMALE                          45                           113
  MALE                            98                           185
[1] 2 2
[1] FALSE
D43V8, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P26.1) MUTATED   103  26
  DEL PEAK  7(3P26.1) WILD-TYPE 219  50
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P26.1) MUTATED    103   26
  DEL PEAK  7(3P26.1) WILD-TYPE  219   50
     clus
vv    DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE
  NO                          103                           219
  YES                          26                            50
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK  7(3P26.1) MUTATED                                          3
  DEL PEAK  7(3P26.1) WILD-TYPE                                       10
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK  7(3P26.1) MUTATED                                      16
  DEL PEAK  7(3P26.1) WILD-TYPE                                    56
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  7(3P26.1) MUTATED                                                       49
  DEL PEAK  7(3P26.1) WILD-TYPE                                                    114
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK  7(3P26.1) MUTATED                                                   5
  DEL PEAK  7(3P26.1) WILD-TYPE                                                16
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  7(3P26.1) MUTATED                                                                  38
  DEL PEAK  7(3P26.1) WILD-TYPE                                                                44
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK  7(3P26.1) MUTATED                                                    3
  DEL PEAK  7(3P26.1) WILD-TYPE                                                  5
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK  7(3P26.1) MUTATED                                                 29
  DEL PEAK  7(3P26.1) WILD-TYPE                                               50
D43V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK  7(3P26.1) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                      16
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     49
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           5
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          38
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           29
                                                                   clus
vv                                                                  DEL PEAK  7(3P26.1) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        56
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      114
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            16
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            44
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             50
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  7(3P26.1) MUTATED   116   5   8   5
  DEL PEAK  7(3P26.1) WILD-TYPE 233  13  11  20
D43V10, multiclass
    clus
vv   DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE
  R0                         116                           233
  R1                           5                            13
  R2                           8                            11
  RX                           5                            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"
D43V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  7(3P26.1) MUTATED      25                         4
  DEL PEAK  7(3P26.1) WILD-TYPE    63                         8
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  7(3P26.1) MUTATED                                           1    93
  DEL PEAK  7(3P26.1) WILD-TYPE                                         0   185
D43V12, multiclass
                                           clus
vv                                          DEL PEAK  7(3P26.1) MUTATED
  ASIAN                                                              25
  BLACK OR AFRICAN AMERICAN                                           4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              93
                                           clus
vv                                          DEL PEAK  7(3P26.1) WILD-TYPE
  ASIAN                                                                63
  BLACK OR AFRICAN AMERICAN                                             8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               185
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V13, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P26.1) MUTATED     1  95
  DEL PEAK  7(3P26.1) WILD-TYPE   4 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P26.1) MUTATED      1   95
  DEL PEAK  7(3P26.1) WILD-TYPE    4  221
                        clus
vv                       DEL PEAK  7(3P26.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          95
                        clus
vv                       DEL PEAK  7(3P26.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           221
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK  8(3P21.1) MUTATION ANALYSIS
D44V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(3P21.1) MUTATED    89  58
  DEL PEAK  8(3P21.1) WILD-TYPE 157 111
  DEL PEAK  8(3P21.1) MUTATED DEL PEAK  8(3P21.1) WILD-TYPE 
                          147                           268 
  DEL PEAK  8(3P21.1) MUTATED DEL PEAK  8(3P21.1) WILD-TYPE 
                           58                           111 
$`DEL PEAK  8(3P21.1) MUTATED`
TCGA-CG-4444 TCGA-EQ-A4SO TCGA-MX-A663 TCGA-VQ-A94U TCGA-B7-A5TI TCGA-B7-A5TJ 
       47.05        16.24         9.86        26.93        19.56        11.01 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-6456 TCGA-BR-6458 
        9.44         6.61         4.08         4.08        17.29        19.33 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6803 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
        9.17        25.61        31.20        35.24        33.63        39.78 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 
        3.45         9.07        33.21        37.25        11.44         0.69 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        2.66        19.96         7.40         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
       20.22        20.88         8.22         7.53        34.98         1.48 
TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       12.89         0.72         0.53        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        1.15        21.44        13.02        13.15        13.18        13.35 
TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8531 TCGA-CD-8533 TCGA-CG-4300 
       12.10        12.76        12.53        12.59        15.39        20.02 
TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4455 
        3.02         7.99         8.05        54.08         4.01        12.03 
TCGA-CG-4466 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5730 TCGA-D7-5578 
       18.97        36.00         1.02        12.03         4.01        12.66 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 
       20.55        18.84        18.54        13.35        17.19        15.22 
TCGA-D7-6817 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YY TCGA-D7-A6EX TCGA-D7-A6F2 
       12.79        14.27        16.44        13.78        11.31        15.65 
TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 
       19.96         0.62         7.99        19.53        14.07        17.06 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8249 
        0.56         5.52         6.21        26.47        18.15        28.96 
TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 
       24.26         3.25        22.75         6.58        20.25         2.10 
TCGA-HU-A4H4 TCGA-IN-7806 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RS 
       23.84        36.36        18.38        13.35         6.44        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
        6.51        10.62        13.51         5.56        63.62        37.64 
TCGA-KB-A93J TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-RD-A7C1 
       36.95        45.67        18.21         8.52        74.53        16.67 
TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU 
       37.91       115.69         8.94         5.79         0.92         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PJ 
       13.25        18.48        37.41         7.73        22.19         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PS TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A 
       17.85         9.27        13.35        64.57        14.33        39.45 
TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 
       42.64         9.50         9.73         9.04         2.01         4.54 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B 
        5.72        66.81        42.54        18.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       54.12        12.43         0.79 

$`DEL PEAK  8(3P21.1) WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A8PU 
       21.99        22.98        79.07         0.23        20.15        27.35 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 
       58.03        26.70        11.70         9.47         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
        7.43        18.35        30.90         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 
        9.57         6.61        34.68        15.95        13.87        13.68 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       39.12        26.10        32.78        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        30.90        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7958 
       36.16        35.84        18.15        15.32        28.73        29.56 
TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       14.43        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       29.42         2.20        15.58         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.05         3.72         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 
       32.58         9.86        10.68        34.13        13.87         6.08 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 
       27.55        28.57         8.98        14.17        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5803 
       32.52         0.46        16.14         5.13        13.41        11.21 
TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 
       12.59         7.17        12.33        12.30        12.39        11.64 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
       27.02        15.95         1.02        14.01        29.98        19.07 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01         7.07        12.00        30.97         6.97 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 
       65.10        69.04        21.07         7.99        25.71        20.91 
TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6818 
       19.13        18.61        17.85        10.26        15.98        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX 
       18.21        14.66        21.14        20.91         5.92        36.43 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.44        20.32        22.29 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        8.38         4.34         7.13        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       11.38         3.48        22.29        59.54         5.03        13.58 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        30.51         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
        5.59        22.68        24.20        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H2 
       29.98         8.98         0.10         6.51         0.26        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR 
        3.45        18.81         3.39        12.46        19.53         6.74 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
       11.70        15.75         2.53         3.72        19.73        14.04 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
      122.30        40.64       116.38        71.38        57.44        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DT TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       16.87        19.04        48.79        13.02        43.36        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       38.14        37.22        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
        2.50        12.79         1.87        23.41        15.65        29.59 
TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       73.41        11.70        21.83        61.22        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A924 TCGA-VQ-A927 
       32.88         1.71        60.85        55.56        55.43         6.58 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D 
       21.04         2.66        11.24        43.66        28.41        17.13 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       26.04        16.14        27.55        17.26 

  DEL PEAK  8(3P21.1) MUTATED DEL PEAK  8(3P21.1) WILD-TYPE 
                         0.53                          0.00 
  DEL PEAK  8(3P21.1) MUTATED DEL PEAK  8(3P21.1) WILD-TYPE 
                       115.69                        122.30 
  DEL PEAK  8(3P21.1) MUTATED DEL PEAK  8(3P21.1) WILD-TYPE 
                        13.35                         15.85 
[1] "0.5 - 115.7 (13.3)" "0.0 - 122.3 (15.8)"
[1] "hr=" "1.1"
D44V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  8(3P21.1) MUTATED         1        5       12       10         9
  DEL PEAK  8(3P21.1) WILD-TYPE       1       11       29       22        31
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  8(3P21.1) MUTATED          22         0         35         21
  DEL PEAK  8(3P21.1) WILD-TYPE        34         3         46         42
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  8(3P21.1) MUTATED           14       17
  DEL PEAK  8(3P21.1) WILD-TYPE         25       27
D44V3, multiclass
            clus
vv           DEL PEAK  8(3P21.1) MUTATED DEL PEAK  8(3P21.1) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             5                            11
  STAGE IB                            12                            29
  STAGE II                            10                            22
  STAGE IIA                            9                            31
  STAGE IIB                           22                            34
  STAGE III                            0                             3
  STAGE IIIA                          35                            46
  STAGE IIIB                          21                            42
  STAGE IIIC                          14                            25
  STAGE IV                            17                            27
[1] 11  2
[1] TRUE
[1] "dimension of 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(3P21.1) MUTATED     9  28  73  42
  DEL PEAK  8(3P21.1) WILD-TYPE  14  65 123  77
D44V4, multiclass
    clus
vv   DEL PEAK  8(3P21.1) MUTATED DEL PEAK  8(3P21.1) WILD-TYPE
  T1                           9                            14
  T2                          28                            65
  T3                          73                           123
  T4                          42                            77
[1] 4 2
[1] TRUE
[1] "dimension of 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(3P21.1) MUTATED   37 46 38 28
  DEL PEAK  8(3P21.1) WILD-TYPE 93 73 48 60
D44V5, multiclass
    clus
vv   DEL PEAK  8(3P21.1) MUTATED DEL PEAK  8(3P21.1) WILD-TYPE
  N0                          37                            93
  N1                          46                            73
  N2                          38                            48
  N3                          28                            60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P21.1) MUTATED   130  14
  DEL PEAK  8(3P21.1) WILD-TYPE 259  16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P21.1) MUTATED    130   14
  DEL PEAK  8(3P21.1) WILD-TYPE  259   16
   clus
vv  DEL PEAK  8(3P21.1) MUTATED DEL PEAK  8(3P21.1) WILD-TYPE
  0                         130                           259
  1                          14                            16
[1] 2 2
[1] FALSE
D44V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P21.1) MUTATED    55  98
  DEL PEAK  8(3P21.1) WILD-TYPE 103 185
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P21.1) MUTATED     55   98
  DEL PEAK  8(3P21.1) WILD-TYPE  103  185
        clus
vv       DEL PEAK  8(3P21.1) MUTATED DEL PEAK  8(3P21.1) WILD-TYPE
  FEMALE                          55                           103
  MALE                            98                           185
[1] 2 2
[1] FALSE
D44V8, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P21.1) MUTATED   111  29
  DEL PEAK  8(3P21.1) WILD-TYPE 211  47
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P21.1) MUTATED    111   29
  DEL PEAK  8(3P21.1) WILD-TYPE  211   47
     clus
vv    DEL PEAK  8(3P21.1) MUTATED DEL PEAK  8(3P21.1) WILD-TYPE
  NO                          111                           211
  YES                          29                            47
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK  8(3P21.1) MUTATED                                          5
  DEL PEAK  8(3P21.1) WILD-TYPE                                        8
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK  8(3P21.1) MUTATED                                      21
  DEL PEAK  8(3P21.1) WILD-TYPE                                    51
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  8(3P21.1) MUTATED                                                       50
  DEL PEAK  8(3P21.1) WILD-TYPE                                                    113
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK  8(3P21.1) MUTATED                                                   5
  DEL PEAK  8(3P21.1) WILD-TYPE                                                16
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  8(3P21.1) MUTATED                                                                  35
  DEL PEAK  8(3P21.1) WILD-TYPE                                                                47
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK  8(3P21.1) MUTATED                                                    4
  DEL PEAK  8(3P21.1) WILD-TYPE                                                  4
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK  8(3P21.1) MUTATED                                                 32
  DEL PEAK  8(3P21.1) WILD-TYPE                                               47
D44V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK  8(3P21.1) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                      21
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     50
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           5
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          35
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           32
                                                                   clus
vv                                                                  DEL PEAK  8(3P21.1) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        51
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      113
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            16
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            47
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             47
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  8(3P21.1) MUTATED   126   4   8   5
  DEL PEAK  8(3P21.1) WILD-TYPE 223  14  11  20
D44V10, multiclass
    clus
vv   DEL PEAK  8(3P21.1) MUTATED DEL PEAK  8(3P21.1) WILD-TYPE
  R0                         126                           223
  R1                           4                            14
  R2                           8                            11
  RX                           5                            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"
D44V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  8(3P21.1) MUTATED      26                         2
  DEL PEAK  8(3P21.1) WILD-TYPE    62                        10
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  8(3P21.1) MUTATED                                           0   104
  DEL PEAK  8(3P21.1) WILD-TYPE                                         1   174
D44V12, multiclass
                                           clus
vv                                          DEL PEAK  8(3P21.1) MUTATED
  ASIAN                                                              26
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             104
                                           clus
vv                                          DEL PEAK  8(3P21.1) WILD-TYPE
  ASIAN                                                                62
  BLACK OR AFRICAN AMERICAN                                            10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               174
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V13, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P21.1) MUTATED     2 103
  DEL PEAK  8(3P21.1) WILD-TYPE   3 213
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P21.1) MUTATED      2  103
  DEL PEAK  8(3P21.1) WILD-TYPE    3  213
                        clus
vv                       DEL PEAK  8(3P21.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         103
                        clus
vv                       DEL PEAK  8(3P21.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           213
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK  9(3P14.2) MUTATION ANALYSIS
D45V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(3P14.2) MUTATED    86  66
  DEL PEAK  9(3P14.2) WILD-TYPE 160 103
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                          152                           263 
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                           66                           103 
$`DEL PEAK  9(3P14.2) MUTATED`
TCGA-CG-4444 TCGA-MX-A663 TCGA-VQ-A94U TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ 
       47.05         9.86        26.93        26.70        19.56        11.01 
TCGA-BR-4183 TCGA-BR-4255 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6705 
        6.61         4.08        17.29        19.33         9.17        25.61 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 
       31.20        44.94        35.24        33.63        39.78        15.32 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 
        3.45         9.07        33.21        37.25        11.44         0.69 
TCGA-BR-8289 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8686 
        2.66         5.39        25.18         9.21        20.22        20.88 
TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY 
        8.22        13.87         7.53        34.98         1.48        12.89 
TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI 
        0.72         0.53        13.51        20.65         1.15        21.44 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 
       13.02        13.15        13.18        12.10        12.76        12.53 
TCGA-CD-8527 TCGA-CD-8533 TCGA-CD-A487 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 
        7.17        15.39        12.30        20.02         3.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 
        7.99         8.05        54.08         4.01        14.01        12.03 
TCGA-CG-4466 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 
       18.97        36.00         1.02        12.03        15.02         4.01 
TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 
       25.71        20.55        18.84        18.54        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-A4YT TCGA-D7-A4YY 
       10.26        15.22        12.79        12.33        14.27        13.78 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 
       11.31        11.44        20.32        19.96         0.62         7.99 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       19.53        14.07        17.06         0.56         5.52         6.21 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        18.15        28.96        22.32        22.82 
TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
       24.26         3.25        22.75        25.81        11.77         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-IN-7806 
        0.10         6.58         2.10        23.84        14.07        36.36 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       18.38        13.35         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J 
       10.62        13.51         5.56        63.62        37.64        36.95 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-RD-A7C1 TCGA-RD-A8MW 
       45.67        18.21         8.52        74.53        16.67        37.91 
TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E7 TCGA-VQ-A8P5 
        8.94         5.79         5.46        13.25        37.41         7.73 
TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PS TCGA-VQ-A8PY 
       22.19         2.70        17.85         9.27        13.35        14.33 
TCGA-VQ-A91N TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
       18.74        42.64         9.50         9.04         2.01        55.43 
TCGA-VQ-A925 TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
        4.54        18.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       12.43         0.79 

$`DEL PEAK  9(3P14.2) WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       21.99        22.98        79.07        16.24         0.23        20.15 
TCGA-VQ-A8PU TCGA-3M-AB46 TCGA-B7-5818 TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 
       27.35        58.03        11.70         9.47         9.44         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 
        4.64         7.43        18.35        30.90         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6706 
       13.87        13.68        39.12        26.10        32.78        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-7196 
       19.89        12.16         8.98        40.21        30.90        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7958 
        9.21        36.16        35.84        18.15        28.73        29.56 
TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       14.43        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       29.42        19.96         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       31.10        13.08         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 
       14.79         7.36        25.05         3.72         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44T 
       24.79        31.96        32.58         9.86        10.68        34.13 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 
        6.08        27.55        28.57         8.98        14.17        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM 
        0.66        32.52         0.46        20.42        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 
       13.41        13.35        11.21        12.59        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.39        12.59        11.64        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        6.31        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4443 TCGA-CG-4449 
       11.77        12.62        27.02         1.02        29.98        19.07 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01         7.07        12.00        30.97         6.97 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 
        0.99         6.02         0.99       105.07        28.96        65.10 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04        21.07         7.99        12.66        20.91        19.13 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 
       18.61        17.85        15.98        12.36        11.31        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET 
       20.91        16.44         5.92        36.43        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       11.24        22.29        15.65         8.38         4.34         7.13 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7998 
       14.47        72.23        21.27        11.38         3.48        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       59.54         5.03        13.58        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       30.51         1.51        24.39        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT 
        5.59        22.68        24.20        21.37        29.98         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 
       20.25         0.26        12.95        29.00        23.80        21.17 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ 
       15.68        33.40         3.45        18.81         3.39        12.46 
TCGA-IN-A6RN TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-MX-A5UG TCGA-MX-A5UJ 
       19.53        11.70        15.75         2.53         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       14.04         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
        5.13       122.30        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT 
       57.44        35.61        16.87        19.04         0.92        48.79 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.02        18.48        43.36        21.73        38.14        37.22 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH 
       30.97        34.29        46.26        16.31         2.50        12.79 
TCGA-VQ-A8PM TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ 
        1.87        23.41        15.65        29.59        64.57        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S 
       39.45        11.70        21.83        61.22        20.81        32.88 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A927 TCGA-VQ-A928 
        1.71        60.85         9.73        55.56         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA68 
       66.81        21.04         2.66        42.54        11.24        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       28.41        17.13        16.14        27.55        17.26 

  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                          0.1                           0.0 
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                        74.53                        122.30 
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                        13.51                         16.14 
[1] "0.1 - 74.5 (13.5)"  "0.0 - 122.3 (16.1)"
[1] "hr=" "1.3"
D45V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  9(3P14.2) MUTATED         1        5       12       13        13
  DEL PEAK  9(3P14.2) WILD-TYPE       1       11       29       19        27
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  9(3P14.2) MUTATED          24         0         35         19
  DEL PEAK  9(3P14.2) WILD-TYPE        32         3         46         44
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  9(3P14.2) MUTATED           13       17
  DEL PEAK  9(3P14.2) WILD-TYPE         26       27
D45V3, multiclass
            clus
vv           DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             5                            11
  STAGE IB                            12                            29
  STAGE II                            13                            19
  STAGE IIA                           13                            27
  STAGE IIB                           24                            32
  STAGE III                            0                             3
  STAGE IIIA                          35                            46
  STAGE IIIB                          19                            44
  STAGE IIIC                          13                            26
  STAGE IV                            17                            27
[1] 11  2
[1] TRUE
[1] "dimension of 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(3P14.2) MUTATED    10  33  72  41
  DEL PEAK  9(3P14.2) WILD-TYPE  13  60 124  78
D45V4, multiclass
    clus
vv   DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  T1                          10                            13
  T2                          33                            60
  T3                          72                           124
  T4                          41                            78
[1] 4 2
[1] TRUE
[1] "dimension of 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(3P14.2) MUTATED   41 50 36 28
  DEL PEAK  9(3P14.2) WILD-TYPE 89 69 50 60
D45V5, multiclass
    clus
vv   DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  N0                          41                            89
  N1                          50                            69
  N2                          36                            50
  N3                          28                            60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P14.2) MUTATED   136  14
  DEL PEAK  9(3P14.2) WILD-TYPE 253  16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P14.2) MUTATED    136   14
  DEL PEAK  9(3P14.2) WILD-TYPE  253   16
   clus
vv  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  0                         136                           253
  1                          14                            16
[1] 2 2
[1] FALSE
D45V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P14.2) MUTATED    58  99
  DEL PEAK  9(3P14.2) WILD-TYPE 100 184
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P14.2) MUTATED     58   99
  DEL PEAK  9(3P14.2) WILD-TYPE  100  184
        clus
vv       DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  FEMALE                          58                           100
  MALE                            99                           184
[1] 2 2
[1] FALSE
D45V8, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P14.2) MUTATED   121  23
  DEL PEAK  9(3P14.2) WILD-TYPE 201  53
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P14.2) MUTATED    121   23
  DEL PEAK  9(3P14.2) WILD-TYPE  201   53
     clus
vv    DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  NO                          121                           201
  YES                          23                            53
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK  9(3P14.2) MUTATED                                          5
  DEL PEAK  9(3P14.2) WILD-TYPE                                        8
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK  9(3P14.2) MUTATED                                      20
  DEL PEAK  9(3P14.2) WILD-TYPE                                    52
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  9(3P14.2) MUTATED                                                       51
  DEL PEAK  9(3P14.2) WILD-TYPE                                                    112
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK  9(3P14.2) MUTATED                                                   4
  DEL PEAK  9(3P14.2) WILD-TYPE                                                17
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  9(3P14.2) MUTATED                                                                  36
  DEL PEAK  9(3P14.2) WILD-TYPE                                                                46
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK  9(3P14.2) MUTATED                                                    4
  DEL PEAK  9(3P14.2) WILD-TYPE                                                  4
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK  9(3P14.2) MUTATED                                                 37
  DEL PEAK  9(3P14.2) WILD-TYPE                                               42
D45V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK  9(3P14.2) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                      20
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     51
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          36
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           37
                                                                   clus
vv                                                                  DEL PEAK  9(3P14.2) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        52
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      112
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            17
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            46
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             42
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  9(3P14.2) MUTATED   136   3   7   3
  DEL PEAK  9(3P14.2) WILD-TYPE 213  15  12  22
D45V10, multiclass
    clus
vv   DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  R0                         136                           213
  R1                           3                            15
  R2                           7                            12
  RX                           3                            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"
D45V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  9(3P14.2) MUTATED      33                         1
  DEL PEAK  9(3P14.2) WILD-TYPE    55                        11
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  9(3P14.2) MUTATED                                           0    98
  DEL PEAK  9(3P14.2) WILD-TYPE                                         1   180
D45V12, multiclass
                                           clus
vv                                          DEL PEAK  9(3P14.2) MUTATED
  ASIAN                                                              33
  BLACK OR AFRICAN AMERICAN                                           1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              98
                                           clus
vv                                          DEL PEAK  9(3P14.2) WILD-TYPE
  ASIAN                                                                55
  BLACK OR AFRICAN AMERICAN                                            11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V13, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P14.2) MUTATED     2 109
  DEL PEAK  9(3P14.2) WILD-TYPE   3 207
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P14.2) MUTATED      2  109
  DEL PEAK  9(3P14.2) WILD-TYPE    3  207
                        clus
vv                       DEL PEAK  9(3P14.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         109
                        clus
vv                       DEL PEAK  9(3P14.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           207
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 10(3Q26.31) MUTATION ANALYSIS
D46V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 10(3Q26.31) MUTATED    30  15
  DEL PEAK 10(3Q26.31) WILD-TYPE 216 154
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                            45                            370 
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                            15                            154 
$`DEL PEAK 10(3Q26.31) MUTATED`
TCGA-MX-A663 TCGA-VQ-A94U TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7959 TCGA-BR-8077 
        9.86        26.93        35.24        33.63        33.21         0.69 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4IY TCGA-BR-A4J1 
        9.21        20.22        10.68        13.87        12.89         0.72 
TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-CD-8533 TCGA-CD-A487 TCGA-CG-4438 TCGA-CG-4441 
       13.51         1.15        15.39        12.30        54.08        14.01 
TCGA-CG-4466 TCGA-D7-5578 TCGA-D7-6526 TCGA-D7-6822 TCGA-D7-8573 TCGA-D7-A6EX 
       18.97        12.66        17.19        12.33        19.50        11.31 
TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-FP-A4BF TCGA-HU-8249 TCGA-HU-A4GF 
       11.44        22.29         7.99         5.52        28.96        25.81 
TCGA-HU-A4GU TCGA-IN-7806 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-R5-A7ZF TCGA-RD-A7C1 
        6.58        36.36         5.56        37.64         8.52        16.67 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A91V TCGA-VQ-A91X 
        5.46        13.25        43.36        22.19        42.64         9.50 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA6B 
       21.04        42.54        32.94 

$`DEL PEAK 10(3Q26.31) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-VQ-A8PU TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
       20.15        27.35        58.03        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        36.16        35.84        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 
       28.73         3.45         9.07        29.56        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       29.42         2.66        19.96         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        31.10        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       25.18         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 
        9.86        20.88         8.22        34.13         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 
       34.98         1.48        27.55        28.57         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 
       13.15        13.18        13.35        11.21        12.10        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       12.59        11.64        12.07        12.82        12.43         6.31 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
        7.99         8.05         4.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01         7.07        12.00        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
       21.07         7.99        25.71        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 
       18.84        18.54        18.61        17.85        13.35        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 
       15.22        15.98        12.79        12.36        11.31        24.72 
TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       16.80        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       26.43        11.24        20.32        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
       19.96         7.13         0.62        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 
       59.54         5.03        13.58         0.56         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        18.15        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93J 
       11.70        15.75        13.51         2.53        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZI 
        3.72        19.73        14.04        45.67        18.21        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       57.44         8.94        35.61        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        0.92        48.79        13.02        18.48        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       38.14        37.22         7.73        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       16.31         2.50        12.79         2.70        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y 
       18.74        20.81        32.88         1.71        60.85         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       55.56         9.04         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        5.72        66.81         2.66        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       27.55        12.43        17.26         0.79 

  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                          0.69                           0.00 
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                         54.08                         122.30 
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                        14.010                         14.905 
[1] "0.7 - 54.1 (14.0)"  "0.0 - 122.3 (14.9)"
[1] "hr=" "1.3"
D46V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 10(3Q26.31) MUTATED         0        1        6        2         4
  DEL PEAK 10(3Q26.31) WILD-TYPE       2       15       35       30        36
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 10(3Q26.31) MUTATED           7         0         11         10
  DEL PEAK 10(3Q26.31) WILD-TYPE        49         3         70         53
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 10(3Q26.31) MUTATED            3        2
  DEL PEAK 10(3Q26.31) WILD-TYPE         36       42
D46V3, multiclass
            clus
vv           DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              1                             15
  STAGE IB                              6                             35
  STAGE II                              2                             30
  STAGE IIA                             4                             36
  STAGE IIB                             7                             49
  STAGE III                             0                              3
  STAGE IIIA                           11                             70
  STAGE IIIB                           10                             53
  STAGE IIIC                            3                             36
  STAGE IV                              2                             42
[1] 11  2
[1] TRUE
[1] "dimension of 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(3Q26.31) MUTATED     1   7  28  12
  DEL PEAK 10(3Q26.31) WILD-TYPE  22  86 168 107
D46V4, multiclass
    clus
vv   DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  T1                            1                             22
  T2                            7                             86
  T3                           28                            168
  T4                           12                            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"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 10(3Q26.31) MUTATED    15   9  15   8
  DEL PEAK 10(3Q26.31) WILD-TYPE 115 110  71  80
D46V5, multiclass
    clus
vv   DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  N0                           15                            115
  N1                            9                            110
  N2                           15                             71
  N3                            8                             80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                                cls
clus                               0   1
  DEL PEAK 10(3Q26.31) MUTATED    45   1
  DEL PEAK 10(3Q26.31) WILD-TYPE 344  29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q26.31) MUTATED     45    1
  DEL PEAK 10(3Q26.31) WILD-TYPE  344   29
   clus
vv  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  0                           45                            344
  1                            1                             29
[1] 2 2
[1] FALSE
D46V7, binary
                                cls
clus                               0   1
  DEL PEAK 10(3Q26.31) MUTATED    16  33
  DEL PEAK 10(3Q26.31) WILD-TYPE 142 250
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q26.31) MUTATED     16   33
  DEL PEAK 10(3Q26.31) WILD-TYPE  142  250
        clus
vv       DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  FEMALE                           16                            142
  MALE                             33                            250
[1] 2 2
[1] FALSE
D46V8, binary
                                cls
clus                               0   1
  DEL PEAK 10(3Q26.31) MUTATED    36   7
  DEL PEAK 10(3Q26.31) WILD-TYPE 286  69
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q26.31) MUTATED     36    7
  DEL PEAK 10(3Q26.31) WILD-TYPE  286   69
     clus
vv    DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  NO                            36                            286
  YES                            7                             69
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 10(3Q26.31) MUTATED                                          2
  DEL PEAK 10(3Q26.31) WILD-TYPE                                       11
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 10(3Q26.31) MUTATED                                       4
  DEL PEAK 10(3Q26.31) WILD-TYPE                                    68
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 10(3Q26.31) MUTATED                                                       15
  DEL PEAK 10(3Q26.31) WILD-TYPE                                                    148
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 10(3Q26.31) MUTATED                                                   1
  DEL PEAK 10(3Q26.31) WILD-TYPE                                                20
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 10(3Q26.31) MUTATED                                                                  13
  DEL PEAK 10(3Q26.31) WILD-TYPE                                                                69
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 10(3Q26.31) MUTATED                                                    0
  DEL PEAK 10(3Q26.31) WILD-TYPE                                                  8
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 10(3Q26.31) MUTATED                                                 14
  DEL PEAK 10(3Q26.31) WILD-TYPE                                               65
D46V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 10(3Q26.31) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      15
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           13
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            14
                                                                   clus
vv                                                                  DEL PEAK 10(3Q26.31) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             69
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             8
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              65
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 10(3Q26.31) MUTATED    44   1   0   2
  DEL PEAK 10(3Q26.31) WILD-TYPE 305  17  19  23
D46V10, multiclass
    clus
vv   DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  R0                           44                            305
  R1                            1                             17
  R2                            0                             19
  RX                            2                             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"
D46V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 10(3Q26.31) MUTATED       9                         2
  DEL PEAK 10(3Q26.31) WILD-TYPE    79                        10
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 10(3Q26.31) MUTATED                                           0
  DEL PEAK 10(3Q26.31) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 10(3Q26.31) MUTATED      32
  DEL PEAK 10(3Q26.31) WILD-TYPE   246
D46V12, multiclass
                                           clus
vv                                          DEL PEAK 10(3Q26.31) MUTATED
  ASIAN                                                                9
  BLACK OR AFRICAN AMERICAN                                            2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               32
                                           clus
vv                                          DEL PEAK 10(3Q26.31) WILD-TYPE
  ASIAN                                                                 79
  BLACK OR AFRICAN AMERICAN                                             10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                246
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V13, binary
                                cls
clus                               0   1
  DEL PEAK 10(3Q26.31) MUTATED     0  33
  DEL PEAK 10(3Q26.31) WILD-TYPE   5 283
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q26.31) MUTATED      0   33
  DEL PEAK 10(3Q26.31) WILD-TYPE    5  283
                        clus
vv                       DEL PEAK 10(3Q26.31) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           33
                        clus
vv                       DEL PEAK 10(3Q26.31) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            283
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 11(4P16.3) MUTATION ANALYSIS
D47V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(4P16.3) MUTATED    96  65
  DEL PEAK 11(4P16.3) WILD-TYPE 150 104
  DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE 
                          161                           254 
  DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE 
                           65                           104 
$`DEL PEAK 11(4P16.3) MUTATED`
TCGA-CG-4444 TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-A5TJ 
       47.05         9.86        27.35        26.93        58.03        11.01 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4255 TCGA-BR-4257 
        9.44         6.61         7.43        18.35         4.08         9.67 
TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 
       17.29         9.17        31.20         9.21        36.16        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 
       39.78        18.15        28.73         3.45         9.07        33.21 
TCGA-BR-8058 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       37.25         9.60        29.42         2.66        19.96         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8373 
       15.58         7.40        22.19        17.52        14.04        14.79 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8677 TCGA-BR-8678 
        3.72         5.39         9.21        20.22        26.73        24.79 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
        9.86        20.88        10.68         7.53        34.98         1.48 
TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-CD-5802 
        0.72         0.66        13.51         0.46        21.44        13.35 
TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 
       11.21        12.59        12.53        12.30        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MH 
       12.07        12.82        12.30        11.31        11.61        12.20 
TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4449 
       20.02         7.99         8.05        54.08         4.01        19.07 
TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5725 TCGA-D7-6518 TCGA-D7-6519 
       12.03        18.97         7.07        15.02        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6820 TCGA-D7-8570 
       18.84        17.19        10.26        15.22        11.31        24.72 
TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F0 
       19.50        18.21        21.14        16.44        11.31        22.29 
TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 
       19.96         7.99        72.23        11.38        14.07        17.06 
TCGA-FP-A4BF TCGA-HF-7133 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        5.52        63.06        30.51        26.47         1.51         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GP 
       18.15        28.96        22.82        22.75        25.81         8.98 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 
        6.58         0.26         2.10        12.95        23.84        21.17 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RP TCGA-IP-7968 
       33.40        36.36        18.81        12.46         6.44         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
        5.56        63.62         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 
        6.08         9.24        11.05        16.67        37.91       115.69 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E2 
        8.94        35.61         5.79         5.46        13.25        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE 
       21.73        37.41        37.22         7.73        46.26        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91V 
       12.79         2.70         1.87        73.41        39.45        42.64 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A94O 
        9.50         9.73        55.56         9.04         4.54        21.04 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       42.54        11.24        38.93        32.94        54.12 

$`DEL PEAK 11(4P16.3) WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       21.99        22.98        79.07        16.24         0.23        20.15 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 
       26.70        11.70        19.56         9.47         6.97         4.64 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
       30.90         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       34.68        15.95        13.87        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7704 
        8.98        40.21        30.90        44.94        21.90        35.24 
TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       35.84        15.32        29.56        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8360 TCGA-BR-8361 
       29.59        32.25         8.05         0.56         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 
       13.08         0.26         0.95        26.33         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8484 TCGA-BR-8487 
       11.80        31.27         7.36        25.05        25.18         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 
       31.96        32.58         8.22        34.13        13.87         6.08 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57        12.89         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL 
       28.34        32.52        20.65        20.42         1.15        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5804 
        5.13        13.41        13.02        13.15        13.18        12.10 
TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8536 
       12.76         7.17        12.33        12.39        12.59        12.43 
TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 
        6.31        12.43         6.58        11.77        12.62         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4462 
       27.02        15.95         1.02        14.01        29.98         0.00 
TCGA-CG-4465 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        9.01        12.00        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       12.66        20.91        18.54        18.61        17.85        13.35 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8574 
       15.98        12.79        12.36        12.33        16.80        17.19 
TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       14.66        20.91        14.27         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 
       14.76        26.43        11.24        11.44        20.32        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-A448 
        8.38         4.34         7.13         0.62        14.47        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        3.48        19.53        22.29        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HU-8244 TCGA-HU-8602 
        0.56         6.21        77.29        52.21        24.39        22.32 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
       24.20         3.25        11.77        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB 
        6.51        20.25        29.00        23.80        14.07        15.68 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR 
        3.45         3.39        18.38        13.35        19.53         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
       37.64        36.95        19.73         8.52        74.53         4.60 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
        8.61         5.13       122.30        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DZ 
       57.44        16.87        19.04         0.92        48.79        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF 
       18.48        38.14        30.97        34.29        16.31         2.50 
TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
       17.85         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       64.57        14.33        11.70        21.83        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A924 
       20.81        32.88         1.71        60.85         2.01        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-AA64 TCGA-VQ-AA68 
        6.58         5.72        66.81         2.66        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       28.41        17.13        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

  DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE 
                         0.26                          0.00 
  DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE 
                       115.69                        122.30 
  DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE 
                        14.79                         15.04 
[1] "0.3 - 115.7 (14.8)" "0.0 - 122.3 (15.0)"
[1] "hr=" "1"  
D47V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 11(4P16.3) MUTATED         0        5       12       13        19
  DEL PEAK 11(4P16.3) WILD-TYPE       2       11       29       19        21
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 11(4P16.3) MUTATED          19         1         37         23
  DEL PEAK 11(4P16.3) WILD-TYPE        37         2         44         40
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 11(4P16.3) MUTATED           17       13
  DEL PEAK 11(4P16.3) WILD-TYPE         22       31
D47V3, multiclass
            clus
vv           DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             5                            11
  STAGE IB                            12                            29
  STAGE II                            13                            19
  STAGE IIA                           19                            21
  STAGE IIB                           19                            37
  STAGE III                            1                             2
  STAGE IIIA                          37                            44
  STAGE IIIB                          23                            40
  STAGE IIIC                          17                            22
  STAGE IV                            13                            31
[1] 11  2
[1] TRUE
[1] "dimension of 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(4P16.3) MUTATED     6  29  89  40
  DEL PEAK 11(4P16.3) WILD-TYPE  17  64 107  79
D47V4, multiclass
    clus
vv   DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE
  T1                           6                            17
  T2                          29                            64
  T3                          89                           107
  T4                          40                            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"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 11(4P16.3) MUTATED   45 47 37 32
  DEL PEAK 11(4P16.3) WILD-TYPE 85 72 49 56
D47V5, multiclass
    clus
vv   DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE
  N0                          45                            85
  N1                          47                            72
  N2                          37                            49
  N3                          32                            56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                               cls
clus                              0   1
  DEL PEAK 11(4P16.3) MUTATED   154   7
  DEL PEAK 11(4P16.3) WILD-TYPE 235  23
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P16.3) MUTATED    154    7
  DEL PEAK 11(4P16.3) WILD-TYPE  235   23
   clus
vv  DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE
  0                         154                           235
  1                           7                            23
[1] 2 2
[1] FALSE
D47V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(4P16.3) MUTATED    55 114
  DEL PEAK 11(4P16.3) WILD-TYPE 103 169
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P16.3) MUTATED     55  114
  DEL PEAK 11(4P16.3) WILD-TYPE  103  169
        clus
vv       DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE
  FEMALE                          55                           103
  MALE                           114                           169
[1] 2 2
[1] FALSE
D47V8, binary
                               cls
clus                              0   1
  DEL PEAK 11(4P16.3) MUTATED   125  32
  DEL PEAK 11(4P16.3) WILD-TYPE 197  44
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P16.3) MUTATED    125   32
  DEL PEAK 11(4P16.3) WILD-TYPE  197   44
     clus
vv    DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE
  NO                          125                           197
  YES                          32                            44
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 11(4P16.3) MUTATED                                          6
  DEL PEAK 11(4P16.3) WILD-TYPE                                        7
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 11(4P16.3) MUTATED                                      23
  DEL PEAK 11(4P16.3) WILD-TYPE                                    49
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 11(4P16.3) MUTATED                                                       57
  DEL PEAK 11(4P16.3) WILD-TYPE                                                    106
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 11(4P16.3) MUTATED                                                  10
  DEL PEAK 11(4P16.3) WILD-TYPE                                                11
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 11(4P16.3) MUTATED                                                                  30
  DEL PEAK 11(4P16.3) WILD-TYPE                                                                52
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 11(4P16.3) MUTATED                                                    3
  DEL PEAK 11(4P16.3) WILD-TYPE                                                  5
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 11(4P16.3) MUTATED                                                 40
  DEL PEAK 11(4P16.3) WILD-TYPE                                               39
D47V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 11(4P16.3) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    6
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                      23
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     57
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                          10
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          30
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           40
                                                                   clus
vv                                                                  DEL PEAK 11(4P16.3) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        49
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      106
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            11
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            52
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             39
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 11(4P16.3) MUTATED   133   8   4   9
  DEL PEAK 11(4P16.3) WILD-TYPE 216  10  15  16
D47V10, multiclass
    clus
vv   DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE
  R0                         133                           216
  R1                           8                            10
  R2                           4                            15
  RX                           9                            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"
D47V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 11(4P16.3) MUTATED      38                         3
  DEL PEAK 11(4P16.3) WILD-TYPE    50                         9
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 11(4P16.3) MUTATED                                           0   107
  DEL PEAK 11(4P16.3) WILD-TYPE                                         1   171
D47V12, multiclass
                                           clus
vv                                          DEL PEAK 11(4P16.3) MUTATED
  ASIAN                                                              38
  BLACK OR AFRICAN AMERICAN                                           3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             107
                                           clus
vv                                          DEL PEAK 11(4P16.3) WILD-TYPE
  ASIAN                                                                50
  BLACK OR AFRICAN AMERICAN                                             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               171
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V13, binary
                               cls
clus                              0   1
  DEL PEAK 11(4P16.3) MUTATED     2 122
  DEL PEAK 11(4P16.3) WILD-TYPE   3 194
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P16.3) MUTATED      2  122
  DEL PEAK 11(4P16.3) WILD-TYPE    3  194
                        clus
vv                       DEL PEAK 11(4P16.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         122
                        clus
vv                       DEL PEAK 11(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           194
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 12(4Q22.1) MUTATION ANALYSIS
D48V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(4Q22.1) MUTATED   106  77
  DEL PEAK 12(4Q22.1) WILD-TYPE 140  92
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                          183                           232 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                           77                            92 
$`DEL PEAK 12(4Q22.1) MUTATED`
TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-MX-A663 TCGA-VQ-A94U 
       47.05        22.98        79.07         0.23         9.86        26.93 
TCGA-3M-AB46 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4255 
       58.03        11.01         9.44         6.61        18.35         4.08 
TCGA-BR-4257 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6801 TCGA-BR-6803 
        9.67        17.29        19.33         9.17        40.21        31.20 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       39.78        18.15         9.07        33.21        37.25        14.43 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        0.69         9.60        29.42         2.66        19.96         2.20 
TCGA-BR-8296 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8373 
       15.58        31.10        22.19        17.52        14.04        14.79 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8589 
        3.72         5.39        25.18         9.21        20.22        27.12 
TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
       24.79         9.86        10.68         7.53        34.98         1.48 
TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
        0.72         0.66        13.51         1.15        21.44         5.13 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 
       13.02        13.15        13.35        11.21        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
        7.17        12.33        12.39        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.82        11.31        12.43        11.61         6.58        12.20 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       20.02         3.02         7.99         8.05        54.08         4.01 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5720 
       19.07        12.03        18.97         7.07        30.97         0.99 
TCGA-CG-5724 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       12.03         4.01        69.04        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       19.13        20.55        17.19        10.26        15.22        15.98 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A6EX 
       12.36        11.31        19.50        18.21        16.44        11.31 
TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 
       19.96         0.62         7.99        72.23        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A9TM 
       19.53        14.07        17.06        13.58         5.52         6.21 
TCGA-HF-7133 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
       63.06         1.51         5.92        18.15        28.96        22.82 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY 
        0.76         5.59        22.75         8.98         6.58         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD 
        2.10        12.95        23.84        23.80        21.17        33.40 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RP TCGA-IN-A6RR 
       36.36        18.81         3.39        12.46         6.44         6.74 
TCGA-IN-A7NT TCGA-IP-7968 TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR 
       10.62         2.53        14.04        45.67        18.21         6.08 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 
        9.24        11.05         8.61        16.67        37.91       115.69 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        8.94        35.61        48.79        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       43.36        21.73         7.73        46.26        12.79         2.70 
TCGA-VQ-A8PO TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91N 
        9.27        13.35        14.33        73.41        39.45        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-A928 
       20.81         9.50         9.73        55.56         4.54         5.72 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       21.04        42.54        43.66        38.93        32.94        54.12 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       16.14        27.55        12.43 

$`DEL PEAK 12(4Q22.1) WILD-TYPE`
TCGA-CG-4460 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-VQ-A8PU TCGA-B7-5816 TCGA-B7-5818 
       21.99        16.24        20.15        27.35        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
       19.56         9.47         6.97         4.64         7.43        30.90 
TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       15.95        13.87        13.68        39.12        26.10        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 
       25.61        18.05        19.89        12.16         8.98        30.90 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8060 
       33.63        15.32        28.73         3.45        29.56        11.44 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8297 TCGA-BR-8360 
       29.59        32.25         8.05         0.56         7.40         6.18 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 
       13.08         0.26         0.95        26.33         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8588 
       11.80        31.27         7.36        25.05         1.12        12.79 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        9.34        28.14         6.28         7.53        26.73        31.96 
TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 
       32.58        20.88         8.22        34.13        13.87         6.08 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57        12.89         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL 
       28.34        32.52         0.46        20.65        20.42        16.14 
TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8529 TCGA-CD-8531 
       13.41        13.18        12.10        12.76        12.30        12.59 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 
       12.43         6.31        12.30        11.77        12.62        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4462 TCGA-CG-4465 
       15.95         1.02        14.01        29.98         0.00         9.01 
TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5721 TCGA-CG-5722 
       12.00         6.97        36.00         1.02         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 
      105.07        15.02        28.96        65.10        21.07         7.99 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6817 
       18.84        18.54        18.61        17.85        13.35        12.79 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 
       12.33        24.72        16.80        17.19        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7998 
        8.38         4.34         7.13        14.47        21.27        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB 
       59.54         5.03         0.56        77.29        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G6 
       26.47        24.39        22.32        21.07        24.30        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       22.68        24.20         3.25        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H8 
       29.98         0.10         6.51        20.25        29.00        14.07 
TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS 
       15.68         3.45        18.38        13.35        19.53        12.59 
TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 
        6.51        11.70        15.75        13.51         5.56        63.62 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI 
       37.64        36.95         3.72        19.73         8.52        74.53 
TCGA-R5-A804 TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
        4.60         5.13       122.30        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU 
       57.44        16.87        19.04         5.79         0.92         5.46 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       37.41        38.14        37.22        30.97        34.29        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       22.19         2.50        17.85         1.87        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S 
       29.59        64.57        11.70        21.83        61.22        32.88 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
        1.71        42.64        60.85         9.04         2.01        55.43 
TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 
        6.58        66.81         2.66        11.24        18.41        28.41 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.13        26.04        17.26         0.79 

  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                         0.23                          0.00 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                       115.69                        122.30 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                        13.35                         16.19 
[1] "0.2 - 115.7 (13.3)" "0.0 - 122.3 (16.2)"
[1] "hr=" "1.2"
D48V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 12(4Q22.1) MUTATED         0        5       13       17        19
  DEL PEAK 12(4Q22.1) WILD-TYPE       2       11       28       15        21
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 12(4Q22.1) MUTATED          26         2         39         24
  DEL PEAK 12(4Q22.1) WILD-TYPE        30         1         42         39
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 12(4Q22.1) MUTATED           19       19
  DEL PEAK 12(4Q22.1) WILD-TYPE         20       25
D48V3, multiclass
            clus
vv           DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             5                            11
  STAGE IB                            13                            28
  STAGE II                            17                            15
  STAGE IIA                           19                            21
  STAGE IIB                           26                            30
  STAGE III                            2                             1
  STAGE IIIA                          39                            42
  STAGE IIIB                          24                            39
  STAGE IIIC                          19                            20
  STAGE IV                            19                            25
[1] 11  2
[1] TRUE
[1] "dimension of 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     6  39  95  48
  DEL PEAK 12(4Q22.1) WILD-TYPE  17  54 101  71
D48V4, multiclass
    clus
vv   DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  T1                           6                            17
  T2                          39                            54
  T3                          95                           101
  T4                          48                            71
[1] 4 2
[1] TRUE
[1] "dimension of 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   50 53 42 40
  DEL PEAK 12(4Q22.1) WILD-TYPE 80 66 44 48
D48V5, multiclass
    clus
vv   DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  N0                          50                            80
  N1                          53                            66
  N2                          42                            44
  N3                          40                            48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V6, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q22.1) MUTATED   173  10
  DEL PEAK 12(4Q22.1) WILD-TYPE 216  20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED    173   10
  DEL PEAK 12(4Q22.1) WILD-TYPE  216   20
   clus
vv  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  0                         173                           216
  1                          10                            20
[1] 2 2
[1] FALSE
D48V7, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q22.1) MUTATED    66 127
  DEL PEAK 12(4Q22.1) WILD-TYPE  92 156
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED     66  127
  DEL PEAK 12(4Q22.1) WILD-TYPE   92  156
        clus
vv       DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  FEMALE                          66                            92
  MALE                           127                           156
[1] 2 2
[1] FALSE
D48V8, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q22.1) MUTATED   135  41
  DEL PEAK 12(4Q22.1) WILD-TYPE 187  35
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED    135   41
  DEL PEAK 12(4Q22.1) WILD-TYPE  187   35
     clus
vv    DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  NO                          135                           187
  YES                          41                            35
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 12(4Q22.1) MUTATED                                          8
  DEL PEAK 12(4Q22.1) WILD-TYPE                                        5
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 12(4Q22.1) MUTATED                                      23
  DEL PEAK 12(4Q22.1) WILD-TYPE                                    49
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 12(4Q22.1) MUTATED                                                       68
  DEL PEAK 12(4Q22.1) WILD-TYPE                                                     95
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 12(4Q22.1) MUTATED                                                   9
  DEL PEAK 12(4Q22.1) WILD-TYPE                                                12
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 12(4Q22.1) MUTATED                                                                  41
  DEL PEAK 12(4Q22.1) WILD-TYPE                                                                41
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 12(4Q22.1) MUTATED                                                    5
  DEL PEAK 12(4Q22.1) WILD-TYPE                                                  3
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 12(4Q22.1) MUTATED                                                 38
  DEL PEAK 12(4Q22.1) WILD-TYPE                                               41
D48V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 12(4Q22.1) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                      23
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     68
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           9
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          41
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           38
                                                                   clus
vv                                                                  DEL PEAK 12(4Q22.1) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        49
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       95
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            12
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            41
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             41
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 12(4Q22.1) MUTATED   147  10  10   8
  DEL PEAK 12(4Q22.1) WILD-TYPE 202   8   9  17
D48V10, multiclass
    clus
vv   DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  R0                         147                           202
  R1                          10                             8
  R2                          10                             9
  RX                           8                            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"
D48V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 12(4Q22.1) MUTATED      43                         7
  DEL PEAK 12(4Q22.1) WILD-TYPE    45                         5
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 12(4Q22.1) MUTATED                                           1   116
  DEL PEAK 12(4Q22.1) WILD-TYPE                                         0   162
D48V12, multiclass
                                           clus
vv                                          DEL PEAK 12(4Q22.1) MUTATED
  ASIAN                                                              43
  BLACK OR AFRICAN AMERICAN                                           7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             116
                                           clus
vv                                          DEL PEAK 12(4Q22.1) WILD-TYPE
  ASIAN                                                                45
  BLACK OR AFRICAN AMERICAN                                             5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               162
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V13, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q22.1) MUTATED     2 137
  DEL PEAK 12(4Q22.1) WILD-TYPE   3 179
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED      2  137
  DEL PEAK 12(4Q22.1) WILD-TYPE    3  179
                        clus
vv                       DEL PEAK 12(4Q22.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         137
                        clus
vv                       DEL PEAK 12(4Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           179
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 13(4Q35.1) MUTATION ANALYSIS
D49V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(4Q35.1) MUTATED   117  77
  DEL PEAK 13(4Q35.1) WILD-TYPE 129  92
  DEL PEAK 13(4Q35.1) MUTATED DEL PEAK 13(4Q35.1) WILD-TYPE 
                          194                           221 
  DEL PEAK 13(4Q35.1) MUTATED DEL PEAK 13(4Q35.1) WILD-TYPE 
                           77                            92 
$`DEL PEAK 13(4Q35.1) MUTATED`
TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-MX-A663 
       47.05        22.98        79.07        16.24         0.23         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN 
       27.35        26.93        58.03        19.56        11.01         9.44 
TCGA-BR-4191 TCGA-BR-4257 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6705 
       18.35         9.67        17.29        19.33         9.17        25.61 
TCGA-BR-6709 TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 
       12.16        31.20         9.21        35.24        33.63        18.15 
TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
       28.73         9.07        33.21        37.25        14.43         0.69 
TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        9.60         2.66        19.96         2.20        15.58         7.40 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8483 
       31.10        22.19        17.52        14.79         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8683 
       25.18         9.21        20.22        26.73        24.79         9.86 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 
        7.53        34.98         1.48         0.72         0.66        13.51 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 
       20.65         1.15        21.44         5.13        13.02        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.35        11.21        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.33        12.30        12.39        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 
       12.82        11.31        12.43        11.61        12.20        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
        3.02        27.02         7.99         8.05        54.08         4.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 
       29.98        19.07        12.03        18.97        30.97         6.97 
TCGA-CG-5719 TCGA-CG-5725 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6525 TCGA-D7-6526 
        1.02        15.02        12.66        19.13        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.22        15.98        12.79        11.31        12.33 
TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6EX 
       19.50        18.21        14.27        16.44        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-A72C 
       11.44        22.29        19.96         0.62         7.99        11.38 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-A4BF TCGA-HF-7133 
       19.53        14.07        17.06        13.58         5.52        63.06 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4GD 
        1.51         5.92        18.15        22.82         0.76        22.75 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        8.98         6.58         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL 
       23.80        21.17        33.40         3.39        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X 
       19.53         6.44         6.74        10.62        11.70        13.51 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        2.53        63.62        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
        6.08         9.24        11.05        16.67       122.30        37.91 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        8.94        35.61         0.92        48.79        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE 
       18.48        43.36        21.73         7.73        46.26        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PS TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91N 
       12.79        13.35        64.57        73.41        39.45        18.74 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A925 
       32.88         1.71         9.50         9.73        55.56         4.54 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A 
       21.04        42.54        11.24        18.41        43.66        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       32.94        17.13        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       12.43         0.79 

$`DEL PEAK 13(4Q35.1) WILD-TYPE`
TCGA-CG-4460 TCGA-KB-A93G TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK TCGA-BR-4183 
       21.99        20.15        26.70        11.70         9.47         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.34         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6706 
       13.87        13.68        39.12        26.10        32.78        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 
       19.89         8.98        40.21        30.90        44.94        21.90 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7958 
       36.16        35.84        39.78        15.32         3.45        29.56 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       11.44        29.59        32.25         8.05         0.56        29.42 
TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        6.18        13.08         0.26         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        31.27         7.36        25.05 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
        7.53        31.96        32.58        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       34.13        13.87         6.08        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 
        8.98        14.17         0.53        28.34        32.52         0.46 
TCGA-BR-A4PE TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8531 
       20.42        16.14        13.41        13.18        12.10        12.59 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43         6.31        12.30         6.58        11.77        12.62 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
       15.95         1.02        14.01         0.00         9.01         7.07 
TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       12.00        36.00         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
        7.99        25.71        20.91        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6818 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 
       18.61        17.85        12.36        24.72        16.80        17.19 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       14.66        21.14        20.91         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       14.76        26.43        20.32        15.65         8.38         4.34 
TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7998 
        7.13        14.47        72.23        21.27         3.48        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 
       59.54         5.03         0.56         6.21        77.29        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 
       30.51        26.47        24.39        28.96        22.32        21.07 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       20.25        29.00        14.07        15.68        36.36         3.45 
TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-KB-A6F5 
       18.81        18.38        12.59         6.51        15.75         5.56 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-R5-A804 
       37.64        36.95         3.72        19.73        74.53         4.60 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
        8.61         5.13        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8E7 
       57.44        16.87        19.04         5.79         5.46        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF 
       38.14        37.22        30.97        34.29        16.31         2.50 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.70        17.85         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q 
       29.59        14.33        11.70        21.83        61.22        20.81 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
       42.64        60.85         9.04         2.01        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-AA69 TCGA-ZA-A8F6 
        5.72        66.81         2.66        28.41        17.26 

  DEL PEAK 13(4Q35.1) MUTATED DEL PEAK 13(4Q35.1) WILD-TYPE 
                         0.23                          0.00 
  DEL PEAK 13(4Q35.1) MUTATED DEL PEAK 13(4Q35.1) WILD-TYPE 
                       122.30                        116.38 
  DEL PEAK 13(4Q35.1) MUTATED DEL PEAK 13(4Q35.1) WILD-TYPE 
                        13.51                         15.95 
[1] "0.2 - 122.3 (13.5)" "0.0 - 116.4 (15.9)"
[1] "hr=" "1"  
D49V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 13(4Q35.1) MUTATED         0        6       15       20        22
  DEL PEAK 13(4Q35.1) WILD-TYPE       2       10       26       12        18
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 13(4Q35.1) MUTATED          24         2         40         31
  DEL PEAK 13(4Q35.1) WILD-TYPE        32         1         41         32
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 13(4Q35.1) MUTATED           22       14
  DEL PEAK 13(4Q35.1) WILD-TYPE         17       30
D49V3, multiclass
            clus
vv           DEL PEAK 13(4Q35.1) MUTATED DEL PEAK 13(4Q35.1) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             6                            10
  STAGE IB                            15                            26
  STAGE II                            20                            12
  STAGE IIA                           22                            18
  STAGE IIB                           24                            32
  STAGE III                            2                             1
  STAGE IIIA                          40                            41
  STAGE IIIB                          31                            32
  STAGE IIIC                          22                            17
  STAGE IV                            14                            30
[1] 11  2
[1] TRUE
[1] "dimension of 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(4Q35.1) MUTATED     9  38  95  57
  DEL PEAK 13(4Q35.1) WILD-TYPE  14  55 101  62
D49V4, multiclass
    clus
vv   DEL PEAK 13(4Q35.1) MUTATED DEL PEAK 13(4Q35.1) WILD-TYPE
  T1                           9                            14
  T2                          38                            55
  T3                          95                           101
  T4                          57                            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"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 13(4Q35.1) MUTATED   59 53 42 42
  DEL PEAK 13(4Q35.1) WILD-TYPE 71 66 44 46
D49V5, multiclass
    clus
vv   DEL PEAK 13(4Q35.1) MUTATED DEL PEAK 13(4Q35.1) WILD-TYPE
  N0                          59                            71
  N1                          53                            66
  N2                          42                            44
  N3                          42                            46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V6, binary
                               cls
clus                              0   1
  DEL PEAK 13(4Q35.1) MUTATED   183  10
  DEL PEAK 13(4Q35.1) WILD-TYPE 206  20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q35.1) MUTATED    183   10
  DEL PEAK 13(4Q35.1) WILD-TYPE  206   20
   clus
vv  DEL PEAK 13(4Q35.1) MUTATED DEL PEAK 13(4Q35.1) WILD-TYPE
  0                         183                           206
  1                          10                            20
[1] 2 2
[1] FALSE
D49V7, binary
                               cls
clus                              0   1
  DEL PEAK 13(4Q35.1) MUTATED    74 130
  DEL PEAK 13(4Q35.1) WILD-TYPE  84 153
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q35.1) MUTATED     74  130
  DEL PEAK 13(4Q35.1) WILD-TYPE   84  153
        clus
vv       DEL PEAK 13(4Q35.1) MUTATED DEL PEAK 13(4Q35.1) WILD-TYPE
  FEMALE                          74                            84
  MALE                           130                           153
[1] 2 2
[1] FALSE
D49V8, binary
                               cls
clus                              0   1
  DEL PEAK 13(4Q35.1) MUTATED   143  44
  DEL PEAK 13(4Q35.1) WILD-TYPE 179  32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q35.1) MUTATED    143   44
  DEL PEAK 13(4Q35.1) WILD-TYPE  179   32
     clus
vv    DEL PEAK 13(4Q35.1) MUTATED DEL PEAK 13(4Q35.1) WILD-TYPE
  NO                          143                           179
  YES                          44                            32
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 13(4Q35.1) MUTATED                                          7
  DEL PEAK 13(4Q35.1) WILD-TYPE                                        6
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 13(4Q35.1) MUTATED                                      21
  DEL PEAK 13(4Q35.1) WILD-TYPE                                    51
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 13(4Q35.1) MUTATED                                                       69
  DEL PEAK 13(4Q35.1) WILD-TYPE                                                     94
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 13(4Q35.1) MUTATED                                                   9
  DEL PEAK 13(4Q35.1) WILD-TYPE                                                12
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 13(4Q35.1) MUTATED                                                                  49
  DEL PEAK 13(4Q35.1) WILD-TYPE                                                                33
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 13(4Q35.1) MUTATED                                                    4
  DEL PEAK 13(4Q35.1) WILD-TYPE                                                  4
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 13(4Q35.1) MUTATED                                                 43
  DEL PEAK 13(4Q35.1) WILD-TYPE                                               36
D49V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 13(4Q35.1) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                      21
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     69
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           9
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          49
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           43
                                                                   clus
vv                                                                  DEL PEAK 13(4Q35.1) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      6
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        51
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       94
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            12
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            33
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             36
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 13(4Q35.1) MUTATED   165   8   6   6
  DEL PEAK 13(4Q35.1) WILD-TYPE 184  10  13  19
D49V10, multiclass
    clus
vv   DEL PEAK 13(4Q35.1) MUTATED DEL PEAK 13(4Q35.1) WILD-TYPE
  R0                         165                           184
  R1                           8                            10
  R2                           6                            13
  RX                           6                            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"
D49V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 13(4Q35.1) MUTATED      43                         7
  DEL PEAK 13(4Q35.1) WILD-TYPE    45                         5
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 13(4Q35.1) MUTATED                                           0   126
  DEL PEAK 13(4Q35.1) WILD-TYPE                                         1   152
D49V12, multiclass
                                           clus
vv                                          DEL PEAK 13(4Q35.1) MUTATED
  ASIAN                                                              43
  BLACK OR AFRICAN AMERICAN                                           7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             126
                                           clus
vv                                          DEL PEAK 13(4Q35.1) WILD-TYPE
  ASIAN                                                                45
  BLACK OR AFRICAN AMERICAN                                             5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               152
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V13, binary
                               cls
clus                              0   1
  DEL PEAK 13(4Q35.1) MUTATED     2 142
  DEL PEAK 13(4Q35.1) WILD-TYPE   3 174
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q35.1) MUTATED      2  142
  DEL PEAK 13(4Q35.1) WILD-TYPE    3  174
                        clus
vv                       DEL PEAK 13(4Q35.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         142
                        clus
vv                       DEL PEAK 13(4Q35.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           174
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 14(5Q12.1) MUTATION ANALYSIS
D50V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(5Q12.1) MUTATED   100  64
  DEL PEAK 14(5Q12.1) WILD-TYPE 146 105
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                          164                           251 
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                           64                           105 
$`DEL PEAK 14(5Q12.1) MUTATED`
TCGA-CG-4444 TCGA-CG-4475 TCGA-MX-A663 TCGA-VQ-A8PU TCGA-3M-AB46 TCGA-B7-A5TI 
       47.05        22.98         9.86        27.35        58.03        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4257 TCGA-BR-6458 TCGA-BR-6565 
       11.01         9.44         6.61         9.67        19.33         9.17 
TCGA-BR-6709 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7901 TCGA-BR-7958 
       12.16        35.24        33.63        39.78         3.45        29.56 
TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 
       33.21        11.44         0.69        29.42         2.66         2.20 
TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 
       14.04        14.79         5.39         9.21        20.22        24.79 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ 
        9.86         8.22        10.68        13.87         7.53        34.98 
TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5800 
        1.48         0.72        20.42         1.15        21.44        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.18        13.35        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
       12.33        12.30        12.07        12.82         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4440 
       11.31        11.61        12.20        27.02         7.99         4.01 
TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5718 
       14.01        19.07        12.03        18.97        30.97        36.00 
TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-6526 
       15.02        69.04        20.91        18.84        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.22        15.98        12.79        11.31        12.33 
TCGA-D7-8570 TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A 
       24.72        11.24        11.31        22.29        15.65        19.96 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8211 
        0.62         7.99        72.23        19.53        17.06        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HU-8238 TCGA-HU-8243 
        0.56         5.52         6.21        63.06         1.51         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4GC TCGA-HU-A4GD 
       18.15        28.96         0.76         5.59         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
       25.81        11.77         6.58         2.10        12.95        23.84 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       21.17        33.40        36.36        18.81         3.39        18.38 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT 
       13.35        19.53         6.44         6.74         6.51        10.62 
TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A666 
       15.75         2.53        63.62        37.64        36.95        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 
       45.67        18.21         8.52        37.91       115.69         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
        5.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
        7.73        46.26        22.19        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91U 
        1.87        13.35        14.33        39.45        18.74         1.71 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A94O 
        9.73        55.56         9.04         4.54         5.72        21.04 
TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6F 
       42.54        18.41        43.66        38.93        17.13        54.12 
TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       27.55         0.79 

$`DEL PEAK 14(5Q12.1) WILD-TYPE`
TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A94U 
       21.99        79.07        16.24         0.23        20.15        26.93 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         9.47         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 
       18.35        30.90         4.08         4.08         9.34         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.68        39.12        26.10        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       19.89         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 
       21.90         9.21        36.16        35.84        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 
       28.73         9.07        37.25        14.43        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 
       32.25         8.05         0.56        19.96        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        31.10        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33         4.31         3.32        11.80        31.27 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 
        7.36        25.05         3.72        25.18         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU 
       31.96        32.58        20.88        34.13         6.08        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57        12.89         8.98        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4QL 
        0.66        32.52        13.51         0.46        20.65        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8530 
        5.13        13.41        13.02        11.21        12.10        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A48A TCGA-CD-A4MG 
       12.59        11.64        15.39        12.43        12.43         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 
       11.77        12.62        20.02         3.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
        8.05        54.08        29.98         0.00         9.01         7.07 
TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       12.00         6.97         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 
      105.07        12.03        28.96        65.10         4.01        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 
        7.99        25.71        12.66        19.13        20.55        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6818 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       18.61        17.85        12.36        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY 
        5.92        36.43        13.78        14.76        26.43        11.44 
TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 
       20.32         8.38         4.34         7.13        14.47        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
       11.38         3.48        14.07        22.29        59.54         5.03 
TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8602 
       77.29        52.21        30.51        26.47        24.39        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       22.82        21.07        24.30        24.26        22.68        24.20 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 
        0.26        29.00        23.80        14.07        15.68         3.45 
TCGA-IN-A6RJ TCGA-IN-A6RS TCGA-IN-A7NU TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-MX-A5UG 
       12.46        12.59        11.70        13.51         5.56         3.72 
TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       19.73        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 
        8.61         5.13        16.67       122.30        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL 
       71.38        57.44        35.61        16.87        19.04         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       48.79        18.48        21.73        38.14        37.22        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       34.29        16.31         2.50         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       29.59        64.57        73.41        11.70        21.83        61.22 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A923 
       20.81        32.88        42.64        60.85         9.50         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA69 
       55.43         6.58        66.81         2.66        11.24        28.41 
TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       32.94        26.04        16.14        12.43        17.26 

  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                         0.56                          0.00 
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                       115.69                        122.30 
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                        13.35                         16.24 
[1] "0.6 - 115.7 (13.3)" "0.0 - 122.3 (16.2)"
[1] "hr=" "1"  
D50V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 14(5Q12.1) MUTATED         1        5       14       12        13
  DEL PEAK 14(5Q12.1) WILD-TYPE       1       11       27       20        27
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 14(5Q12.1) MUTATED          27         0         40         22
  DEL PEAK 14(5Q12.1) WILD-TYPE        29         3         41         41
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 14(5Q12.1) MUTATED           13       16
  DEL PEAK 14(5Q12.1) WILD-TYPE         26       28
D50V3, multiclass
            clus
vv           DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             5                            11
  STAGE IB                            14                            27
  STAGE II                            12                            20
  STAGE IIA                           13                            27
  STAGE IIB                           27                            29
  STAGE III                            0                             3
  STAGE IIIA                          40                            41
  STAGE IIIB                          22                            41
  STAGE IIIC                          13                            26
  STAGE IV                            16                            28
[1] 11  2
[1] TRUE
[1] "dimension of 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(5Q12.1) MUTATED    10  38  79  40
  DEL PEAK 14(5Q12.1) WILD-TYPE  13  55 117  79
D50V4, multiclass
    clus
vv   DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  T1                          10                            13
  T2                          38                            55
  T3                          79                           117
  T4                          40                            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"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 14(5Q12.1) MUTATED   41 50 40 33
  DEL PEAK 14(5Q12.1) WILD-TYPE 89 69 46 55
D50V5, multiclass
    clus
vv   DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  N0                          41                            89
  N1                          50                            69
  N2                          40                            46
  N3                          33                            55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q12.1) MUTATED   152  10
  DEL PEAK 14(5Q12.1) WILD-TYPE 237  20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q12.1) MUTATED    152   10
  DEL PEAK 14(5Q12.1) WILD-TYPE  237   20
   clus
vv  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  0                         152                           237
  1                          10                            20
[1] 2 2
[1] FALSE
D50V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q12.1) MUTATED    59 111
  DEL PEAK 14(5Q12.1) WILD-TYPE  99 172
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q12.1) MUTATED     59  111
  DEL PEAK 14(5Q12.1) WILD-TYPE   99  172
        clus
vv       DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  FEMALE                          59                            99
  MALE                           111                           172
[1] 2 2
[1] FALSE
D50V8, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q12.1) MUTATED   126  33
  DEL PEAK 14(5Q12.1) WILD-TYPE 196  43
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q12.1) MUTATED    126   33
  DEL PEAK 14(5Q12.1) WILD-TYPE  196   43
     clus
vv    DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  NO                          126                           196
  YES                          33                            43
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 14(5Q12.1) MUTATED                                          4
  DEL PEAK 14(5Q12.1) WILD-TYPE                                        9
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 14(5Q12.1) MUTATED                                      12
  DEL PEAK 14(5Q12.1) WILD-TYPE                                    60
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 14(5Q12.1) MUTATED                                                       61
  DEL PEAK 14(5Q12.1) WILD-TYPE                                                    102
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 14(5Q12.1) MUTATED                                                  10
  DEL PEAK 14(5Q12.1) WILD-TYPE                                                11
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 14(5Q12.1) MUTATED                                                                  33
  DEL PEAK 14(5Q12.1) WILD-TYPE                                                                49
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 14(5Q12.1) MUTATED                                                    4
  DEL PEAK 14(5Q12.1) WILD-TYPE                                                  4
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 14(5Q12.1) MUTATED                                                 45
  DEL PEAK 14(5Q12.1) WILD-TYPE                                               34
D50V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 14(5Q12.1) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    4
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                      12
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     61
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                          10
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          33
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           45
                                                                   clus
vv                                                                  DEL PEAK 14(5Q12.1) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      9
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        60
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      102
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            11
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            49
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             34
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 14(5Q12.1) MUTATED   136   9   6   5
  DEL PEAK 14(5Q12.1) WILD-TYPE 213   9  13  20
D50V10, multiclass
    clus
vv   DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  R0                         136                           213
  R1                           9                             9
  R2                           6                            13
  RX                           5                            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"
D50V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 14(5Q12.1) MUTATED      38                         5
  DEL PEAK 14(5Q12.1) WILD-TYPE    50                         7
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 14(5Q12.1) MUTATED                                           0   107
  DEL PEAK 14(5Q12.1) WILD-TYPE                                         1   171
D50V12, multiclass
                                           clus
vv                                          DEL PEAK 14(5Q12.1) MUTATED
  ASIAN                                                              38
  BLACK OR AFRICAN AMERICAN                                           5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             107
                                           clus
vv                                          DEL PEAK 14(5Q12.1) WILD-TYPE
  ASIAN                                                                50
  BLACK OR AFRICAN AMERICAN                                             7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               171
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V13, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q12.1) MUTATED     2 119
  DEL PEAK 14(5Q12.1) WILD-TYPE   3 197
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q12.1) MUTATED      2  119
  DEL PEAK 14(5Q12.1) WILD-TYPE    3  197
                        clus
vv                       DEL PEAK 14(5Q12.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         119
                        clus
vv                       DEL PEAK 14(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           197
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 15(5Q23.2) MUTATION ANALYSIS
D51V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(5Q23.2) MUTATED    95  58
  DEL PEAK 15(5Q23.2) WILD-TYPE 151 111
  DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE 
                          153                           262 
  DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE 
                           58                           111 
$`DEL PEAK 15(5Q23.2) MUTATED`
TCGA-CG-4444 TCGA-EQ-A4SO TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 
       47.05        16.24         9.86        27.35        26.93        58.03 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4257 TCGA-BR-4267 
       19.56        11.01         9.44         6.61         9.67         6.18 
TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       19.33         9.17         9.21        35.24        33.63        39.78 
TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8289 
        3.45        29.56        33.21        11.44        29.42         2.66 
TCGA-BR-8295 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8485 
        2.20         4.31        14.04        14.79         5.39         9.21 
TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A452 
       20.22        24.79         9.86         8.22        10.68         7.53 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI 
       34.98         1.48         0.72        20.65        20.42        21.44 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.15        13.18        13.35        12.76        12.59        12.53 
TCGA-CD-8528 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A4MH TCGA-CG-4304 
       12.33        15.39        12.82        11.31        12.20        27.02 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        7.99        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5725 TCGA-D7-5579 TCGA-D7-6520 
       18.97        30.97        36.00        15.02        20.91        18.84 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8570 
       17.19        10.26        15.98        12.79        12.33        24.72 
TCGA-D7-8573 TCGA-D7-A4YT TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 
       19.50        14.27        11.24        11.31        22.29        15.65 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
        7.99        72.23        19.53        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8610 TCGA-HU-A4GC 
        6.21         1.51         5.92        18.15         0.76         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 
       22.75        25.81        11.77         8.98         6.58         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
       12.95        23.84        21.17        33.40        36.36        18.81 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR 
       18.38        13.35        19.53         6.44         6.74         6.51 
TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7O7 
       10.62        15.75         2.53        63.62        37.64        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A8MW TCGA-RD-A8N1 
       18.21         8.52         6.08         8.61        37.91       115.69 
TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        8.94         5.79         0.92         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH 
       43.36        37.41         7.73        46.26        22.19        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91Q 
        2.70        17.85        13.35        39.45        18.74        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
        1.71        42.64         9.73        55.56         9.04         2.01 
TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A 
        4.54        21.04        42.54        18.41        43.66        38.93 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-ZQ-A9CR 
       17.13        54.12         0.79 

$`DEL PEAK 15(5Q23.2) WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-B7-5816 
       21.99        22.98        79.07         0.23        20.15        26.70 
TCGA-B7-5818 TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         9.47         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-4280 
       30.90         4.08         4.08         9.34         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 
       34.68        15.95        13.87        17.29        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 
       36.16        35.84        18.15        15.32        28.73         9.07 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        8.05         0.56        19.96        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       31.10        13.08         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
       26.33         3.32        11.80        31.27         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        3.72        25.18         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        31.96        32.58 
TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
       20.88        34.13        13.87         6.08        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         8.98        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM 
       32.52        13.51         0.46         1.15        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8527 TCGA-CD-8529 
       13.41        13.02        11.21        12.10         7.17        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 
       12.39        12.59        11.64        12.07        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.30        12.43        11.61         6.58        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4455 
       20.02         3.02        15.95         1.02         8.05        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5719 
        0.00         9.01         7.07        12.00         6.97         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       12.66        19.13        20.55        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8572 TCGA-D7-8574 
       13.35        15.22        12.36        11.31        16.80        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV 
       18.21        14.66        21.14        20.91        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ 
       36.43        13.78        14.76        26.43        11.44        20.32 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 
        8.38         4.34        19.96         7.13         0.62        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27        11.38         3.48        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
       59.54         5.03        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       26.47        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ 
       24.30         5.59        24.26        22.68        24.20        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 
       29.98         0.10         6.51        20.25         0.26        29.00 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ 
       23.80        14.07        15.68         3.45         3.39        12.46 
TCGA-IN-A6RS TCGA-IN-A7NU TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A93J TCGA-MX-A5UG 
       12.59        11.70        13.51         5.56        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       19.73        14.04        74.53         4.60         9.24        11.05 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
        5.13        16.67       122.30        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DT TCGA-VQ-A8E0 
       57.44        35.61        16.87        19.04        48.79        18.48 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       21.73        38.14        37.22        30.97        34.29        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
        2.50         1.87         9.27        23.41        15.65        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       64.57        14.33        73.41        11.70        21.83        61.22 
TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
       32.88        60.85         9.50        55.43         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6G 
       66.81         2.66        11.24        28.41        32.94        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE 
                         0.56                          0.00 
  DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE 
                       115.69                        122.30 
  DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE 
                       13.580                        15.665 
[1] "0.6 - 115.7 (13.6)" "0.0 - 122.3 (15.7)"
[1] "hr=" "1"  
D51V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 15(5Q23.2) MUTATED         1        7       15       10        13
  DEL PEAK 15(5Q23.2) WILD-TYPE       1        9       26       22        27
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 15(5Q23.2) MUTATED          23         1         40         17
  DEL PEAK 15(5Q23.2) WILD-TYPE        33         2         41         46
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 15(5Q23.2) MUTATED           13       13
  DEL PEAK 15(5Q23.2) WILD-TYPE         26       31
D51V3, multiclass
            clus
vv           DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             7                             9
  STAGE IB                            15                            26
  STAGE II                            10                            22
  STAGE IIA                           13                            27
  STAGE IIB                           23                            33
  STAGE III                            1                             2
  STAGE IIIA                          40                            41
  STAGE IIIB                          17                            46
  STAGE IIIC                          13                            26
  STAGE IV                            13                            31
[1] 11  2
[1] TRUE
[1] "dimension of 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(5Q23.2) MUTATED    11  31  76  38
  DEL PEAK 15(5Q23.2) WILD-TYPE  12  62 120  81
D51V4, multiclass
    clus
vv   DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE
  T1                          11                            12
  T2                          31                            62
  T3                          76                           120
  T4                          38                            81
[1] 4 2
[1] TRUE
[1] "dimension of 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(5Q23.2) MUTATED   46 45 34 29
  DEL PEAK 15(5Q23.2) WILD-TYPE 84 74 52 59
D51V5, multiclass
    clus
vv   DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE
  N0                          46                            84
  N1                          45                            74
  N2                          34                            52
  N3                          29                            59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q23.2) MUTATED   143   8
  DEL PEAK 15(5Q23.2) WILD-TYPE 246  22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q23.2) MUTATED    143    8
  DEL PEAK 15(5Q23.2) WILD-TYPE  246   22
   clus
vv  DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE
  0                         143                           246
  1                           8                            22
[1] 2 2
[1] FALSE
D51V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q23.2) MUTATED    54 104
  DEL PEAK 15(5Q23.2) WILD-TYPE 104 179
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q23.2) MUTATED     54  104
  DEL PEAK 15(5Q23.2) WILD-TYPE  104  179
        clus
vv       DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE
  FEMALE                          54                           104
  MALE                           104                           179
[1] 2 2
[1] FALSE
D51V8, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q23.2) MUTATED   114  34
  DEL PEAK 15(5Q23.2) WILD-TYPE 208  42
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q23.2) MUTATED    114   34
  DEL PEAK 15(5Q23.2) WILD-TYPE  208   42
     clus
vv    DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE
  NO                          114                           208
  YES                          34                            42
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 15(5Q23.2) MUTATED                                          4
  DEL PEAK 15(5Q23.2) WILD-TYPE                                        9
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 15(5Q23.2) MUTATED                                       9
  DEL PEAK 15(5Q23.2) WILD-TYPE                                    63
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 15(5Q23.2) MUTATED                                                       56
  DEL PEAK 15(5Q23.2) WILD-TYPE                                                    107
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 15(5Q23.2) MUTATED                                                   7
  DEL PEAK 15(5Q23.2) WILD-TYPE                                                14
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 15(5Q23.2) MUTATED                                                                  32
  DEL PEAK 15(5Q23.2) WILD-TYPE                                                                50
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 15(5Q23.2) MUTATED                                                    3
  DEL PEAK 15(5Q23.2) WILD-TYPE                                                  5
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 15(5Q23.2) MUTATED                                                 46
  DEL PEAK 15(5Q23.2) WILD-TYPE                                               33
D51V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 15(5Q23.2) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    4
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       9
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     56
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           7
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          32
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           46
                                                                   clus
vv                                                                  DEL PEAK 15(5Q23.2) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      9
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        63
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      107
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            14
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            50
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             33
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 15(5Q23.2) MUTATED   129   7   6   4
  DEL PEAK 15(5Q23.2) WILD-TYPE 220  11  13  21
D51V10, multiclass
    clus
vv   DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE
  R0                         129                           220
  R1                           7                            11
  R2                           6                            13
  RX                           4                            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"
D51V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 15(5Q23.2) MUTATED      33                         5
  DEL PEAK 15(5Q23.2) WILD-TYPE    55                         7
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 15(5Q23.2) MUTATED                                           1    99
  DEL PEAK 15(5Q23.2) WILD-TYPE                                         0   179
D51V12, multiclass
                                           clus
vv                                          DEL PEAK 15(5Q23.2) MUTATED
  ASIAN                                                              33
  BLACK OR AFRICAN AMERICAN                                           5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              99
                                           clus
vv                                          DEL PEAK 15(5Q23.2) WILD-TYPE
  ASIAN                                                                55
  BLACK OR AFRICAN AMERICAN                                             7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               179
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V13, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q23.2) MUTATED     2 109
  DEL PEAK 15(5Q23.2) WILD-TYPE   3 207
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q23.2) MUTATED      2  109
  DEL PEAK 15(5Q23.2) WILD-TYPE    3  207
                        clus
vv                       DEL PEAK 15(5Q23.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         109
                        clus
vv                       DEL PEAK 15(5Q23.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           207
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 16(6P25.3) MUTATION ANALYSIS
D52V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 16(6P25.3) MUTATED    64  45
  DEL PEAK 16(6P25.3) WILD-TYPE 182 124
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                          109                           306 
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                           45                           124 
$`DEL PEAK 16(6P25.3) MUTATED`
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-VQ-A8PU TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6456 
       79.07        16.24        27.35        26.70         6.97        17.29 
TCGA-BR-6458 TCGA-BR-6709 TCGA-BR-6803 TCGA-BR-7716 TCGA-BR-7901 TCGA-BR-8077 
       19.33        12.16        31.20        39.78         3.45         0.69 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8683 
        6.18        31.10         9.21        20.22        24.79         9.86 
TCGA-BR-8687 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J8 
        8.22        34.98         1.48        12.89         0.72        13.51 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8525 TCGA-CD-8527 
       20.65         1.15        13.15        13.35        12.59         7.17 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CG-4437 
       11.64        12.82        12.30        11.31        12.43         8.05 
TCGA-CG-4466 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5728 TCGA-CG-5732 TCGA-D7-5578 
       18.97         1.02        12.03        65.10        69.04        12.66 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6528 
       19.13        20.55        18.84        18.54        13.35        15.22 
TCGA-D7-6815 TCGA-D7-6822 TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F2 TCGA-D7-A74A 
       15.98        12.33        11.31        11.44        15.65        19.96 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-A9TM TCGA-HF-7133 
       72.23        11.38        17.06        13.58         6.21        63.06 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8604 TCGA-HU-A4G3 TCGA-HU-A4GD 
       30.51        26.47         5.92        22.82         5.59        22.75 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-HU-A4HD 
       11.77         8.98         6.58        12.95        21.17        33.40 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93J 
       12.46        13.35         6.74        11.70         5.56        36.95 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7C1 TCGA-RD-A8MV 
       45.67        18.21         6.08         9.24        16.67       122.30 
TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8P3 
      115.69        57.44         8.94         0.92         5.46        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PS 
        7.73        22.19         2.70        17.85         1.87        13.35 
TCGA-VQ-A8PY TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A928 
       14.33        18.74        20.81        55.56         9.04         5.72 
TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       42.54        43.66        38.93        54.12        26.04        16.14 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK 16(6P25.3) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       47.05        21.99        22.98         0.23        20.15         9.86 
TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       26.93        58.03        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        6.61        34.68        15.95        13.87        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        30.90        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.24        35.84        33.63        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       28.73         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       29.42         2.66        19.96         2.20        15.58         7.40 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8487 
        7.36        25.05         3.72         5.39        25.18         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T 
       26.73        31.96        32.58        20.88        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
       13.87         7.53         6.08        27.55        28.57         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 
       14.17         0.53        28.34         0.66        32.52         0.46 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8528 
       13.18        11.21        12.10        12.76        12.53        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 
       12.30        12.39        12.59        15.39        12.07        12.43 
TCGA-CD-A486 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
        6.31        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01         7.07        12.00        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 
       36.00         0.99         6.02         0.99       105.07        15.02 
TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 
       28.96         4.01        21.07         7.99        25.71        20.91 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 
       18.61        17.85        17.19        10.26        12.79        12.36 
TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EZ 
       36.43        13.78        14.76        26.43        11.24        20.32 
TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
       22.29         8.38         4.34         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       14.47        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-7132 TCGA-HF-7134 
       59.54         5.03         0.56         5.52        77.29        52.21 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 
        1.51        24.39        18.15        28.96        22.32        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30        24.26        22.68        24.20         3.25 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       25.81        21.37        29.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 
        0.26         2.10        29.00        23.84        23.80        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       15.68        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V 
       19.53         6.44        12.59         6.51        10.62        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
       13.51         2.53        63.62        37.64         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT 
       14.04         8.52        74.53         4.60        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 
        5.13        37.91        40.64       116.38        71.38        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       16.87        19.04         5.79        48.79        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P8 
       18.48        43.36        21.73        37.41        38.14        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PO 
       34.29        46.26        16.31         2.50        12.79         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A 
       23.41        15.65        29.59        64.57        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       11.70        21.83        61.22        32.88         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
       60.85         9.50         9.73         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 
        6.58        66.81        21.04         2.66        11.24        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       28.41        32.94        17.13        27.55        12.43        17.26 

  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                         0.69                          0.00 
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                       122.30                        116.38 
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                       13.510                        15.355 
[1] "0.7 - 122.3 (13.5)" "0.0 - 116.4 (15.4)"
[1] "hr=" "1"  
D52V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 16(6P25.3) MUTATED         0        5        8        7        11
  DEL PEAK 16(6P25.3) WILD-TYPE       2       11       33       25        29
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 16(6P25.3) MUTATED          14         1         24         16
  DEL PEAK 16(6P25.3) WILD-TYPE        42         2         57         47
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 16(6P25.3) MUTATED            9       11
  DEL PEAK 16(6P25.3) WILD-TYPE         30       33
D52V3, multiclass
            clus
vv           DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             5                            11
  STAGE IB                             8                            33
  STAGE II                             7                            25
  STAGE IIA                           11                            29
  STAGE IIB                           14                            42
  STAGE III                            1                             2
  STAGE IIIA                          24                            57
  STAGE IIIB                          16                            47
  STAGE IIIC                           9                            30
  STAGE IV                            11                            33
[1] 11  2
[1] TRUE
[1] "dimension of 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(6P25.3) MUTATED     5  25  57  26
  DEL PEAK 16(6P25.3) WILD-TYPE  18  68 139  93
D52V4, multiclass
    clus
vv   DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  T1                           5                            18
  T2                          25                            68
  T3                          57                           139
  T4                          26                            93
[1] 4 2
[1] TRUE
[1] "dimension of 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(6P25.3) MUTATED   31 31 24 23
  DEL PEAK 16(6P25.3) WILD-TYPE 99 88 62 65
D52V5, multiclass
    clus
vv   DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  N0                          31                            99
  N1                          31                            88
  N2                          24                            62
  N3                          23                            65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                               cls
clus                              0   1
  DEL PEAK 16(6P25.3) MUTATED   103   4
  DEL PEAK 16(6P25.3) WILD-TYPE 286  26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6P25.3) MUTATED    103    4
  DEL PEAK 16(6P25.3) WILD-TYPE  286   26
   clus
vv  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  0                         103                           286
  1                           4                            26
[1] 2 2
[1] FALSE
D52V7, binary
                               cls
clus                              0   1
  DEL PEAK 16(6P25.3) MUTATED    43  72
  DEL PEAK 16(6P25.3) WILD-TYPE 115 211
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6P25.3) MUTATED     43   72
  DEL PEAK 16(6P25.3) WILD-TYPE  115  211
        clus
vv       DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  FEMALE                          43                           115
  MALE                            72                           211
[1] 2 2
[1] FALSE
D52V8, binary
                               cls
clus                              0   1
  DEL PEAK 16(6P25.3) MUTATED    82  23
  DEL PEAK 16(6P25.3) WILD-TYPE 240  53
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6P25.3) MUTATED     82   23
  DEL PEAK 16(6P25.3) WILD-TYPE  240   53
     clus
vv    DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  NO                           82                           240
  YES                          23                            53
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 16(6P25.3) MUTATED                                          2
  DEL PEAK 16(6P25.3) WILD-TYPE                                       11
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 16(6P25.3) MUTATED                                      14
  DEL PEAK 16(6P25.3) WILD-TYPE                                    58
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 16(6P25.3) MUTATED                                                       35
  DEL PEAK 16(6P25.3) WILD-TYPE                                                    128
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 16(6P25.3) MUTATED                                                   4
  DEL PEAK 16(6P25.3) WILD-TYPE                                                17
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 16(6P25.3) MUTATED                                                                  22
  DEL PEAK 16(6P25.3) WILD-TYPE                                                                60
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 16(6P25.3) MUTATED                                                    2
  DEL PEAK 16(6P25.3) WILD-TYPE                                                  6
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 16(6P25.3) MUTATED                                                 35
  DEL PEAK 16(6P25.3) WILD-TYPE                                               44
D52V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 16(6P25.3) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                      14
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     35
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          22
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           35
                                                                   clus
vv                                                                  DEL PEAK 16(6P25.3) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        58
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      128
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            17
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            60
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             44
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 16(6P25.3) MUTATED    93   7   2   6
  DEL PEAK 16(6P25.3) WILD-TYPE 256  11  17  19
D52V10, multiclass
    clus
vv   DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  R0                          93                           256
  R1                           7                            11
  R2                           2                            17
  RX                           6                            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"
D52V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 16(6P25.3) MUTATED      24                         2
  DEL PEAK 16(6P25.3) WILD-TYPE    64                        10
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 16(6P25.3) MUTATED                                           0    75
  DEL PEAK 16(6P25.3) WILD-TYPE                                         1   203
D52V12, multiclass
                                           clus
vv                                          DEL PEAK 16(6P25.3) MUTATED
  ASIAN                                                              24
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              75
                                           clus
vv                                          DEL PEAK 16(6P25.3) WILD-TYPE
  ASIAN                                                                64
  BLACK OR AFRICAN AMERICAN                                            10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               203
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V13, binary
                               cls
clus                              0   1
  DEL PEAK 16(6P25.3) MUTATED     1  81
  DEL PEAK 16(6P25.3) WILD-TYPE   4 235
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6P25.3) MUTATED      1   81
  DEL PEAK 16(6P25.3) WILD-TYPE    4  235
                        clus
vv                       DEL PEAK 16(6P25.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          81
                        clus
vv                       DEL PEAK 16(6P25.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           235
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 17(6Q14.1) MUTATION ANALYSIS
D53V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 17(6Q14.1) MUTATED    50  33
  DEL PEAK 17(6Q14.1) WILD-TYPE 196 136
  DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE 
                           83                           332 
  DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE 
                           33                           136 
$`DEL PEAK 17(6Q14.1) MUTATED`
TCGA-CG-4444 TCGA-EQ-A4SO TCGA-VQ-A8PU TCGA-B7-A5TI TCGA-BR-4191 TCGA-BR-4267 
       47.05        16.24        27.35        19.56        18.35         6.18 
TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-8080 TCGA-BR-8486 
       17.29         9.17        39.78        15.32         9.60        20.22 
TCGA-BR-A4CQ TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5803 
       34.98         0.53        13.51        20.65         1.15        11.21 
TCGA-CD-5804 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A48A 
       12.10        12.39        11.64        12.82         6.31        12.43 
TCGA-CG-4301 TCGA-CG-4437 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-5718 TCGA-CG-5719 
        3.02         8.05        29.98        12.03        36.00         1.02 
TCGA-CG-5724 TCGA-CG-5725 TCGA-D7-5578 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 
       12.03        15.02        12.66        18.84        18.54        13.35 
TCGA-D7-6527 TCGA-D7-8570 TCGA-D7-8576 TCGA-D7-A4YY TCGA-D7-A6EX TCGA-D7-A74A 
       10.26        24.72        14.66        13.78        11.31        19.96 
TCGA-F1-A72C TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 TCGA-HJ-7597 TCGA-HU-A4GD 
       11.38        17.06        13.58         0.56        26.47        22.75 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-A6RL 
       11.77         8.98        23.80        33.40        36.36        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A93J 
       19.53         6.44        12.59        10.62        11.70        36.95 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N5 
       45.67        18.21         6.08        16.67       122.30        57.44 
TCGA-SW-A7EA TCGA-VQ-A8E0 TCGA-VQ-A8P5 TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A91A 
       19.04        18.48         7.73        13.35        14.33        39.45 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-AA68 
       18.74        20.81         2.01         4.54        21.04        43.66 
TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       54.12        16.14        27.55        17.26         0.79 

$`DEL PEAK 17(6Q14.1) WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       21.99        22.98        79.07         0.23        20.15         9.86 
TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       26.93        58.03        26.70        11.70        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
        9.44         6.61         6.97         4.64         7.43        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         9.67         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       34.68        15.95        13.87        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 
        9.21        36.16        35.24        35.84        33.63        18.15 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69        29.59        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.56        29.42         2.66        19.96         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       34.13        13.87         7.53         6.08         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 
       28.57        12.89         8.98         0.72        14.17        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL 
        0.66        32.52         0.46        20.42        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 
       12.59        15.39        12.07        12.43        12.30        11.31 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         1.02         7.99        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       14.01        19.07         0.00         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       12.00        30.97         6.97         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
      105.07        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6522 
        7.99        25.71        20.91        19.13        20.55        18.61 
TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.85        17.19        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        12.33        16.80        19.50        17.19        18.21 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
       15.65         8.38         4.34         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       22.29        59.54         5.03         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        30.51         1.51         5.92        24.39 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       18.15        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        21.37        29.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       21.17        14.07        15.68         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X 
       18.38        12.46         6.74         6.51        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        37.64         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       14.04         8.52        74.53         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        8.61         5.13        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL 
       71.38         8.94        35.61        16.87         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       48.79         5.46        13.25        13.02        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       37.41        38.14        37.22        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       16.31        22.19         2.50        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX 
        1.87         9.27        23.41        15.65        29.59        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91U 
       73.41        11.70        21.83        61.22        32.88         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       42.64        60.85         9.50         9.73        55.56         9.04 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R 
       55.43         6.58         5.72        66.81         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       11.24        18.41        28.41        38.93        32.94        17.13 
TCGA-VQ-AA6G TCGA-VQ-AA6K 
       26.04        12.43 

  DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE 
                         0.53                          0.00 
  DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE 
                       122.30                        116.38 
  DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE 
                       15.020                        14.775 
[1] "0.5 - 122.3 (15.0)" "0.0 - 116.4 (14.8)"
[1] "hr=" "1"  
D53V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 17(6Q14.1) MUTATED         0        5        8        8         7
  DEL PEAK 17(6Q14.1) WILD-TYPE       2       11       33       24        33
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 17(6Q14.1) MUTATED          10         1         18         13
  DEL PEAK 17(6Q14.1) WILD-TYPE        46         2         63         50
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 17(6Q14.1) MUTATED            7        6
  DEL PEAK 17(6Q14.1) WILD-TYPE         32       38
D53V3, multiclass
            clus
vv           DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             5                            11
  STAGE IB                             8                            33
  STAGE II                             8                            24
  STAGE IIA                            7                            33
  STAGE IIB                           10                            46
  STAGE III                            1                             2
  STAGE IIIA                          18                            63
  STAGE IIIB                          13                            50
  STAGE IIIC                           7                            32
  STAGE IV                             6                            38
[1] 11  2
[1] TRUE
[1] "dimension of 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(6Q14.1) MUTATED     7  20  43  17
  DEL PEAK 17(6Q14.1) WILD-TYPE  16  73 153 102
D53V4, multiclass
    clus
vv   DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE
  T1                           7                            16
  T2                          20                            73
  T3                          43                           153
  T4                          17                           102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 17(6Q14.1) MUTATED    24  27  18  17
  DEL PEAK 17(6Q14.1) WILD-TYPE 106  92  68  71
D53V5, multiclass
    clus
vv   DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE
  N0                          24                           106
  N1                          27                            92
  N2                          18                            68
  N3                          17                            71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V6, binary
                               cls
clus                              0   1
  DEL PEAK 17(6Q14.1) MUTATED    76   4
  DEL PEAK 17(6Q14.1) WILD-TYPE 313  26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(6Q14.1) MUTATED     76    4
  DEL PEAK 17(6Q14.1) WILD-TYPE  313   26
   clus
vv  DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE
  0                          76                           313
  1                           4                            26
[1] 2 2
[1] FALSE
D53V7, binary
                               cls
clus                              0   1
  DEL PEAK 17(6Q14.1) MUTATED    26  63
  DEL PEAK 17(6Q14.1) WILD-TYPE 132 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(6Q14.1) MUTATED     26   63
  DEL PEAK 17(6Q14.1) WILD-TYPE  132  220
        clus
vv       DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE
  FEMALE                          26                           132
  MALE                            63                           220
[1] 2 2
[1] FALSE
D53V8, binary
                               cls
clus                              0   1
  DEL PEAK 17(6Q14.1) MUTATED    59  21
  DEL PEAK 17(6Q14.1) WILD-TYPE 263  55
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(6Q14.1) MUTATED     59   21
  DEL PEAK 17(6Q14.1) WILD-TYPE  263   55
     clus
vv    DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE
  NO                           59                           263
  YES                          21                            55
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 17(6Q14.1) MUTATED                                          1
  DEL PEAK 17(6Q14.1) WILD-TYPE                                       12
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 17(6Q14.1) MUTATED                                      12
  DEL PEAK 17(6Q14.1) WILD-TYPE                                    60
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 17(6Q14.1) MUTATED                                                       33
  DEL PEAK 17(6Q14.1) WILD-TYPE                                                    130
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 17(6Q14.1) MUTATED                                                   4
  DEL PEAK 17(6Q14.1) WILD-TYPE                                                17
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 17(6Q14.1) MUTATED                                                                  15
  DEL PEAK 17(6Q14.1) WILD-TYPE                                                                67
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 17(6Q14.1) MUTATED                                                    2
  DEL PEAK 17(6Q14.1) WILD-TYPE                                                  6
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 17(6Q14.1) MUTATED                                                 21
  DEL PEAK 17(6Q14.1) WILD-TYPE                                               58
D53V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 17(6Q14.1) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                      12
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     33
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          15
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           21
                                                                   clus
vv                                                                  DEL PEAK 17(6Q14.1) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     12
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        60
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      130
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            17
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 17(6Q14.1) MUTATED    73   1   3   5
  DEL PEAK 17(6Q14.1) WILD-TYPE 276  17  16  20
D53V10, multiclass
    clus
vv   DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE
  R0                          73                           276
  R1                           1                            17
  R2                           3                            16
  RX                           5                            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"
D53V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 17(6Q14.1) MUTATED      15                         4
  DEL PEAK 17(6Q14.1) WILD-TYPE    73                         8
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 17(6Q14.1) MUTATED                                           0    57
  DEL PEAK 17(6Q14.1) WILD-TYPE                                         1   221
D53V12, multiclass
                                           clus
vv                                          DEL PEAK 17(6Q14.1) MUTATED
  ASIAN                                                              15
  BLACK OR AFRICAN AMERICAN                                           4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              57
                                           clus
vv                                          DEL PEAK 17(6Q14.1) WILD-TYPE
  ASIAN                                                                73
  BLACK OR AFRICAN AMERICAN                                             8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V13, binary
                               cls
clus                              0   1
  DEL PEAK 17(6Q14.1) MUTATED     1  61
  DEL PEAK 17(6Q14.1) WILD-TYPE   4 255
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(6Q14.1) MUTATED      1   61
  DEL PEAK 17(6Q14.1) WILD-TYPE    4  255
                        clus
vv                       DEL PEAK 17(6Q14.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          61
                        clus
vv                       DEL PEAK 17(6Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           255
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 18(6Q24.3) MUTATION ANALYSIS
D54V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 18(6Q24.3) MUTATED    38  35
  DEL PEAK 18(6Q24.3) WILD-TYPE 208 134
  DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE 
                           73                           342 
  DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE 
                           35                           134 
$`DEL PEAK 18(6Q24.3) MUTATED`
TCGA-CG-4475 TCGA-MX-A663 TCGA-B7-A5TI TCGA-BR-4267 TCGA-BR-6565 TCGA-BR-7716 
       22.98         9.86        19.56         6.18         9.17        39.78 
TCGA-BR-7722 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8360 TCGA-BR-A4J1 TCGA-BR-A4J8 
       15.32         0.69         9.60         6.18         0.72        13.51 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8530 TCGA-CD-8532 
        1.15        21.44        11.21        12.10        12.39        11.64 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       15.39        12.82         6.31         4.01        14.01        29.98 
TCGA-CG-4455 TCGA-CG-4472 TCGA-CG-5725 TCGA-D7-5578 TCGA-D7-6521 TCGA-D7-6525 
       12.03        12.00        15.02        12.66        18.54        13.35 
TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A6EX 
       12.79        24.72        19.50        18.21        14.66        11.31 
TCGA-D7-A6F2 TCGA-D7-A74A TCGA-F1-A72C TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 
       15.65        19.96        11.38        17.06        13.58         0.56 
TCGA-HJ-7597 TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NT 
       26.47         6.58        23.84        13.35         6.44        10.62 
TCGA-KB-A93H TCGA-KB-A93J TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A7C1 
       37.64        36.95        18.21         6.08         8.61        16.67 
TCGA-RD-A8MV TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PC 
      122.30        57.44         8.94        43.36        21.73        46.26 
TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A923 
       13.35        14.33        18.74        20.81        32.88         2.01 
TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-AA68 TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J 
        4.54        21.04        43.66        54.12        16.14        27.55 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK 18(6Q24.3) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        79.07        16.24         0.23        20.15 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ 
       27.35        26.93        58.03        26.70        11.70        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
       13.68        19.33        39.12        26.10        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       35.84        33.63        18.15        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 
       29.56        33.21        37.25        14.43        11.44        29.59 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
        2.20        15.58         7.40        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 
       14.17         0.53        28.34         0.66        32.52         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.65        20.42        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.15        13.18        13.35        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8534 TCGA-CD-8536 
        7.17        12.33        12.30        12.59        12.07        12.43 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-4462 
        1.02         7.99         8.05        54.08        19.07         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
       25.71        20.91        19.13        20.55        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 
       17.85        17.19        10.26        15.22        15.98        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-8579 
       11.31        12.33        16.80        17.19        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 
       26.43        11.24        11.44        20.32        22.29         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
        4.34         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
       21.27         3.48        19.53        14.07        22.29        59.54 
TCGA-FP-8210 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        5.03         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
       30.51         1.51         5.92        24.39        18.15        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        29.00        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR 
       18.81         3.39        18.38        12.46        19.53         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
       12.59         6.51        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        63.62         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW 
        8.52        74.53         4.60         9.24        11.05         5.13 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 
       37.91        40.64       115.69       116.38        71.38        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       16.87        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        18.48        37.41        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
        7.73        30.97        34.29        16.31        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       12.79         2.70        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       15.65        29.59        64.57        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       21.83        61.22         1.71        42.64        60.85         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
        9.73        55.56         9.04        55.43         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 
       66.81         2.66        42.54        11.24        18.41        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZA-A8F6 
       38.93        32.94        17.13        26.04        12.43        17.26 

  DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE 
                         0.56                          0.00 
  DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE 
                       122.30                        116.38 
  DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE 
                       14.010                        15.615 
[1] "0.6 - 122.3 (14.0)" "0.0 - 116.4 (15.6)"
[1] "hr=" "1.3"
D54V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 18(6Q24.3) MUTATED         0        1        5        6         8
  DEL PEAK 18(6Q24.3) WILD-TYPE       2       15       36       26        32
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 18(6Q24.3) MUTATED          10         1         19         11
  DEL PEAK 18(6Q24.3) WILD-TYPE        46         2         62         52
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 18(6Q24.3) MUTATED            7        5
  DEL PEAK 18(6Q24.3) WILD-TYPE         32       39
D54V3, multiclass
            clus
vv           DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             1                            15
  STAGE IB                             5                            36
  STAGE II                             6                            26
  STAGE IIA                            8                            32
  STAGE IIB                           10                            46
  STAGE III                            1                             2
  STAGE IIIA                          19                            62
  STAGE IIIB                          11                            52
  STAGE IIIC                           7                            32
  STAGE IV                             5                            39
[1] 11  2
[1] TRUE
[1] "dimension of 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(6Q24.3) MUTATED     2  15  45  14
  DEL PEAK 18(6Q24.3) WILD-TYPE  21  78 151 105
D54V4, multiclass
    clus
vv   DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE
  T1                           2                            21
  T2                          15                            78
  T3                          45                           151
  T4                          14                           105
[1] 4 2
[1] TRUE
[1] "dimension of 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(6Q24.3) MUTATED    19  23  17  16
  DEL PEAK 18(6Q24.3) WILD-TYPE 111  96  69  72
D54V5, multiclass
    clus
vv   DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE
  N0                          19                           111
  N1                          23                            96
  N2                          17                            69
  N3                          16                            72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                               cls
clus                              0   1
  DEL PEAK 18(6Q24.3) MUTATED    72   1
  DEL PEAK 18(6Q24.3) WILD-TYPE 317  29
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(6Q24.3) MUTATED     72    1
  DEL PEAK 18(6Q24.3) WILD-TYPE  317   29
   clus
vv  DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE
  0                          72                           317
  1                           1                            29
[1] 2 2
[1] FALSE
D54V7, binary
                               cls
clus                              0   1
  DEL PEAK 18(6Q24.3) MUTATED    21  57
  DEL PEAK 18(6Q24.3) WILD-TYPE 137 226
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(6Q24.3) MUTATED     21   57
  DEL PEAK 18(6Q24.3) WILD-TYPE  137  226
        clus
vv       DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE
  FEMALE                          21                           137
  MALE                            57                           226
[1] 2 2
[1] FALSE
D54V8, binary
                               cls
clus                              0   1
  DEL PEAK 18(6Q24.3) MUTATED    54  14
  DEL PEAK 18(6Q24.3) WILD-TYPE 268  62
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(6Q24.3) MUTATED     54   14
  DEL PEAK 18(6Q24.3) WILD-TYPE  268   62
     clus
vv    DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE
  NO                           54                           268
  YES                          14                            62
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 18(6Q24.3) MUTATED                                          2
  DEL PEAK 18(6Q24.3) WILD-TYPE                                       11
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 18(6Q24.3) MUTATED                                       8
  DEL PEAK 18(6Q24.3) WILD-TYPE                                    64
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 18(6Q24.3) MUTATED                                                       24
  DEL PEAK 18(6Q24.3) WILD-TYPE                                                    139
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 18(6Q24.3) MUTATED                                                   3
  DEL PEAK 18(6Q24.3) WILD-TYPE                                                18
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 18(6Q24.3) MUTATED                                                                  16
  DEL PEAK 18(6Q24.3) WILD-TYPE                                                                66
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 18(6Q24.3) MUTATED                                                    0
  DEL PEAK 18(6Q24.3) WILD-TYPE                                                  8
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 18(6Q24.3) MUTATED                                                 23
  DEL PEAK 18(6Q24.3) WILD-TYPE                                               56
D54V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 18(6Q24.3) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       8
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     24
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          16
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           23
                                                                   clus
vv                                                                  DEL PEAK 18(6Q24.3) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      139
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            8
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 18(6Q24.3) MUTATED    64   2   3   4
  DEL PEAK 18(6Q24.3) WILD-TYPE 285  16  16  21
D54V10, multiclass
    clus
vv   DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE
  R0                          64                           285
  R1                           2                            16
  R2                           3                            16
  RX                           4                            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"
D54V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 18(6Q24.3) MUTATED      13                         4
  DEL PEAK 18(6Q24.3) WILD-TYPE    75                         8
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 18(6Q24.3) MUTATED                                           1    49
  DEL PEAK 18(6Q24.3) WILD-TYPE                                         0   229
D54V12, multiclass
                                           clus
vv                                          DEL PEAK 18(6Q24.3) MUTATED
  ASIAN                                                              13
  BLACK OR AFRICAN AMERICAN                                           4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              49
                                           clus
vv                                          DEL PEAK 18(6Q24.3) WILD-TYPE
  ASIAN                                                                75
  BLACK OR AFRICAN AMERICAN                                             8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               229
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V13, binary
                               cls
clus                              0   1
  DEL PEAK 18(6Q24.3) MUTATED     0  52
  DEL PEAK 18(6Q24.3) WILD-TYPE   5 264
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(6Q24.3) MUTATED      0   52
  DEL PEAK 18(6Q24.3) WILD-TYPE    5  264
                        clus
vv                       DEL PEAK 18(6Q24.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          52
                        clus
vv                       DEL PEAK 18(6Q24.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           264
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 19(6Q26) MUTATION ANALYSIS
D55V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 19(6Q26) MUTATED    54  44
  DEL PEAK 19(6Q26) WILD-TYPE 192 125
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                         98                         317 
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                         44                         125 
$`DEL PEAK 19(6Q26) MUTATED`
TCGA-FP-A8CX TCGA-MX-A663 TCGA-B7-A5TI TCGA-BR-4183 TCGA-BR-6458 TCGA-BR-6565 
        0.23         9.86        19.56         6.61        19.33         9.17 
TCGA-BR-6709 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7958 
       12.16        39.78        18.15        15.32        28.73        29.56 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8680 TCGA-BR-A4IY TCGA-BR-A4J8 TCGA-BR-A4PE 
        0.69         9.60        31.96        12.89        13.51        20.42 
TCGA-BR-A4PF TCGA-CD-5800 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8529 TCGA-CD-8530 
        1.15        13.15        11.21        12.10        12.30        12.39 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CG-4301 
       11.64        15.39        12.82         6.31        12.30         3.02 
TCGA-CG-4305 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4469 
       15.95         8.05         4.01        29.98        12.03         7.07 
TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5732 
       12.00         6.97         1.02        12.03        15.02        69.04 
TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-8570 
       12.66        20.55        18.54        13.35        17.19        24.72 
TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F2 
       19.50        18.21        14.66        11.31        11.44        15.65 
TCGA-D7-A74A TCGA-F1-A72C TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       19.96        11.38        17.06        13.58         0.56         5.52 
TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-A4G3 TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-HU-A4HD 
       63.06        26.47         5.59         6.58        23.84        33.40 
TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A93J TCGA-R5-A7O7 
       13.35         6.44        10.62        11.70        36.95        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N5 TCGA-RD-A8N6 
       18.21         6.08        16.67       122.30        57.44         8.94 
TCGA-VQ-A8DL TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PF 
        0.92        13.02        43.36         7.73        46.26         2.50 
TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A91Q TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A925 
       13.35        14.33        20.81        55.56         2.01         4.54 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6I 
       21.04        42.54        43.66        17.13        54.12        16.14 
TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       27.55         0.79 

$`DEL PEAK 19(6Q26) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G 
       47.05        21.99        22.98        79.07        16.24        20.15 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ 
       27.35        26.93        58.03        26.70        11.70        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.68        39.12        26.10        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       19.89         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        3.45         9.07        33.21        37.25        14.43        11.44 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       29.59        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       19.96         2.20        15.58         7.40         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
        6.08        34.98         1.48        27.55        28.57         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.65        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.02        13.18        13.35        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8531 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A489 
        7.17        12.33        12.59        12.07        12.43        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4441 
       20.02        27.02         1.02         7.99        54.08        14.01 
TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5718 
       19.07         0.00         9.01        18.97        30.97        36.00 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 
        0.99         6.02         0.99       105.07        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 
        4.01        21.07         7.99        25.71        20.91        19.13 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.84        18.61        17.85        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8574 
       12.79        12.36        11.31        12.33        16.80        17.19 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F0 
       13.78        14.76        26.43        11.24        20.32        22.29 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        8.38         4.34         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB 
       59.54         5.03         6.21        77.29        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        1.51         5.92        24.39        18.15        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 
       22.82        21.07         0.76        24.30        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        29.00        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       15.68        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V 
       12.46        19.53         6.74        12.59         6.51        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        37.64         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 
       19.73        14.04         8.52        74.53         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
       11.05         8.61         5.13        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
      116.38        71.38        35.61        16.87        19.04         5.79 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       48.79         5.46        13.25        18.48        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE 
       38.14        37.22        30.97        34.29        16.31        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       12.79         2.70        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       15.65        29.59        64.57        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       21.83        61.22        18.74        32.88         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 
       60.85         9.50         9.73         9.04        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 
        5.72        66.81         2.66        11.24        18.41        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZA-A8F6 
       38.93        32.94        26.04        12.43        17.26 

  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                       0.23                        0.00 
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                     122.30                      116.38 
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                      13.35                       15.75 
[1] "0.2 - 122.3 (13.3)" "0.0 - 116.4 (15.8)"
[1] "hr=" "1.2"
D55V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 19(6Q26) MUTATED         0        1        5       10         7
  DEL PEAK 19(6Q26) WILD-TYPE       2       15       36       22        33
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 19(6Q26) MUTATED          12         1         22         16
  DEL PEAK 19(6Q26) WILD-TYPE        44         2         59         47
                             vv
clus                          STAGE IIIC STAGE IV
  DEL PEAK 19(6Q26) MUTATED            8       14
  DEL PEAK 19(6Q26) WILD-TYPE         31       30
D55V3, multiclass
            clus
vv           DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  STAGE I                            0                           2
  STAGE IA                           1                          15
  STAGE IB                           5                          36
  STAGE II                          10                          22
  STAGE IIA                          7                          33
  STAGE IIB                         12                          44
  STAGE III                          1                           2
  STAGE IIIA                        22                          59
  STAGE IIIB                        16                          47
  STAGE IIIC                         8                          31
  STAGE IV                          14                          30
[1] 11  2
[1] TRUE
[1] "dimension of 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     2  20  57  22
  DEL PEAK 19(6Q26) WILD-TYPE  21  73 139  97
D55V4, multiclass
    clus
vv   DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  T1                         2                          21
  T2                        20                          73
  T3                        57                         139
  T4                        22                          97
[1] 4 2
[1] TRUE
[1] "dimension of 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    23  31  22  24
  DEL PEAK 19(6Q26) WILD-TYPE 107  88  64  64
D55V5, multiclass
    clus
vv   DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  N0                        23                         107
  N1                        31                          88
  N2                        22                          64
  N3                        24                          64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V6, binary
                             cls
clus                            0   1
  DEL PEAK 19(6Q26) MUTATED    88   8
  DEL PEAK 19(6Q26) WILD-TYPE 301  22
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(6Q26) MUTATED     88    8
  DEL PEAK 19(6Q26) WILD-TYPE  301   22
   clus
vv  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  0                        88                         301
  1                         8                          22
[1] 2 2
[1] FALSE
D55V7, binary
                             cls
clus                            0   1
  DEL PEAK 19(6Q26) MUTATED    32  70
  DEL PEAK 19(6Q26) WILD-TYPE 126 213
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(6Q26) MUTATED     32   70
  DEL PEAK 19(6Q26) WILD-TYPE  126  213
        clus
vv       DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  FEMALE                        32                         126
  MALE                          70                         213
[1] 2 2
[1] FALSE
D55V8, binary
                             cls
clus                            0   1
  DEL PEAK 19(6Q26) MUTATED    73  18
  DEL PEAK 19(6Q26) WILD-TYPE 249  58
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(6Q26) MUTATED     73   18
  DEL PEAK 19(6Q26) WILD-TYPE  249   58
     clus
vv    DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  NO                         73                         249
  YES                        18                          58
[1] 2 2
[1] FALSE
                             vv
clus                          STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 19(6Q26) MUTATED                                          5
  DEL PEAK 19(6Q26) WILD-TYPE                                        8
                             vv
clus                          STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 19(6Q26) MUTATED                                      11
  DEL PEAK 19(6Q26) WILD-TYPE                                    61
                             vv
clus                          STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 19(6Q26) MUTATED                                                       32
  DEL PEAK 19(6Q26) WILD-TYPE                                                    131
                             vv
clus                          STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 19(6Q26) MUTATED                                                   5
  DEL PEAK 19(6Q26) WILD-TYPE                                                16
                             vv
clus                          STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 19(6Q26) MUTATED                                                                  18
  DEL PEAK 19(6Q26) WILD-TYPE                                                                64
                             vv
clus                          STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 19(6Q26) MUTATED                                                    1
  DEL PEAK 19(6Q26) WILD-TYPE                                                  7
                             vv
clus                          STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 19(6Q26) MUTATED                                                 29
  DEL PEAK 19(6Q26) WILD-TYPE                                               50
D55V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 19(6Q26) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                  5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                    11
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                   32
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        18
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                        1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                         29
                                                                   clus
vv                                                                  DEL PEAK 19(6Q26) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                      61
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                    131
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                          16
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           50
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 19(6Q26) MUTATED    82   6   5   3
  DEL PEAK 19(6Q26) WILD-TYPE 267  12  14  22
D55V10, multiclass
    clus
vv   DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  R0                        82                         267
  R1                         6                          12
  R2                         5                          14
  RX                         3                          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"
D55V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 19(6Q26) MUTATED      18                         4
  DEL PEAK 19(6Q26) WILD-TYPE    70                         8
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 19(6Q26) MUTATED                                           0    61
  DEL PEAK 19(6Q26) WILD-TYPE                                         1   217
D55V12, multiclass
                                           clus
vv                                          DEL PEAK 19(6Q26) MUTATED
  ASIAN                                                            18
  BLACK OR AFRICAN AMERICAN                                         4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         0
  WHITE                                                            61
                                           clus
vv                                          DEL PEAK 19(6Q26) WILD-TYPE
  ASIAN                                                              70
  BLACK OR AFRICAN AMERICAN                                           8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V13, binary
                             cls
clus                            0   1
  DEL PEAK 19(6Q26) MUTATED     1  65
  DEL PEAK 19(6Q26) WILD-TYPE   4 251
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(6Q26) MUTATED      1   65
  DEL PEAK 19(6Q26) WILD-TYPE    4  251
                        clus
vv                       DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             1                           4
  NOT HISPANIC OR LATINO                        65                         251
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK 20(7Q31.1) MUTATION ANALYSIS
D56V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 20(7Q31.1) MUTATED    42  26
  DEL PEAK 20(7Q31.1) WILD-TYPE 204 143
  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                           68                           347 
  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                           26                           143 
$`DEL PEAK 20(7Q31.1) MUTATED`
TCGA-CG-4475 TCGA-VQ-A94U TCGA-BR-4255 TCGA-BR-6564 TCGA-BR-6706 TCGA-BR-7723 
       22.98        26.93         4.08        26.10        18.05        28.73 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8369 TCGA-BR-8678 TCGA-BR-A452 TCGA-BR-A4CS 
        6.18        31.10        14.04        24.79         7.53         1.48 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8534 TCGA-CD-A486 
        1.15        21.44        12.76         7.17        12.07         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CG-4301 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4449 
       12.30        11.31         3.02         8.05        54.08        19.07 
TCGA-CG-4455 TCGA-CG-4472 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-8575 TCGA-D7-A4YX 
       12.03        12.00        15.98        11.31        18.21        36.43 
TCGA-D7-A6EX TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-8631 TCGA-HU-A4GD TCGA-HU-A4GH 
       11.31        72.23        19.53         0.56        22.75        11.77 
TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD 
        6.58        12.95        23.84        21.17        14.07        33.40 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RN TCGA-IN-AB1V TCGA-IP-7968 
       18.81         3.39        18.38        19.53        15.75         2.53 
TCGA-KB-A93H TCGA-KB-A93J TCGA-RD-A7BT TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-RD-A8N9 
       37.64        36.95         8.61        37.91         8.94        35.61 
TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PS 
        5.46        13.02        18.48        37.22         7.73        13.35 
TCGA-VQ-A91Q TCGA-VQ-A923 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6D TCGA-VQ-AA6F 
       20.81         2.01         5.72        43.66        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I 
       26.04        16.14 

$`DEL PEAK 20(7Q31.1) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A8PU TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        9.86        27.35        58.03        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35        30.90         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 
       17.29        13.68        19.33        39.12         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 
       35.84        33.63        39.78        18.15        15.32         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       29.42         2.66        19.96         2.20        15.58         7.40 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
        4.31         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ 
        8.22        10.68        34.13        13.87         6.08        34.98 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.53        28.34         0.66        32.52        13.51         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.65        20.42        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 
       13.15        13.18        13.35        11.21        12.10        12.59 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
       12.53        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
       15.39        12.82        12.43        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 
       12.20        11.77        12.62        20.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4462 
        1.02         7.99         4.01        14.01        29.98         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 
       10.26        15.22        12.79        12.36        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44         5.92        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27        11.38         3.48        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       59.54         5.03        13.58         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       24.39        18.15        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        25.81        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H5 
        6.51        20.25         0.26         2.10        29.00        23.80 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP 
       15.68        36.36         3.45        12.46        13.35         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X 
        6.74        12.59         6.51        10.62        11.70        13.51 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        63.62         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 
       11.05         5.13        16.67       122.30        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
      116.38        71.38        57.44        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        0.92        48.79        13.25        43.36        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
       38.14        30.97        34.29        46.26        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
        2.50        12.79         2.70        17.85         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       23.41        15.65        29.59        64.57        14.33        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S 
       39.45        11.70        21.83        61.22        18.74        32.88 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
        1.71        42.64        60.85         9.50         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O 
        9.04        55.43         4.54         6.58        66.81        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A 
        2.66        42.54        11.24        18.41        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       32.94        27.55        12.43        17.26         0.79 

  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                         0.56                          0.00 
  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                        72.23                        122.30 
  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                       15.865                        14.760 
[1] "0.6 - 72.2 (15.9)"  "0.0 - 122.3 (14.8)"
[1] "hr=" "1"  
D56V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 20(7Q31.1) MUTATED         1        3        2        8         8
  DEL PEAK 20(7Q31.1) WILD-TYPE       1       13       39       24        32
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 20(7Q31.1) MUTATED          14         0         17          7
  DEL PEAK 20(7Q31.1) WILD-TYPE        42         3         64         56
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 20(7Q31.1) MUTATED            3        7
  DEL PEAK 20(7Q31.1) WILD-TYPE         36       37
D56V3, multiclass
            clus
vv           DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             3                            13
  STAGE IB                             2                            39
  STAGE II                             8                            24
  STAGE IIA                            8                            32
  STAGE IIB                           14                            42
  STAGE III                            0                             3
  STAGE IIIA                          17                            64
  STAGE IIIB                           7                            56
  STAGE IIIC                           3                            36
  STAGE IV                             7                            37
[1] 11  2
[1] TRUE
[1] "dimension of 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(7Q31.1) MUTATED     5  14  39  12
  DEL PEAK 20(7Q31.1) WILD-TYPE  18  79 157 107
D56V4, multiclass
    clus
vv   DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  T1                           5                            18
  T2                          14                            79
  T3                          39                           157
  T4                          12                           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"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 20(7Q31.1) MUTATED    15  27  18  10
  DEL PEAK 20(7Q31.1) WILD-TYPE 115  92  68  78
D56V5, multiclass
    clus
vv   DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  N0                          15                           115
  N1                          27                            92
  N2                          18                            68
  N3                          10                            78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
                               cls
clus                              0   1
  DEL PEAK 20(7Q31.1) MUTATED    67   2
  DEL PEAK 20(7Q31.1) WILD-TYPE 322  28
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(7Q31.1) MUTATED     67    2
  DEL PEAK 20(7Q31.1) WILD-TYPE  322   28
   clus
vv  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  0                          67                           322
  1                           2                            28
[1] 2 2
[1] FALSE
D56V7, binary
                               cls
clus                              0   1
  DEL PEAK 20(7Q31.1) MUTATED    19  52
  DEL PEAK 20(7Q31.1) WILD-TYPE 139 231
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(7Q31.1) MUTATED     19   52
  DEL PEAK 20(7Q31.1) WILD-TYPE  139  231
        clus
vv       DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  FEMALE                          19                           139
  MALE                            52                           231
[1] 2 2
[1] FALSE
D56V8, binary
                               cls
clus                              0   1
  DEL PEAK 20(7Q31.1) MUTATED    52  13
  DEL PEAK 20(7Q31.1) WILD-TYPE 270  63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(7Q31.1) MUTATED     52   13
  DEL PEAK 20(7Q31.1) WILD-TYPE  270   63
     clus
vv    DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  NO                           52                           270
  YES                          13                            63
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 20(7Q31.1) MUTATED                                          2
  DEL PEAK 20(7Q31.1) WILD-TYPE                                       11
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 20(7Q31.1) MUTATED                                       7
  DEL PEAK 20(7Q31.1) WILD-TYPE                                    65
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 20(7Q31.1) MUTATED                                                       22
  DEL PEAK 20(7Q31.1) WILD-TYPE                                                    141
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 20(7Q31.1) MUTATED                                                   3
  DEL PEAK 20(7Q31.1) WILD-TYPE                                                18
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 20(7Q31.1) MUTATED                                                                  15
  DEL PEAK 20(7Q31.1) WILD-TYPE                                                                67
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 20(7Q31.1) MUTATED                                                    1
  DEL PEAK 20(7Q31.1) WILD-TYPE                                                  7
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 20(7Q31.1) MUTATED                                                 19
  DEL PEAK 20(7Q31.1) WILD-TYPE                                               60
D56V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 20(7Q31.1) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       7
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     22
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          15
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           19
                                                                   clus
vv                                                                  DEL PEAK 20(7Q31.1) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      141
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 20(7Q31.1) MUTATED    63   1   3   2
  DEL PEAK 20(7Q31.1) WILD-TYPE 286  17  16  23
D56V10, multiclass
    clus
vv   DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  R0                          63                           286
  R1                           1                            17
  R2                           3                            16
  RX                           2                            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"
D56V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 20(7Q31.1) MUTATED      17                         3
  DEL PEAK 20(7Q31.1) WILD-TYPE    71                         9
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 20(7Q31.1) MUTATED                                           1    40
  DEL PEAK 20(7Q31.1) WILD-TYPE                                         0   238
D56V12, multiclass
                                           clus
vv                                          DEL PEAK 20(7Q31.1) MUTATED
  ASIAN                                                              17
  BLACK OR AFRICAN AMERICAN                                           3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              40
                                           clus
vv                                          DEL PEAK 20(7Q31.1) WILD-TYPE
  ASIAN                                                                71
  BLACK OR AFRICAN AMERICAN                                             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V13, binary
                               cls
clus                              0   1
  DEL PEAK 20(7Q31.1) MUTATED     0  46
  DEL PEAK 20(7Q31.1) WILD-TYPE   5 270
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(7Q31.1) MUTATED      0   46
  DEL PEAK 20(7Q31.1) WILD-TYPE    5  270
                        clus
vv                       DEL PEAK 20(7Q31.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          46
                        clus
vv                       DEL PEAK 20(7Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           270
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK 21(7Q36.3) MUTATION ANALYSIS
D57V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 21(7Q36.3) MUTATED    58  36
  DEL PEAK 21(7Q36.3) WILD-TYPE 188 133
  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                           94                           321 
  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                           36                           133 
$`DEL PEAK 21(7Q36.3) MUTATED`
TCGA-CG-4475 TCGA-EQ-A4SO TCGA-VQ-A94U TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4255 
       22.98        16.24        26.93        19.56         9.44         4.08 
TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-7704 TCGA-BR-7723 TCGA-BR-7901 
       17.29        19.33        26.10        35.24        28.73         3.45 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8296 TCGA-BR-8369 TCGA-BR-8485 TCGA-BR-8678 
       11.44         0.69        15.58        14.04         9.21        24.79 
TCGA-BR-A4CS TCGA-BR-A4PF TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8528 
        1.48         1.15        13.35        12.76        12.59        12.33 
TCGA-CD-8529 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.30        12.07        12.82         6.31        12.30        11.31 
TCGA-CD-A48C TCGA-CG-4301 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-4455 
       11.61         3.02         8.05        54.08        19.07        12.03 
TCGA-CG-4472 TCGA-CG-5724 TCGA-D7-6519 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 
       12.00        12.03        20.55        13.35        17.19        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8575 TCGA-D7-A6EV TCGA-D7-A6EX 
       12.79        12.36        11.31        18.21        11.24        11.31 
TCGA-D7-A6F0 TCGA-D7-A74A TCGA-FP-7829 TCGA-FP-8631 TCGA-HU-8243 TCGA-HU-A4GD 
       22.29        19.96        19.53         0.56         5.92        22.75 
TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD 
       11.77         6.58        12.95        23.84        21.17        33.40 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
        3.45        18.81         3.39        18.38        12.46        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-KB-A93H TCGA-MX-A666 
        6.44         6.74        10.62        15.75        37.64        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-RD-A8MW TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DZ 
       45.67        18.21        37.91        35.61         5.46        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PS 
       18.48        37.22         7.73         2.70        17.85        13.35 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-AA64 TCGA-VQ-AA68 
       18.74        20.81         5.72        66.81        18.41        43.66 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-ZQ-A9CR 
       54.12        26.04        16.14         0.79 

$`DEL PEAK 21(7Q36.3) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       47.05        21.99        79.07         0.23        20.15         9.86 
TCGA-VQ-A8PU TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       27.35        58.03        26.70        11.70        11.01         9.47 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6565 
       34.68        15.95        13.87        13.68        39.12         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 
        9.07        29.56        33.21        37.25        14.43        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       19.96         2.20         7.40         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        3.72         5.39        25.18        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU 
       34.13        13.87         7.53         6.08        34.98        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
       28.34         0.66        32.52        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8526 TCGA-CD-8527 
       13.15        13.18        11.21        12.10        12.53         7.17 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A48A 
       12.39        12.59        11.64        15.39        12.43        12.43 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 
        6.58        12.20        11.77        12.62        20.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       15.95         1.02         7.99         4.01        14.01        29.98 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 
        7.99        25.71        12.66        20.91        19.13        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6822 
       18.54        18.61        17.85        10.26        15.22        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 
       24.72        16.80        19.50        17.19        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 
       14.76        26.43        11.44        20.32        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
        4.34         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27        11.38         3.48        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       59.54         5.03        13.58         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 
       63.06        52.21        30.51        26.47         1.51        24.39 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       18.15        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 
       20.25         0.26         2.10        29.00        23.80        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-A6RL TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU 
       15.68        36.36        13.35        12.59         6.51        11.70 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       19.73         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 
       11.05         8.61         5.13        16.67       122.30        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB 
      115.69       116.38        71.38        57.44         8.94        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E2 
       19.04         5.79         0.92        48.79        13.25        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       21.73        37.41        38.14        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO 
       16.31        22.19         2.50        12.79         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       23.41        15.65        29.59        64.57        14.33        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91U 
       39.45        11.70        21.83        61.22        32.88         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       42.64        60.85         9.50         9.73        55.56         9.04 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A94O TCGA-VQ-A94P 
        2.01        55.43         4.54         6.58        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       42.54        11.24        28.41        38.93        32.94        17.13 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                         0.56                          0.00 
  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                        66.81                        122.30 
  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                        13.35                         15.32 
[1] "0.6 - 66.8 (13.3)"  "0.0 - 122.3 (15.3)"
[1] "hr=" "1"  
D57V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 21(7Q36.3) MUTATED         1        3        3        8         7
  DEL PEAK 21(7Q36.3) WILD-TYPE       1       13       38       24        33
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 21(7Q36.3) MUTATED          21         0         22         10
  DEL PEAK 21(7Q36.3) WILD-TYPE        35         3         59         53
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 21(7Q36.3) MUTATED            8       11
  DEL PEAK 21(7Q36.3) WILD-TYPE         31       33
D57V3, multiclass
            clus
vv           DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             3                            13
  STAGE IB                             3                            38
  STAGE II                             8                            24
  STAGE IIA                            7                            33
  STAGE IIB                           21                            35
  STAGE III                            0                             3
  STAGE IIIA                          22                            59
  STAGE IIIB                          10                            53
  STAGE IIIC                           8                            31
  STAGE IV                            11                            33
[1] 11  2
[1] TRUE
[1] "dimension of 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     6  19  50  21
  DEL PEAK 21(7Q36.3) WILD-TYPE  17  74 146  98
D57V4, multiclass
    clus
vv   DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  T1                           6                            17
  T2                          19                            74
  T3                          50                           146
  T4                          21                            98
[1] 4 2
[1] TRUE
[1] "dimension of 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    19  31  24  20
  DEL PEAK 21(7Q36.3) WILD-TYPE 111  88  62  68
D57V5, multiclass
    clus
vv   DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  N0                          19                           111
  N1                          31                            88
  N2                          24                            62
  N3                          20                            68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V6, binary
                               cls
clus                              0   1
  DEL PEAK 21(7Q36.3) MUTATED    87   7
  DEL PEAK 21(7Q36.3) WILD-TYPE 302  23
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q36.3) MUTATED     87    7
  DEL PEAK 21(7Q36.3) WILD-TYPE  302   23
   clus
vv  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  0                          87                           302
  1                           7                            23
[1] 2 2
[1] FALSE
D57V7, binary
                               cls
clus                              0   1
  DEL PEAK 21(7Q36.3) MUTATED    33  65
  DEL PEAK 21(7Q36.3) WILD-TYPE 125 218
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q36.3) MUTATED     33   65
  DEL PEAK 21(7Q36.3) WILD-TYPE  125  218
        clus
vv       DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  FEMALE                          33                           125
  MALE                            65                           218
[1] 2 2
[1] FALSE
D57V8, binary
                               cls
clus                              0   1
  DEL PEAK 21(7Q36.3) MUTATED    70  21
  DEL PEAK 21(7Q36.3) WILD-TYPE 252  55
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q36.3) MUTATED     70   21
  DEL PEAK 21(7Q36.3) WILD-TYPE  252   55
     clus
vv    DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  NO                           70                           252
  YES                          21                            55
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 21(7Q36.3) MUTATED                                          2
  DEL PEAK 21(7Q36.3) WILD-TYPE                                       11
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 21(7Q36.3) MUTATED                                      12
  DEL PEAK 21(7Q36.3) WILD-TYPE                                    60
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 21(7Q36.3) MUTATED                                                       33
  DEL PEAK 21(7Q36.3) WILD-TYPE                                                    130
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 21(7Q36.3) MUTATED                                                   5
  DEL PEAK 21(7Q36.3) WILD-TYPE                                                16
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 21(7Q36.3) MUTATED                                                                  17
  DEL PEAK 21(7Q36.3) WILD-TYPE                                                                65
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 21(7Q36.3) MUTATED                                                    1
  DEL PEAK 21(7Q36.3) WILD-TYPE                                                  7
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 21(7Q36.3) MUTATED                                                 25
  DEL PEAK 21(7Q36.3) WILD-TYPE                                               54
D57V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 21(7Q36.3) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                      12
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     33
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           5
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          17
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           25
                                                                   clus
vv                                                                  DEL PEAK 21(7Q36.3) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        60
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      130
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            16
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             54
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 21(7Q36.3) MUTATED    80   1   4   3
  DEL PEAK 21(7Q36.3) WILD-TYPE 269  17  15  22
D57V10, multiclass
    clus
vv   DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  R0                          80                           269
  R1                           1                            17
  R2                           4                            15
  RX                           3                            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"
D57V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 21(7Q36.3) MUTATED      21                         2
  DEL PEAK 21(7Q36.3) WILD-TYPE    67                        10
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 21(7Q36.3) MUTATED                                           0    63
  DEL PEAK 21(7Q36.3) WILD-TYPE                                         1   215
D57V12, multiclass
                                           clus
vv                                          DEL PEAK 21(7Q36.3) MUTATED
  ASIAN                                                              21
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              63
                                           clus
vv                                          DEL PEAK 21(7Q36.3) WILD-TYPE
  ASIAN                                                                67
  BLACK OR AFRICAN AMERICAN                                            10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V13, binary
                               cls
clus                              0   1
  DEL PEAK 21(7Q36.3) MUTATED     1  69
  DEL PEAK 21(7Q36.3) WILD-TYPE   4 247
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q36.3) MUTATED      1   69
  DEL PEAK 21(7Q36.3) WILD-TYPE    4  247
                        clus
vv                       DEL PEAK 21(7Q36.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          69
                        clus
vv                       DEL PEAK 21(7Q36.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           247
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 22(8P23.2) MUTATION ANALYSIS
D58V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 22(8P23.2) MUTATED    69  46
  DEL PEAK 22(8P23.2) WILD-TYPE 177 123
  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                          115                           300 
  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                           46                           123 
$`DEL PEAK 22(8P23.2) MUTATED`
TCGA-CG-4444 TCGA-CG-4475 TCGA-3M-AB46 TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4191 
       47.05        22.98        58.03        19.56         9.44        18.35 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6709 TCGA-BR-7197 
       17.29        13.68         9.17        25.61        12.16         9.21 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7958 TCGA-BR-8077 TCGA-BR-8080 
       33.63        39.78        28.73        29.56         0.69         9.60 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8362 TCGA-BR-8485 TCGA-BR-8680 
       29.42         2.66        15.58        13.08         9.21        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A4IY TCGA-BR-A4J1 
       32.58         9.86         8.22        13.87        12.89         0.72 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-5802 
       13.51        20.65         1.15        21.44        13.15        13.35 
TCGA-CD-5804 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A48A 
       12.10        12.53         7.17        15.39         6.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
       11.61        12.20         3.02         7.99        54.08         4.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 
       29.98        19.07        36.00        12.03        15.02         4.01 
TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6528 
       69.04        12.66        19.13        18.54        17.19        15.22 
TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-A4YU TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 
       11.31        24.72        16.44        15.65        19.96         0.62 
TCGA-FP-8099 TCGA-HF-7133 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8610 
       17.06        63.06         5.92        18.15        28.96         0.76 
TCGA-HU-A4GD TCGA-HU-A4GU TCGA-HU-A4HD TCGA-IN-8663 TCGA-IN-A6RP TCGA-IN-A6RR 
       22.75         6.58        33.40         3.39         6.44         6.74 
TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93J 
        6.51        11.70        15.75         2.53         5.56        36.95 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A8MV 
       14.04        45.67         8.52         9.24         8.61       122.30 
TCGA-RD-A8MW TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       37.91         5.79         0.92        18.48        43.36        37.41 
TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM 
        7.73        46.26        22.19        12.79        17.85         1.87 
TCGA-VQ-A8PS TCGA-VQ-A91A TCGA-VQ-A91U TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-A94T 
       13.35        39.45         1.71        55.56         4.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J 
       18.41        43.66        32.94        54.12        16.14        27.55 
TCGA-VQ-AA6K 
       12.43 

$`DEL PEAK 22(8P23.2) WILD-TYPE`
TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       21.99        79.07        16.24         0.23        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       27.35        26.93        26.70        11.70        11.01         9.47 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 
        6.61         6.97         4.64         7.43        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       34.68        15.95        13.87        19.33        39.12        26.10 
TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       32.78        18.05        19.89         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        44.94        21.90        36.16        35.24        35.84 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 
       18.15        15.32         3.45         9.07        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       14.43        11.44        29.59        32.25         8.05         0.56 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        3.72         5.39        25.18        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 
       24.79        20.88        10.68        34.13         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 
       34.98         1.48        27.55        28.57         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE 
        0.53        28.34         0.66        32.52         0.46        20.42 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5803 
       16.14         5.13        13.41        13.02        13.18        11.21 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.76        12.59        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 
       11.64        12.07        12.82        12.43        12.30        11.31 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 
        6.58        11.77        12.62        20.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
        1.02         8.05        14.01        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 
       18.97         7.07        12.00        30.97         6.97         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 
        0.99         6.02         0.99       105.07        28.96        65.10 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 
       21.07         7.99        25.71        20.91        20.55        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
       18.61        17.85        13.35        10.26        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.36        12.33        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 
       20.32        22.29         8.38         4.34         7.13         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       14.07        22.29        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52         6.21        77.29        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 
        1.51        24.39        22.32        22.82        21.07        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
        5.59        24.26        22.68        24.20         3.25        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        14.07        15.68        36.36         3.45 
TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS 
       18.81        18.38        12.46        13.35        19.53        12.59 
TCGA-IN-A7NT TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
       10.62        13.51        63.62        37.64         3.72        19.73 
TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BW 
       18.21        74.53         6.08         4.60        11.05         5.13 
TCGA-RD-A7C1 TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       16.67        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DT TCGA-VQ-A8DU 
        8.94        35.61        16.87        19.04        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       13.25        13.02        21.73        38.14        37.22        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP 
       34.29        16.31         2.50         2.70         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D 
       15.65        29.59        64.57        14.33        73.41        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V 
       21.83        61.22        18.74        20.81        32.88        42.64 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
       60.85         9.50         9.73         9.04         2.01        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
        6.58         5.72        66.81        21.04         2.66        42.54 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       28.41        38.93        17.13        26.04        17.26         0.79 

  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                         0.62                          0.00 
  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                       122.30                        116.38 
  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                       14.040                        15.055 
[1] "0.6 - 122.3 (14.0)" "0.0 - 116.4 (15.1)"
[1] "hr=" "1"  
D58V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 22(8P23.2) MUTATED         1        4        5        9        11
  DEL PEAK 22(8P23.2) WILD-TYPE       1       12       36       23        29
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 22(8P23.2) MUTATED          14         0         19         26
  DEL PEAK 22(8P23.2) WILD-TYPE        42         3         62         37
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 22(8P23.2) MUTATED           12       16
  DEL PEAK 22(8P23.2) WILD-TYPE         27       28
D58V3, multiclass
            clus
vv           DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             4                            12
  STAGE IB                             5                            36
  STAGE II                             9                            23
  STAGE IIA                           11                            29
  STAGE IIB                           14                            42
  STAGE III                            0                             3
  STAGE IIIA                          19                            62
  STAGE IIIB                          26                            37
  STAGE IIIC                          12                            27
  STAGE IV                            16                            28
[1] 11  2
[1] TRUE
[1] "dimension of 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     6  19  66  29
  DEL PEAK 22(8P23.2) WILD-TYPE  17  74 130  90
D58V4, multiclass
    clus
vv   DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  T1                           6                            17
  T2                          19                            74
  T3                          66                           130
  T4                          29                            90
[1] 4 2
[1] TRUE
[1] "dimension of 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    29  29  27  33
  DEL PEAK 22(8P23.2) WILD-TYPE 101  90  59  55
D58V5, multiclass
    clus
vv   DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  N0                          29                           101
  N1                          29                            90
  N2                          27                            59
  N3                          33                            55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V6, binary
                               cls
clus                              0   1
  DEL PEAK 22(8P23.2) MUTATED   106  11
  DEL PEAK 22(8P23.2) WILD-TYPE 283  19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(8P23.2) MUTATED    106   11
  DEL PEAK 22(8P23.2) WILD-TYPE  283   19
   clus
vv  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  0                         106                           283
  1                          11                            19
[1] 2 2
[1] FALSE
D58V7, binary
                               cls
clus                              0   1
  DEL PEAK 22(8P23.2) MUTATED    32  90
  DEL PEAK 22(8P23.2) WILD-TYPE 126 193
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(8P23.2) MUTATED     32   90
  DEL PEAK 22(8P23.2) WILD-TYPE  126  193
        clus
vv       DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  FEMALE                          32                           126
  MALE                            90                           193
[1] 2 2
[1] FALSE
D58V8, binary
                               cls
clus                              0   1
  DEL PEAK 22(8P23.2) MUTATED    88  22
  DEL PEAK 22(8P23.2) WILD-TYPE 234  54
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(8P23.2) MUTATED     88   22
  DEL PEAK 22(8P23.2) WILD-TYPE  234   54
     clus
vv    DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  NO                           88                           234
  YES                          22                            54
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 22(8P23.2) MUTATED                                          3
  DEL PEAK 22(8P23.2) WILD-TYPE                                       10
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 22(8P23.2) MUTATED                                       9
  DEL PEAK 22(8P23.2) WILD-TYPE                                    63
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 22(8P23.2) MUTATED                                                       48
  DEL PEAK 22(8P23.2) WILD-TYPE                                                    115
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 22(8P23.2) MUTATED                                                   6
  DEL PEAK 22(8P23.2) WILD-TYPE                                                15
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 22(8P23.2) MUTATED                                                                  27
  DEL PEAK 22(8P23.2) WILD-TYPE                                                                55
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 22(8P23.2) MUTATED                                                    2
  DEL PEAK 22(8P23.2) WILD-TYPE                                                  6
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 22(8P23.2) MUTATED                                                 26
  DEL PEAK 22(8P23.2) WILD-TYPE                                               53
D58V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 22(8P23.2) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       9
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     48
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           6
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          27
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           26
                                                                   clus
vv                                                                  DEL PEAK 22(8P23.2) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        63
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      115
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            15
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            55
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             53
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 22(8P23.2) MUTATED    93   7   7   3
  DEL PEAK 22(8P23.2) WILD-TYPE 256  11  12  22
D58V10, multiclass
    clus
vv   DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  R0                          93                           256
  R1                           7                            11
  R2                           7                            12
  RX                           3                            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"
D58V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 22(8P23.2) MUTATED      25                         4
  DEL PEAK 22(8P23.2) WILD-TYPE    63                         8
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 22(8P23.2) MUTATED                                           1    74
  DEL PEAK 22(8P23.2) WILD-TYPE                                         0   204
D58V12, multiclass
                                           clus
vv                                          DEL PEAK 22(8P23.2) MUTATED
  ASIAN                                                              25
  BLACK OR AFRICAN AMERICAN                                           4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              74
                                           clus
vv                                          DEL PEAK 22(8P23.2) WILD-TYPE
  ASIAN                                                                63
  BLACK OR AFRICAN AMERICAN                                             8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               204
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V13, binary
                               cls
clus                              0   1
  DEL PEAK 22(8P23.2) MUTATED     2  79
  DEL PEAK 22(8P23.2) WILD-TYPE   3 237
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(8P23.2) MUTATED      2   79
  DEL PEAK 22(8P23.2) WILD-TYPE    3  237
                        clus
vv                       DEL PEAK 22(8P23.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          79
                        clus
vv                       DEL PEAK 22(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           237
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK 23(9P23) MUTATION ANALYSIS
D59V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 23(9P23) MUTATED   108  78
  DEL PEAK 23(9P23) WILD-TYPE 138  91
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                        186                         229 
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                         78                          91 
$`DEL PEAK 23(9P23) MUTATED`
TCGA-CG-4444 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-A5TI 
       47.05        27.35        26.93        58.03        26.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
       11.01         9.44         6.61        18.35         4.08         4.08 
TCGA-BR-4257 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6707 TCGA-BR-6709 
        9.67        17.29        13.68        19.33        19.89        12.16 
TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       31.20         9.21        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 
       15.32        28.73         3.45        33.21        37.25        11.44 
TCGA-BR-8077 TCGA-BR-8284 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8364 TCGA-BR-8365 
        0.69         8.05         2.66        19.96        22.19        17.52 
TCGA-BR-8369 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8676 
       14.04         5.39        25.18         9.21        20.22         7.53 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A4CQ 
       32.58         9.86        20.88         8.22        13.87        34.98 
TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF 
        1.48         0.72         0.66        13.51        20.65         1.15 
TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 
       21.44        13.02        13.15        11.21        12.10        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.53         7.17        12.39        11.64        15.39        12.07 
TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CG-4301 TCGA-CG-4437 TCGA-CG-4438 
        6.31        12.43        11.61         3.02         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4472 
        4.01        29.98        19.07        12.03        18.97        12.00 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5730 TCGA-CG-5732 
       36.00         1.02       105.07        12.03         4.01        69.04 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
       18.54        13.35        17.19        10.26        15.98        12.79 
TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YU 
       11.31        19.50        18.21        14.66        21.14        16.44 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-8122 
       11.24        11.31        22.29        15.65        19.96         7.99 
TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF 
       11.38        19.53        14.07        17.06         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7133 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-A4GF 
        6.21        63.06         1.51         5.92        18.15        25.81 
TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 
       11.77         6.58        29.00        21.17        33.40        36.36 
TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR 
       18.81        18.38        12.46        13.35         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 
       12.59         6.51        10.62        15.75        13.51         5.56 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZR 
       37.64        36.95        14.04        45.67         8.52         6.08 
TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
        9.24         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E0 
      115.69         8.94         5.79        48.79        13.25        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH 
       43.36        37.41         7.73        22.19         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91N 
        2.70        17.85         1.87        64.57        14.33        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       20.81         1.71        42.64         9.50         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
        9.04         2.01        21.04        42.54        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       43.66        38.93        54.12        27.55        12.43         0.79 

$`DEL PEAK 23(9P23) WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       21.99        22.98        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-B7-5818 TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.86        11.70         9.47         6.97         4.64         7.43 
TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       30.90         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       15.95        13.87        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 
       25.61        18.05         8.98        40.21        30.90        44.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8059 
       21.90        36.16        35.84         9.07        29.56        14.43 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8295 
       29.59         9.60        32.25         0.56        29.42         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33         4.31         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 
       14.79         7.36        25.05         3.72         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34        28.14         6.28        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU 
       31.96        10.68        34.13         7.53         6.08        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57        12.89         8.98        14.17         0.53        28.34 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       32.52         0.46        20.42        16.14         5.13        13.41 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 
       13.18        13.35        12.76        12.33        12.30        12.59 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MH 
       12.82        12.43        12.30        11.31         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        12.62        20.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4441 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4477 
        7.99        14.01         0.00         9.01         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5725 TCGA-CG-5726 
        6.97         0.99         6.02         0.99        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6528 
       65.10        21.07         7.99        18.61        17.85        15.22 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8579 
       12.36        12.33        24.72        16.80        17.19        20.91 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 
       11.44        20.32         8.38         4.34         7.13         0.62 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7998 TCGA-FP-8209 
       14.47        72.23        21.27         3.48        22.29        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.03        13.58        77.29        52.21        30.51        26.47 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       22.75        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        23.84        23.80 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RN TCGA-IN-A7NU 
       14.07        15.68         3.45         3.39        19.53        11.70 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZE TCGA-R5-A7ZI 
        2.53        63.62         3.72        19.73        18.21        74.53 
TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
        4.60        11.05        40.64       116.38        71.38        57.44 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DZ 
       35.61        16.87        19.04         0.92         5.46        13.02 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       21.73        38.14        37.22        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
       16.31         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S 
       73.41        39.45        11.70        21.83        61.22        32.88 
TCGA-VQ-A91W TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
       60.85        55.43         4.54         6.58         5.72        66.81 
TCGA-VQ-A94P TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I 
        2.66        28.41        32.94        17.13        26.04        16.14 
TCGA-ZA-A8F6 
       17.26 

  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                       0.56                        0.00 
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                     122.30                      116.38 
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                      14.04                       15.65 
[1] "0.6 - 122.3 (14.0)" "0.0 - 116.4 (15.7)"
[1] "hr=" "1.1"
D59V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 23(9P23) MUTATED         1        8       10       17        18
  DEL PEAK 23(9P23) WILD-TYPE       1        8       31       15        22
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 23(9P23) MUTATED          25         1         37         28
  DEL PEAK 23(9P23) WILD-TYPE        31         2         44         35
                             vv
clus                          STAGE IIIC STAGE IV
  DEL PEAK 23(9P23) MUTATED           17       21
  DEL PEAK 23(9P23) WILD-TYPE         22       23
D59V3, multiclass
            clus
vv           DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  STAGE I                            1                           1
  STAGE IA                           8                           8
  STAGE IB                          10                          31
  STAGE II                          17                          15
  STAGE IIA                         18                          22
  STAGE IIB                         25                          31
  STAGE III                          1                           2
  STAGE IIIA                        37                          44
  STAGE IIIB                        28                          35
  STAGE IIIC                        17                          22
  STAGE IV                          21                          23
[1] 11  2
[1] TRUE
[1] "dimension of 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    11  39  95  45
  DEL PEAK 23(9P23) WILD-TYPE  12  54 101  74
D59V4, multiclass
    clus
vv   DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  T1                        11                          12
  T2                        39                          54
  T3                        95                         101
  T4                        45                          74
[1] 4 2
[1] TRUE
[1] "dimension of 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   49 55 42 41
  DEL PEAK 23(9P23) WILD-TYPE 81 64 44 47
D59V5, multiclass
    clus
vv   DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  N0                        49                          81
  N1                        55                          64
  N2                        42                          44
  N3                        41                          47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V6, binary
                             cls
clus                            0   1
  DEL PEAK 23(9P23) MUTATED   176  11
  DEL PEAK 23(9P23) WILD-TYPE 213  19
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 23(9P23) MUTATED    176   11
  DEL PEAK 23(9P23) WILD-TYPE  213   19
   clus
vv  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  0                       176                         213
  1                        11                          19
[1] 2 2
[1] FALSE
D59V7, binary
                             cls
clus                            0   1
  DEL PEAK 23(9P23) MUTATED    67 128
  DEL PEAK 23(9P23) WILD-TYPE  91 155
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 23(9P23) MUTATED     67  128
  DEL PEAK 23(9P23) WILD-TYPE   91  155
        clus
vv       DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  FEMALE                        67                          91
  MALE                         128                         155
[1] 2 2
[1] FALSE
D59V8, binary
                             cls
clus                            0   1
  DEL PEAK 23(9P23) MUTATED   142  36
  DEL PEAK 23(9P23) WILD-TYPE 180  40
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 23(9P23) MUTATED    142   36
  DEL PEAK 23(9P23) WILD-TYPE  180   40
     clus
vv    DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  NO                        142                         180
  YES                        36                          40
[1] 2 2
[1] FALSE
                             vv
clus                          STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 23(9P23) MUTATED                                          4
  DEL PEAK 23(9P23) WILD-TYPE                                        9
                             vv
clus                          STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 23(9P23) MUTATED                                      23
  DEL PEAK 23(9P23) WILD-TYPE                                    49
                             vv
clus                          STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 23(9P23) MUTATED                                                       69
  DEL PEAK 23(9P23) WILD-TYPE                                                     94
                             vv
clus                          STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 23(9P23) MUTATED                                                   9
  DEL PEAK 23(9P23) WILD-TYPE                                                12
                             vv
clus                          STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 23(9P23) MUTATED                                                                  43
  DEL PEAK 23(9P23) WILD-TYPE                                                                39
                             vv
clus                          STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 23(9P23) MUTATED                                                    3
  DEL PEAK 23(9P23) WILD-TYPE                                                  5
                             vv
clus                          STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 23(9P23) MUTATED                                                 43
  DEL PEAK 23(9P23) WILD-TYPE                                               36
D59V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 23(9P23) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                  4
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                    23
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                   69
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                         9
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        43
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                         43
                                                                   clus
vv                                                                  DEL PEAK 23(9P23) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    9
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                      49
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     94
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                          12
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          39
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           36
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 23(9P23) MUTATED   154   9   7   9
  DEL PEAK 23(9P23) WILD-TYPE 195   9  12  16
D59V10, multiclass
    clus
vv   DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  R0                       154                         195
  R1                         9                           9
  R2                         7                          12
  RX                         9                          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"
D59V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 23(9P23) MUTATED      33                         5
  DEL PEAK 23(9P23) WILD-TYPE    55                         7
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 23(9P23) MUTATED                                           1   127
  DEL PEAK 23(9P23) WILD-TYPE                                         0   151
D59V12, multiclass
                                           clus
vv                                          DEL PEAK 23(9P23) MUTATED
  ASIAN                                                            33
  BLACK OR AFRICAN AMERICAN                                         5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         1
  WHITE                                                           127
                                           clus
vv                                          DEL PEAK 23(9P23) WILD-TYPE
  ASIAN                                                              55
  BLACK OR AFRICAN AMERICAN                                           7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             151
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V13, binary
                             cls
clus                            0   1
  DEL PEAK 23(9P23) MUTATED     2 137
  DEL PEAK 23(9P23) WILD-TYPE   3 179
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 23(9P23) MUTATED      2  137
  DEL PEAK 23(9P23) WILD-TYPE    3  179
                        clus
vv                       DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  HISPANIC OR LATINO                             2                           3
  NOT HISPANIC OR LATINO                       137                         179
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 24(9P21.3) MUTATION ANALYSIS
D60V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 24(9P21.3) MUTATED   109  77
  DEL PEAK 24(9P21.3) WILD-TYPE 137  92
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                          186                           229 
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                           77                            92 
$`DEL PEAK 24(9P21.3) MUTATED`
TCGA-CG-4444 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-A5TI TCGA-B7-A5TJ 
       47.05        27.35        26.93        58.03        19.56        11.01 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-6456 
        9.44         6.61        18.35         4.08         9.67        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6709 TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7704 
       13.68        19.33        12.16        31.20         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8291 
       33.21        37.25        14.43        11.44         0.69        19.96 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       22.19        17.52        14.04         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       20.22        26.73        32.58         9.86        20.88         8.22 
TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 
       13.87        34.98         1.48         0.72         0.66        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5799 
       20.65        20.42         1.15        21.44        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.15        11.21        12.76        12.59        12.53         7.17 
TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-A486 TCGA-CD-A48A 
       12.39        11.64        15.39        12.07         6.31        12.43 
TCGA-CD-A48C TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       11.61         3.02        27.02        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4477 
       29.98        19.07        12.03        18.97        12.00        30.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 
       36.00         1.02         0.99        12.03        15.02         4.01 
TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       69.04        12.66        20.91        20.55        18.84        18.54 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 
       13.35        17.19        10.26        15.98        12.79        11.31 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A6EV 
       18.21        14.66        21.14        14.27        16.44        11.24 
TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C 
       11.31        22.29        19.96         7.99        72.23        11.38 
TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7133 TCGA-HU-8238 
       17.06        13.58         0.56         6.21        63.06         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-A4G3 TCGA-HU-A4GH TCGA-HU-A4GU 
        5.92        24.39        18.15         5.59        11.77         6.58 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RJ 
       23.80        21.17        33.40        36.36        18.81        12.46 
TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V 
       13.35         6.74        12.59         6.51        10.62        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J 
       13.51         2.53         5.56        63.62        37.64        36.95 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BT 
       14.04        45.67         8.52         6.08         9.24         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB 
        5.13        16.67        37.91       115.69         8.94         5.79 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       48.79        13.25        13.02        18.48        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH 
       37.41        37.22         7.73        46.26        22.19        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91N 
        2.70        17.85         1.87        64.57        14.33        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       20.81         1.71        42.64         9.50         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        9.04        21.04        42.54        11.24        18.41        43.66 
TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       38.93        54.12        27.55        12.43        17.26         0.79 

$`DEL PEAK 24(9P21.3) WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       21.99        22.98        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 
        9.86        26.70        11.70         9.47         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
        7.43        30.90         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6563 TCGA-BR-6564 
        6.61        34.68        15.95        13.87        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 
       40.21        30.90        44.94        21.90        36.16        35.84 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
        9.07        29.56        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.56        29.42         2.66         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 
        6.18        31.10        13.08         0.26         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
        4.31         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.05         3.72         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8690 
       28.14         6.28         7.53        24.79        31.96        10.68 
TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       34.13         7.53         6.08        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 
        8.98        14.17         0.53        28.34        32.52         0.46 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5804 TCGA-CD-8528 
       16.14         5.13        13.18        13.35        12.10        12.33 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 
       12.30        12.59        12.82        12.43        12.30        11.31 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4305 
        6.58        12.20        11.77        12.62        20.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
        1.02         7.99         8.05         0.00         9.01         7.07 
TCGA-CG-5717 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 
        6.97         6.02         0.99       105.07        28.96        65.10 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 
       21.07         7.99        25.71        19.13        18.61        17.85 
TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       15.22        12.36        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       17.19        20.91         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       26.43        11.44        20.32        15.65         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        7.13         0.62        14.47        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF TCGA-HF-7132 
       14.07        22.29        59.54         5.03         5.52        77.29 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       52.21        30.51        26.47        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       21.07         0.76        24.30        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8663 
       29.00        23.84        14.07        15.68         3.45         3.39 
TCGA-IN-A6RI TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NU TCGA-MX-A5UG TCGA-MX-A5UJ 
       18.38        19.53         6.44        11.70         3.72        19.73 
TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A8MV TCGA-RD-A8N0 
       18.21        74.53         4.60        11.05       122.30        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44        35.61        16.87        19.04 
TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
        0.92         5.46        38.14        30.97        34.29        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        2.50         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S 
       73.41        39.45        11.70        21.83        61.22        32.88 
TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
       60.85         2.01        55.43         4.54         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G 
       66.81         2.66        28.41        32.94        17.13        26.04 
TCGA-VQ-AA6I 
       16.14 

  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                         0.56                          0.00 
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                       115.69                        122.30 
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                        14.30                         15.65 
[1] "0.6 - 115.7 (14.3)" "0.0 - 122.3 (15.7)"
[1] "hr=" "1"  
D60V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 24(9P21.3) MUTATED         0       10       17       17        16
  DEL PEAK 24(9P21.3) WILD-TYPE       2        6       24       15        24
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 24(9P21.3) MUTATED          25         2         36         27
  DEL PEAK 24(9P21.3) WILD-TYPE        31         1         45         36
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 24(9P21.3) MUTATED           13       21
  DEL PEAK 24(9P21.3) WILD-TYPE         26       23
D60V3, multiclass
            clus
vv           DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                            10                             6
  STAGE IB                            17                            24
  STAGE II                            17                            15
  STAGE IIA                           16                            24
  STAGE IIB                           25                            31
  STAGE III                            2                             1
  STAGE IIIA                          36                            45
  STAGE IIIB                          27                            36
  STAGE IIIC                          13                            26
  STAGE IV                            21                            23
[1] 11  2
[1] TRUE
[1] "dimension of 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    11  44  91  43
  DEL PEAK 24(9P21.3) WILD-TYPE  12  49 105  76
D60V4, multiclass
    clus
vv   DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  T1                          11                            12
  T2                          44                            49
  T3                          91                           105
  T4                          43                            76
[1] 4 2
[1] TRUE
[1] "dimension of 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   55 54 43 35
  DEL PEAK 24(9P21.3) WILD-TYPE 75 65 43 53
D60V5, multiclass
    clus
vv   DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  N0                          55                            75
  N1                          54                            65
  N2                          43                            43
  N3                          35                            53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V6, binary
                               cls
clus                              0   1
  DEL PEAK 24(9P21.3) MUTATED   172  11
  DEL PEAK 24(9P21.3) WILD-TYPE 217  19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 24(9P21.3) MUTATED    172   11
  DEL PEAK 24(9P21.3) WILD-TYPE  217   19
   clus
vv  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  0                         172                           217
  1                          11                            19
[1] 2 2
[1] FALSE
D60V7, binary
                               cls
clus                              0   1
  DEL PEAK 24(9P21.3) MUTATED    67 126
  DEL PEAK 24(9P21.3) WILD-TYPE  91 157
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 24(9P21.3) MUTATED     67  126
  DEL PEAK 24(9P21.3) WILD-TYPE   91  157
        clus
vv       DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  FEMALE                          67                            91
  MALE                           126                           157
[1] 2 2
[1] FALSE
D60V8, binary
                               cls
clus                              0   1
  DEL PEAK 24(9P21.3) MUTATED   138  37
  DEL PEAK 24(9P21.3) WILD-TYPE 184  39
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 24(9P21.3) MUTATED    138   37
  DEL PEAK 24(9P21.3) WILD-TYPE  184   39
     clus
vv    DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  NO                          138                           184
  YES                          37                            39
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 24(9P21.3) MUTATED                                          5
  DEL PEAK 24(9P21.3) WILD-TYPE                                        8
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 24(9P21.3) MUTATED                                      19
  DEL PEAK 24(9P21.3) WILD-TYPE                                    53
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 24(9P21.3) MUTATED                                                       69
  DEL PEAK 24(9P21.3) WILD-TYPE                                                     94
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 24(9P21.3) MUTATED                                                   9
  DEL PEAK 24(9P21.3) WILD-TYPE                                                12
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 24(9P21.3) MUTATED                                                                  45
  DEL PEAK 24(9P21.3) WILD-TYPE                                                                37
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 24(9P21.3) MUTATED                                                    4
  DEL PEAK 24(9P21.3) WILD-TYPE                                                  4
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 24(9P21.3) MUTATED                                                 41
  DEL PEAK 24(9P21.3) WILD-TYPE                                               38
D60V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 24(9P21.3) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                      19
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     69
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           9
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          45
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           41
                                                                   clus
vv                                                                  DEL PEAK 24(9P21.3) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        53
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       94
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            12
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            37
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             38
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 24(9P21.3) MUTATED   155   8   8   6
  DEL PEAK 24(9P21.3) WILD-TYPE 194  10  11  19
D60V10, multiclass
    clus
vv   DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  R0                         155                           194
  R1                           8                            10
  R2                           8                            11
  RX                           6                            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"
D60V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 24(9P21.3) MUTATED      34                         7
  DEL PEAK 24(9P21.3) WILD-TYPE    54                         5
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 24(9P21.3) MUTATED                                           1   119
  DEL PEAK 24(9P21.3) WILD-TYPE                                         0   159
D60V12, multiclass
                                           clus
vv                                          DEL PEAK 24(9P21.3) MUTATED
  ASIAN                                                              34
  BLACK OR AFRICAN AMERICAN                                           7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             119
                                           clus
vv                                          DEL PEAK 24(9P21.3) WILD-TYPE
  ASIAN                                                                54
  BLACK OR AFRICAN AMERICAN                                             5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               159
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V13, binary
                               cls
clus                              0   1
  DEL PEAK 24(9P21.3) MUTATED     2 129
  DEL PEAK 24(9P21.3) WILD-TYPE   3 187
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 24(9P21.3) MUTATED      2  129
  DEL PEAK 24(9P21.3) WILD-TYPE    3  187
                        clus
vv                       DEL PEAK 24(9P21.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         129
                        clus
vv                       DEL PEAK 24(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           187
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 25(9Q21.11) MUTATION ANALYSIS
D61V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(9Q21.11) MUTATED    58  50
  DEL PEAK 25(9Q21.11) WILD-TYPE 188 119
  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                           108                            307 
  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                            50                            119 
$`DEL PEAK 25(9Q21.11) MUTATED`
TCGA-VQ-A94U TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4255 TCGA-BR-4257 
       26.93        11.01         9.44         6.61         4.08         9.67 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6803 TCGA-BR-7715 TCGA-BR-7716 
       17.29        13.68        19.33        31.20        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8058 TCGA-BR-8291 TCGA-BR-8364 
       18.15        28.73         3.45        37.25        19.96        22.19 
TCGA-BR-8365 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8682 TCGA-BR-8686 
       17.52         5.39        25.18         9.21        32.58        20.88 
TCGA-BR-8687 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PF 
        8.22        34.98         1.48         0.72        13.51         1.15 
TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 
       21.44        13.02        13.15        13.35        11.21        12.59 
TCGA-CD-8527 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48C 
        7.17        11.64        15.39         6.31        11.31        11.61 
TCGA-CD-A4MH TCGA-CG-4304 TCGA-CG-4438 TCGA-CG-4455 TCGA-CG-5724 TCGA-D7-6519 
       12.20        27.02        54.08        12.03        12.03        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-8575 
       18.84        18.54        13.35        10.26        15.98        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-8122 
       14.66        21.14        16.44        22.29        19.96         7.99 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-7133 
       72.23        11.38        17.06        13.58         0.56        63.06 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GU 
        5.92        18.15        28.96        25.81        11.77         6.58 
TCGA-HU-A4H0 TCGA-HU-A4H6 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RP TCGA-IN-A6RR 
        2.10        21.17        18.38        12.46         6.44         6.74 
TCGA-IN-A7NR TCGA-IN-AB1V TCGA-KB-A93H TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF 
        6.51        15.75        37.64        14.04        45.67         8.52 
TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DV 
        6.08        16.67        37.91         8.94         5.79        13.25 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       18.48        43.36        22.19        12.79         2.70        17.85 
TCGA-VQ-A8PS TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A94O 
       13.35        20.81        42.64         9.73         9.04        21.04 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       42.54        11.24        43.66        38.93        27.55         0.79 

$`DEL PEAK 25(9Q21.11) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
       20.15         9.86        27.35        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       19.56         9.47         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
       30.90         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       34.68        15.95        13.87        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       40.21        30.90        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       35.24        35.84        15.32         9.07        29.56        33.21 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56        29.42         2.66         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 
        7.40         6.18        31.10        13.08         0.26         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8486 TCGA-BR-8487 
       14.79         7.36        25.05         3.72        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44T 
       26.73        24.79        31.96         9.86        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       13.87         7.53         6.08        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.65        20.42        16.14         5.13        13.41 
TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 
       13.18        12.10        12.76        12.53        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 
       12.39        12.59        12.07        12.82        12.43        12.30 
TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       12.43         6.58        11.77        12.62        20.02         3.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         7.99         8.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       29.98        19.07         0.00         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99       105.07        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6528 
       20.91        19.13        18.61        17.85        17.19        15.22 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX 
       19.50        17.19        20.91        14.27         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 
       20.32        15.65         8.38         4.34         7.13         0.62 
TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       14.47        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 
       59.54         5.03         5.52         6.21        77.29        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 
       30.51        26.47         1.51        24.39        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       24.20         3.25        22.75        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 
        0.10         6.51        20.25         0.26        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS 
        3.45        18.81         3.39        13.35        19.53        12.59 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       10.62        11.70        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A804 
       36.95         3.72        19.73        18.21        74.53         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 
        9.24        11.05         8.61         5.13       122.30        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB 
      115.69       116.38        71.38        57.44        35.61        16.87 
TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E3 
       19.04         0.92        48.79         5.46        13.02        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       46.26        16.31         2.50         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        29.59        64.57        14.33        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U 
       11.70        21.83        61.22        18.74        32.88         1.71 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
       60.85         9.50        55.56         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-AA64 TCGA-VQ-AA69 
        6.58         5.72        66.81         2.66        18.41        28.41 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K 
       32.94        17.13        54.12        26.04        16.14        12.43 
TCGA-ZA-A8F6 
       17.26 

  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                          0.56                           0.00 
  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                         72.23                         122.30 
  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                         14.35                          15.02 
[1] "0.6 - 72.2 (14.3)"  "0.0 - 122.3 (15.0)"
[1] "hr=" "1.3"
D61V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 25(9Q21.11) MUTATED         1        4        6        9        14
  DEL PEAK 25(9Q21.11) WILD-TYPE       1       12       35       23        26
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 25(9Q21.11) MUTATED          15         1         20         14
  DEL PEAK 25(9Q21.11) WILD-TYPE        41         2         61         49
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 25(9Q21.11) MUTATED           13       10
  DEL PEAK 25(9Q21.11) WILD-TYPE         26       34
D61V3, multiclass
            clus
vv           DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                              4                             12
  STAGE IB                              6                             35
  STAGE II                              9                             23
  STAGE IIA                            14                             26
  STAGE IIB                            15                             41
  STAGE III                             1                              2
  STAGE IIIA                           20                             61
  STAGE IIIB                           14                             49
  STAGE IIIC                           13                             26
  STAGE IV                             10                             34
[1] 11  2
[1] TRUE
[1] "dimension of 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(9Q21.11) MUTATED     5  19  57  29
  DEL PEAK 25(9Q21.11) WILD-TYPE  18  74 139  90
D61V4, multiclass
    clus
vv   DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  T1                            5                             18
  T2                           19                             74
  T3                           57                            139
  T4                           29                             90
[1] 4 2
[1] TRUE
[1] "dimension of 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(9Q21.11) MUTATED   31 29 25 22
  DEL PEAK 25(9Q21.11) WILD-TYPE 99 90 61 66
D61V5, multiclass
    clus
vv   DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  N0                           31                             99
  N1                           29                             90
  N2                           25                             61
  N3                           22                             66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V6, binary
                                cls
clus                               0   1
  DEL PEAK 25(9Q21.11) MUTATED   102   5
  DEL PEAK 25(9Q21.11) WILD-TYPE 287  25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(9Q21.11) MUTATED    102    5
  DEL PEAK 25(9Q21.11) WILD-TYPE  287   25
   clus
vv  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  0                          102                            287
  1                            5                             25
[1] 2 2
[1] FALSE
D61V7, binary
                                cls
clus                               0   1
  DEL PEAK 25(9Q21.11) MUTATED    36  77
  DEL PEAK 25(9Q21.11) WILD-TYPE 122 206
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(9Q21.11) MUTATED     36   77
  DEL PEAK 25(9Q21.11) WILD-TYPE  122  206
        clus
vv       DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  FEMALE                           36                            122
  MALE                             77                            206
[1] 2 2
[1] FALSE
D61V8, binary
                                cls
clus                               0   1
  DEL PEAK 25(9Q21.11) MUTATED    86  19
  DEL PEAK 25(9Q21.11) WILD-TYPE 236  57
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(9Q21.11) MUTATED     86   19
  DEL PEAK 25(9Q21.11) WILD-TYPE  236   57
     clus
vv    DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  NO                            86                            236
  YES                           19                             57
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 25(9Q21.11) MUTATED                                          1
  DEL PEAK 25(9Q21.11) WILD-TYPE                                       12
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 25(9Q21.11) MUTATED                                      13
  DEL PEAK 25(9Q21.11) WILD-TYPE                                    59
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 25(9Q21.11) MUTATED                                                       46
  DEL PEAK 25(9Q21.11) WILD-TYPE                                                    117
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 25(9Q21.11) MUTATED                                                   5
  DEL PEAK 25(9Q21.11) WILD-TYPE                                                16
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 25(9Q21.11) MUTATED                                                                  19
  DEL PEAK 25(9Q21.11) WILD-TYPE                                                                63
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 25(9Q21.11) MUTATED                                                    3
  DEL PEAK 25(9Q21.11) WILD-TYPE                                                  5
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 25(9Q21.11) MUTATED                                                 26
  DEL PEAK 25(9Q21.11) WILD-TYPE                                               53
D61V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 25(9Q21.11) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       13
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      46
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           19
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            26
                                                                   clus
vv                                                                  DEL PEAK 25(9Q21.11) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      12
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         59
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       117
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             16
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              53
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 25(9Q21.11) MUTATED    87   4   3   5
  DEL PEAK 25(9Q21.11) WILD-TYPE 262  14  16  20
D61V10, multiclass
    clus
vv   DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  R0                           87                            262
  R1                            4                             14
  R2                            3                             16
  RX                            5                             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"
D61V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 25(9Q21.11) MUTATED      26                         6
  DEL PEAK 25(9Q21.11) WILD-TYPE    62                         6
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 25(9Q21.11) MUTATED                                           0
  DEL PEAK 25(9Q21.11) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 25(9Q21.11) MUTATED      70
  DEL PEAK 25(9Q21.11) WILD-TYPE   208
D61V12, multiclass
                                           clus
vv                                          DEL PEAK 25(9Q21.11) MUTATED
  ASIAN                                                               26
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               70
                                           clus
vv                                          DEL PEAK 25(9Q21.11) WILD-TYPE
  ASIAN                                                                 62
  BLACK OR AFRICAN AMERICAN                                              6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                208
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V13, binary
                                cls
clus                               0   1
  DEL PEAK 25(9Q21.11) MUTATED     1  86
  DEL PEAK 25(9Q21.11) WILD-TYPE   4 230
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(9Q21.11) MUTATED      1   86
  DEL PEAK 25(9Q21.11) WILD-TYPE    4  230
                        clus
vv                       DEL PEAK 25(9Q21.11) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           86
                        clus
vv                       DEL PEAK 25(9Q21.11) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            230
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 26(10P15.3) MUTATION ANALYSIS
D62V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(10P15.3) MUTATED    36  37
  DEL PEAK 26(10P15.3) WILD-TYPE 210 132
  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE 
                            73                            342 
  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE 
                            37                            132 
$`DEL PEAK 26(10P15.3) MUTATED`
TCGA-CG-4475 TCGA-FP-A8CX TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-BR-4191 TCGA-BR-4255 
       22.98         0.23        19.56        11.01        18.35         4.08 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-7901 TCGA-BR-8059 
        9.67         6.18        19.33        26.10         3.45        14.43 
TCGA-BR-8060 TCGA-BR-8291 TCGA-BR-8365 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8683 
       11.44        19.96        17.52        20.22        24.79         9.86 
TCGA-BR-A452 TCGA-BR-A4IY TCGA-BR-A4J7 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 
        7.53        12.89        32.52        12.59         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8533 TCGA-CD-A487 TCGA-CG-4301 TCGA-CG-4441 TCGA-CG-4455 
       12.30        15.39        12.30         3.02        14.01        12.03 
TCGA-CG-5732 TCGA-D7-6521 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-8570 
       69.04        18.54        15.22        15.98        11.31        24.72 
TCGA-D7-8575 TCGA-D7-A4YT TCGA-D7-A6EV TCGA-EQ-8122 TCGA-FP-7829 TCGA-FP-8631 
       18.21        14.27        11.24         7.99        19.53         0.56 
TCGA-FP-A4BF TCGA-HF-7133 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-A4GU TCGA-IN-8462 
        5.52        63.06         5.92        28.96         6.58        18.81 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-R5-A7ZF TCGA-R5-A805 TCGA-RD-A8N1 TCGA-RD-A8N6 
        6.44         6.74         8.52         9.24       115.69         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
        5.79         0.92        48.79        13.02        18.48        43.36 
TCGA-VQ-A8P3 TCGA-VQ-A8PS TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A922 TCGA-VQ-A925 
       37.22        13.35        18.74        20.81         9.04         4.54 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6I 
        5.72        66.81        11.24        18.41        43.66        16.14 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK 26(10P15.3) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 
       47.05        21.99        79.07        16.24        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK 
       27.35        26.93        58.03        26.70        11.70         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
        9.44         6.61         6.97         4.64         7.43        30.90 
TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        4.08         9.34         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 
       13.87        17.29        13.68        39.12         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 
       28.73         9.07        29.56        33.21        37.25         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66         2.20        15.58         7.40         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       13.08         0.26        22.19         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 
       25.05         3.72         5.39        25.18         9.21         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       26.73        31.96        32.58        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       34.13        13.87         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 
       13.18        13.35        11.21        12.10        12.76        12.53 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.39        12.59        11.64        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        6.31        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        12.62        20.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 
        7.99         8.05        54.08         4.01        29.98        19.07 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       20.55        18.84        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 
       10.26        12.79        12.36        12.33        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV 
       17.19        14.66        21.14        20.91        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY 
       36.43        13.78        14.76        26.43        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        3.48        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
       13.58         6.21        77.29        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        1.51        24.39        18.15        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI 
       15.68        33.40        36.36         3.45         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       12.46        13.35        19.53        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       37.64        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT 
       18.21        74.53         6.08         4.60        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 
        5.13        16.67       122.30        37.91        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DU 
       71.38        57.44        35.61        16.87        19.04         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       13.25        21.73        37.41        38.14         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH 
       34.29        46.26        16.31        22.19         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.70        17.85         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       29.59        64.57        14.33        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       21.83        61.22        32.88         1.71        42.64        60.85 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
        9.50         9.73        55.56         2.01        55.43         6.58 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       21.04         2.66        42.54        28.41        38.93        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       17.13        54.12        26.04        27.55        12.43        17.26 

  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE 
                          0.23                           0.00 
  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE 
                        115.69                         122.30 
  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE 
                         13.02                          15.65 
[1] "0.2 - 115.7 (13.0)" "0.0 - 122.3 (15.7)"
[1] "hr=" "1.5"
D62V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 26(10P15.3) MUTATED         0        2        4        3         2
  DEL PEAK 26(10P15.3) WILD-TYPE       2       14       37       29        38
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 26(10P15.3) MUTATED          16         1         18          9
  DEL PEAK 26(10P15.3) WILD-TYPE        40         2         63         54
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 26(10P15.3) MUTATED            7       10
  DEL PEAK 26(10P15.3) WILD-TYPE         32       34
D62V3, multiclass
            clus
vv           DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              2                             14
  STAGE IB                              4                             37
  STAGE II                              3                             29
  STAGE IIA                             2                             38
  STAGE IIB                            16                             40
  STAGE III                             1                              2
  STAGE IIIA                           18                             63
  STAGE IIIB                            9                             54
  STAGE IIIC                            7                             32
  STAGE IV                             10                             34
[1] 11  2
[1] TRUE
[1] "dimension of 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(10P15.3) MUTATED     3  17  33  20
  DEL PEAK 26(10P15.3) WILD-TYPE  20  76 163  99
D62V4, multiclass
    clus
vv   DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE
  T1                            3                             20
  T2                           17                             76
  T3                           33                            163
  T4                           20                             99
[1] 4 2
[1] TRUE
[1] "dimension of 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(10P15.3) MUTATED    12  23  20  17
  DEL PEAK 26(10P15.3) WILD-TYPE 118  96  66  71
D62V5, multiclass
    clus
vv   DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE
  N0                           12                            118
  N1                           23                             96
  N2                           20                             66
  N3                           17                             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V6, binary
                                cls
clus                               0   1
  DEL PEAK 26(10P15.3) MUTATED    69   4
  DEL PEAK 26(10P15.3) WILD-TYPE 320  26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10P15.3) MUTATED     69    4
  DEL PEAK 26(10P15.3) WILD-TYPE  320   26
   clus
vv  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE
  0                           69                            320
  1                            4                             26
[1] 2 2
[1] FALSE
D62V7, binary
                                cls
clus                               0   1
  DEL PEAK 26(10P15.3) MUTATED    23  54
  DEL PEAK 26(10P15.3) WILD-TYPE 135 229
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10P15.3) MUTATED     23   54
  DEL PEAK 26(10P15.3) WILD-TYPE  135  229
        clus
vv       DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE
  FEMALE                           23                            135
  MALE                             54                            229
[1] 2 2
[1] FALSE
D62V8, binary
                                cls
clus                               0   1
  DEL PEAK 26(10P15.3) MUTATED    54  16
  DEL PEAK 26(10P15.3) WILD-TYPE 268  60
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10P15.3) MUTATED     54   16
  DEL PEAK 26(10P15.3) WILD-TYPE  268   60
     clus
vv    DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE
  NO                            54                            268
  YES                           16                             60
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 26(10P15.3) MUTATED                                          3
  DEL PEAK 26(10P15.3) WILD-TYPE                                       10
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 26(10P15.3) MUTATED                                       8
  DEL PEAK 26(10P15.3) WILD-TYPE                                    64
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 26(10P15.3) MUTATED                                                       22
  DEL PEAK 26(10P15.3) WILD-TYPE                                                    141
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 26(10P15.3) MUTATED                                                   7
  DEL PEAK 26(10P15.3) WILD-TYPE                                                14
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 26(10P15.3) MUTATED                                                                  14
  DEL PEAK 26(10P15.3) WILD-TYPE                                                                68
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 26(10P15.3) MUTATED                                                    1
  DEL PEAK 26(10P15.3) WILD-TYPE                                                  7
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 26(10P15.3) MUTATED                                                 21
  DEL PEAK 26(10P15.3) WILD-TYPE                                               58
D62V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 26(10P15.3) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        8
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      22
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            7
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           14
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            21
                                                                   clus
vv                                                                  DEL PEAK 26(10P15.3) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       141
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             14
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 26(10P15.3) MUTATED    60   3   3   6
  DEL PEAK 26(10P15.3) WILD-TYPE 289  15  16  19
D62V10, multiclass
    clus
vv   DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE
  R0                           60                            289
  R1                            3                             15
  R2                            3                             16
  RX                            6                             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"
D62V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 26(10P15.3) MUTATED      15                         3
  DEL PEAK 26(10P15.3) WILD-TYPE    73                         9
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 26(10P15.3) MUTATED                                           0
  DEL PEAK 26(10P15.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 26(10P15.3) MUTATED      48
  DEL PEAK 26(10P15.3) WILD-TYPE   230
D62V12, multiclass
                                           clus
vv                                          DEL PEAK 26(10P15.3) MUTATED
  ASIAN                                                               15
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               48
                                           clus
vv                                          DEL PEAK 26(10P15.3) WILD-TYPE
  ASIAN                                                                 73
  BLACK OR AFRICAN AMERICAN                                              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V13, binary
                                cls
clus                               0   1
  DEL PEAK 26(10P15.3) MUTATED     0  54
  DEL PEAK 26(10P15.3) WILD-TYPE   5 262
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10P15.3) MUTATED      0   54
  DEL PEAK 26(10P15.3) WILD-TYPE    5  262
                        clus
vv                       DEL PEAK 26(10P15.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           54
                        clus
vv                       DEL PEAK 26(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            262
[1] 2 2
[1] FALSE

Clustering(63) Variable = DEL PEAK 27(10Q22.3) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(10Q22.3) MUTATED    39  35
  DEL PEAK 27(10Q22.3) WILD-TYPE 207 134
  DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE 
                            74                            341 
  DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE 
                            35                            134 
$`DEL PEAK 27(10Q22.3) MUTATED`
TCGA-CG-4475 TCGA-FP-A8CX TCGA-3M-AB46 TCGA-BR-4257 TCGA-BR-7716 TCGA-BR-7723 
       22.98         0.23        58.03         9.67        39.78        28.73 
TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8291 TCGA-BR-8365 TCGA-BR-8483 TCGA-BR-8486 
        3.45        11.44        19.96        17.52         5.39        20.22 
TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-8526 
       13.87        34.98        21.44        13.02        13.35        12.53 
TCGA-CD-8528 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4436 
       12.33         6.31        12.43         6.58        12.20         7.99 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-5718 TCGA-CG-5730 
        4.01        14.01        12.03        18.97        36.00         4.01 
TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       19.13        18.54        10.26        15.22        15.98        12.79 
TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YX TCGA-EQ-8122 TCGA-FP-7829 TCGA-FP-A4BF 
       21.14        14.27        36.43         7.99        19.53         5.52 
TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G6 TCGA-HU-A4GH TCGA-IN-8462 
        5.92        28.96        22.82        24.26        11.77        18.81 
TCGA-IN-A6RR TCGA-IN-A7NR TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZR 
        6.74         6.51        37.64        45.67         8.52         6.08 
TCGA-R5-A805 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ 
        9.24         8.94         5.79        48.79         5.46        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A91N TCGA-VQ-A91U 
       18.48        22.19        17.85         1.87        18.74         1.71 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94T TCGA-VQ-AA68 
        9.50         9.73        66.81        21.04        11.24        43.66 
TCGA-VQ-AA6A TCGA-ZQ-A9CR 
       38.93         0.79 

$`DEL PEAK 27(10Q22.3) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 
       47.05        21.99        79.07        16.24        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       27.35        26.93        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 
       18.35        30.90         4.08         4.08         9.34         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7957 
       35.24        35.84        33.63        18.15        15.32         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       29.56        33.21        37.25        14.43         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        2.20        15.58         7.40         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
        0.26        22.19         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        3.72        25.18         9.21         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       34.13         7.53         6.08         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.66        32.52        13.51         0.46        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 
        1.15        16.14         5.13        13.41        13.15        13.18 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8529 
       11.21        12.10        12.76        12.59         7.17        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        12.30        11.31        11.61        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         1.02         8.05 
TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
       54.08        29.98        19.07         0.00         9.01         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       12.00        30.97         6.97         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       20.55        18.84        18.61        17.85        13.35        17.19 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV 
       17.19        18.21        14.66        20.91        16.44         5.92 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        3.48        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       13.58         0.56         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       30.51        26.47         1.51        24.39        18.15        22.32 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI 
       15.68        33.40        36.36         3.45         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NT 
       12.46        13.35        19.53         6.44        12.59        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZI 
       36.95         3.72        19.73        14.04        18.21        74.53 
TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        4.60        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8E2 
       35.61        16.87        19.04         0.92        13.25        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        37.41        38.14        37.22         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       34.29        46.26        16.31         2.50        12.79         2.70 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A922 
       20.81        32.88        42.64        60.85        55.56         9.04 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P 
        2.01        55.43         4.54         6.58         5.72         2.66 
TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       42.54        18.41        28.41        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE 
                          0.23                           0.00 
  DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE 
                         66.81                         122.30 
  DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE 
                        13.185                         15.580 
[1] "0.2 - 66.8 (13.2)"  "0.0 - 122.3 (15.6)"
[1] "hr=" "1.4"
D63V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 27(10Q22.3) MUTATED         0        4        6        5         7
  DEL PEAK 27(10Q22.3) WILD-TYPE       2       12       35       27        33
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 27(10Q22.3) MUTATED          11         1         16          8
  DEL PEAK 27(10Q22.3) WILD-TYPE        45         2         65         55
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 27(10Q22.3) MUTATED            8        8
  DEL PEAK 27(10Q22.3) WILD-TYPE         31       36
D63V3, multiclass
            clus
vv           DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              4                             12
  STAGE IB                              6                             35
  STAGE II                              5                             27
  STAGE IIA                             7                             33
  STAGE IIB                            11                             45
  STAGE III                             1                              2
  STAGE IIIA                           16                             65
  STAGE IIIB                            8                             55
  STAGE IIIC                            8                             31
  STAGE IV                              8                             36
[1] 11  2
[1] TRUE
[1] "dimension of 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(10Q22.3) MUTATED     4  20  37  14
  DEL PEAK 27(10Q22.3) WILD-TYPE  19  73 159 105
D63V4, multiclass
    clus
vv   DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE
  T1                            4                             19
  T2                           20                             73
  T3                           37                            159
  T4                           14                            105
[1] 4 2
[1] TRUE
[1] "dimension of 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(10Q22.3) MUTATED    19  21  14  21
  DEL PEAK 27(10Q22.3) WILD-TYPE 111  98  72  67
D63V5, multiclass
    clus
vv   DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE
  N0                           19                            111
  N1                           21                             98
  N2                           14                             72
  N3                           21                             67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V6, binary
                                cls
clus                               0   1
  DEL PEAK 27(10Q22.3) MUTATED    69   6
  DEL PEAK 27(10Q22.3) WILD-TYPE 320  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10Q22.3) MUTATED     69    6
  DEL PEAK 27(10Q22.3) WILD-TYPE  320   24
   clus
vv  DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE
  0                           69                            320
  1                            6                             24
[1] 2 2
[1] FALSE
D63V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(10Q22.3) MUTATED    26  53
  DEL PEAK 27(10Q22.3) WILD-TYPE 132 230
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10Q22.3) MUTATED     26   53
  DEL PEAK 27(10Q22.3) WILD-TYPE  132  230
        clus
vv       DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE
  FEMALE                           26                            132
  MALE                             53                            230
[1] 2 2
[1] FALSE
D63V8, binary
                                cls
clus                               0   1
  DEL PEAK 27(10Q22.3) MUTATED    57  14
  DEL PEAK 27(10Q22.3) WILD-TYPE 265  62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10Q22.3) MUTATED     57   14
  DEL PEAK 27(10Q22.3) WILD-TYPE  265   62
     clus
vv    DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE
  NO                            57                            265
  YES                           14                             62
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 27(10Q22.3) MUTATED                                          4
  DEL PEAK 27(10Q22.3) WILD-TYPE                                        9
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 27(10Q22.3) MUTATED                                       5
  DEL PEAK 27(10Q22.3) WILD-TYPE                                    67
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 27(10Q22.3) MUTATED                                                       26
  DEL PEAK 27(10Q22.3) WILD-TYPE                                                    137
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 27(10Q22.3) MUTATED                                                   3
  DEL PEAK 27(10Q22.3) WILD-TYPE                                                18
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 27(10Q22.3) MUTATED                                                                  19
  DEL PEAK 27(10Q22.3) WILD-TYPE                                                                63
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 27(10Q22.3) MUTATED                                                    2
  DEL PEAK 27(10Q22.3) WILD-TYPE                                                  6
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 27(10Q22.3) MUTATED                                                 19
  DEL PEAK 27(10Q22.3) WILD-TYPE                                               60
D63V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 27(10Q22.3) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     4
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      26
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           19
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            19
                                                                   clus
vv                                                                  DEL PEAK 27(10Q22.3) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                       9
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       137
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 27(10Q22.3) MUTATED    57   2   4   4
  DEL PEAK 27(10Q22.3) WILD-TYPE 292  16  15  21
D63V10, multiclass
    clus
vv   DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE
  R0                           57                            292
  R1                            2                             16
  R2                            4                             15
  RX                            4                             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"
D63V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 27(10Q22.3) MUTATED      16                         5
  DEL PEAK 27(10Q22.3) WILD-TYPE    72                         7
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 27(10Q22.3) MUTATED                                           0
  DEL PEAK 27(10Q22.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 27(10Q22.3) MUTATED      47
  DEL PEAK 27(10Q22.3) WILD-TYPE   231
D63V12, multiclass
                                           clus
vv                                          DEL PEAK 27(10Q22.3) MUTATED
  ASIAN                                                               16
  BLACK OR AFRICAN AMERICAN                                            5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               47
                                           clus
vv                                          DEL PEAK 27(10Q22.3) WILD-TYPE
  ASIAN                                                                 72
  BLACK OR AFRICAN AMERICAN                                              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V13, binary
                                cls
clus                               0   1
  DEL PEAK 27(10Q22.3) MUTATED     2  52
  DEL PEAK 27(10Q22.3) WILD-TYPE   3 264
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10Q22.3) MUTATED      2   52
  DEL PEAK 27(10Q22.3) WILD-TYPE    3  264
                        clus
vv                       DEL PEAK 27(10Q22.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           52
                        clus
vv                       DEL PEAK 27(10Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            264
[1] 2 2
[1] FALSE

Clustering(64) Variable = DEL PEAK 28(10Q23.31) MUTATION ANALYSIS
D64V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 28(10Q23.31) MUTATED    59  52
  DEL PEAK 28(10Q23.31) WILD-TYPE 187 117
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                            111                             304 
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                             52                             117 
$`DEL PEAK 28(10Q23.31) MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-FP-A8CX TCGA-3M-AB46 TCGA-B7-5818 TCGA-BR-4183 
       47.05        21.99         0.23        58.03        11.70         6.61 
TCGA-BR-4191 TCGA-BR-4257 TCGA-BR-6455 TCGA-BR-7704 TCGA-BR-7716 TCGA-BR-7723 
       18.35         9.67        13.87        35.24        39.78        28.73 
TCGA-BR-7901 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8365 
        3.45        37.25        11.44        19.96         2.20        17.52 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        4.31        14.04         5.39        25.18         9.21        20.22 
TCGA-BR-8683 TCGA-BR-A4CQ TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-8524 
        9.86        34.98        21.44        13.02        13.35        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A4MH 
       12.59        12.53        12.33         6.31        12.43        12.20 
TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 
       27.02         7.99         4.01        14.01        29.98        12.03 
TCGA-CG-4466 TCGA-CG-5718 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5577 
       18.97        36.00        15.02         4.01        69.04        25.71 
TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       19.13        18.54        10.26        15.22        15.98        12.79 
TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-FP-7735 TCGA-FP-7829 
       21.14        14.27        22.29         7.99         3.48        19.53 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8604 
       13.58         0.56         5.52         5.92        28.96        22.82 
TCGA-HU-A4GH TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-8462 
       11.77         6.51         6.58        23.80        33.40        18.81 
TCGA-IN-A6RI TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NU TCGA-KB-A93H 
       18.38         6.44         6.74         6.51        11.70        37.64 
TCGA-KB-A93J TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A8N6 
       36.95        45.67         8.52         6.08         9.24         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        5.79         0.92        48.79         5.46        13.02        18.48 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A91A TCGA-VQ-A91N 
       22.19        17.85         1.87        13.35        39.45        18.74 
TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A928 TCGA-VQ-A92D 
        1.71         9.50         9.73         9.04         5.72        66.81 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A 
       21.04        42.54        11.24        18.41        43.66        38.93 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-ZQ-A9CR 
       26.04        16.14         0.79 

$`DEL PEAK 28(10Q23.31) WILD-TYPE`
TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU 
       22.98        79.07        16.24        20.15         9.86        27.35 
TCGA-VQ-A94U TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.93        26.70        19.56        11.01         9.47         9.44 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.34         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7957 
       36.16        35.84        33.63        18.15        15.32         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       29.56        33.21        14.43         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 
       32.25         8.05         0.56        29.42         2.66        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        0.95        26.33         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        7.36        25.05         3.72         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       31.96        32.58        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       13.87         7.53         6.08         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.66        32.52        13.51         0.46        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 
        1.15        16.14         5.13        13.41        13.15        13.18 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       11.21        12.10         7.17        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 
       11.64        15.39        12.07        12.82        12.43        12.30 
TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.31        11.61         6.58        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4449 
        3.02        15.95         1.02         8.05        54.08        19.07 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01         7.07        12.00        30.97         6.97 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 
       28.96        65.10        21.07         7.99        12.66        20.91 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       20.55        18.84        18.61        17.85        13.35        17.19 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV 
       17.19        18.21        14.66        20.91        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.44        20.32        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62        14.47        72.23        21.27        11.38 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A9TM 
       14.07        22.29        17.06        59.54         5.03         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        18.15        22.32        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX 
       25.81        21.37        29.98         8.98         0.10        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
        0.26         2.10        12.95        29.00        23.84        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ 
       14.07        15.68        36.36         3.45         3.39        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X 
       13.35        19.53        12.59        10.62        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        2.53         5.56        63.62         3.72        19.73        14.04 
TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
       18.21        74.53         4.60        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DV 
       71.38        57.44        35.61        16.87        19.04        13.25 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       43.36        21.73        37.41        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH 
       30.97        34.29        46.26        16.31         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX 
        2.70         9.27        23.41        15.65        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q 
       14.33        73.41        11.70        21.83        61.22        20.81 
TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 
       32.88        42.64        60.85        55.56         2.01        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A94P TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D 
        4.54         6.58         2.66        28.41        32.94        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        27.55        12.43        17.26 

  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                           0.23                            0.00 
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                          69.04                          122.30 
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                          13.58                           15.65 
[1] "0.2 - 69.0 (13.6)"  "0.0 - 122.3 (15.7)"
[1] "hr=" "1.3"
D64V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 28(10Q23.31) MUTATED         1        4       13        8         9
  DEL PEAK 28(10Q23.31) WILD-TYPE       1       12       28       24        31
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 28(10Q23.31) MUTATED          13         1         24         14
  DEL PEAK 28(10Q23.31) WILD-TYPE        43         2         57         49
                                 vv
clus                              STAGE IIIC STAGE IV
  DEL PEAK 28(10Q23.31) MUTATED           10       12
  DEL PEAK 28(10Q23.31) WILD-TYPE         29       32
D64V3, multiclass
            clus
vv           DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  STAGE I                                1                               1
  STAGE IA                               4                              12
  STAGE IB                              13                              28
  STAGE II                               8                              24
  STAGE IIA                              9                              31
  STAGE IIB                             13                              43
  STAGE III                              1                               2
  STAGE IIIA                            24                              57
  STAGE IIIB                            14                              49
  STAGE IIIC                            10                              29
  STAGE IV                              12                              32
[1] 11  2
[1] TRUE
[1] "dimension of 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     6  31  52  22
  DEL PEAK 28(10Q23.31) WILD-TYPE  17  62 144  97
D64V4, multiclass
    clus
vv   DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  T1                             6                              17
  T2                            31                              62
  T3                            52                             144
  T4                            22                              97
[1] 4 2
[1] TRUE
[1] "dimension of 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   32 30 21 29
  DEL PEAK 28(10Q23.31) WILD-TYPE 98 89 65 59
D64V5, multiclass
    clus
vv   DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  N0                            32                              98
  N1                            30                              89
  N2                            21                              65
  N3                            29                              59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V6, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10Q23.31) MUTATED   102   7
  DEL PEAK 28(10Q23.31) WILD-TYPE 287  23
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10Q23.31) MUTATED    102    7
  DEL PEAK 28(10Q23.31) WILD-TYPE  287   23
   clus
vv  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  0                           102                             287
  1                             7                              23
[1] 2 2
[1] FALSE
D64V7, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10Q23.31) MUTATED    40  76
  DEL PEAK 28(10Q23.31) WILD-TYPE 118 207
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10Q23.31) MUTATED     40   76
  DEL PEAK 28(10Q23.31) WILD-TYPE  118  207
        clus
vv       DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  FEMALE                            40                             118
  MALE                              76                             207
[1] 2 2
[1] FALSE
D64V8, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10Q23.31) MUTATED    83  22
  DEL PEAK 28(10Q23.31) WILD-TYPE 239  54
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10Q23.31) MUTATED     83   22
  DEL PEAK 28(10Q23.31) WILD-TYPE  239   54
     clus
vv    DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  NO                             83                             239
  YES                            22                              54
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 28(10Q23.31) MUTATED                                          4
  DEL PEAK 28(10Q23.31) WILD-TYPE                                        9
                                 vv
clus                              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 28(10Q23.31) MUTATED                                       8
  DEL PEAK 28(10Q23.31) WILD-TYPE                                    64
                                 vv
clus                              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 28(10Q23.31) MUTATED                                                       40
  DEL PEAK 28(10Q23.31) WILD-TYPE                                                    123
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 28(10Q23.31) MUTATED                                                   5
  DEL PEAK 28(10Q23.31) WILD-TYPE                                                16
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 28(10Q23.31) MUTATED                                                                  31
  DEL PEAK 28(10Q23.31) WILD-TYPE                                                                51
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 28(10Q23.31) MUTATED                                                    3
  DEL PEAK 28(10Q23.31) WILD-TYPE                                                  5
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 28(10Q23.31) MUTATED                                                 25
  DEL PEAK 28(10Q23.31) WILD-TYPE                                               54
D64V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 28(10Q23.31) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      4
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         8
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       40
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            31
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             25
                                                                   clus
vv                                                                  DEL PEAK 28(10Q23.31) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                        9
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                          64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                        123
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                              16
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                              51
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                               54
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 28(10Q23.31) MUTATED    91   3   5   6
  DEL PEAK 28(10Q23.31) WILD-TYPE 258  15  14  19
D64V10, multiclass
    clus
vv   DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  R0                            91                             258
  R1                             3                              15
  R2                             5                              14
  RX                             6                              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"
D64V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 28(10Q23.31) MUTATED      21                         6
  DEL PEAK 28(10Q23.31) WILD-TYPE    67                         6
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 28(10Q23.31) MUTATED                                           0
  DEL PEAK 28(10Q23.31) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 28(10Q23.31) MUTATED      72
  DEL PEAK 28(10Q23.31) WILD-TYPE   206
D64V12, multiclass
                                           clus
vv                                          DEL PEAK 28(10Q23.31) MUTATED
  ASIAN                                                                21
  BLACK OR AFRICAN AMERICAN                                             6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                72
                                           clus
vv                                          DEL PEAK 28(10Q23.31) WILD-TYPE
  ASIAN                                                                  67
  BLACK OR AFRICAN AMERICAN                                               6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 206
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V13, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10Q23.31) MUTATED     2  74
  DEL PEAK 28(10Q23.31) WILD-TYPE   3 242
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10Q23.31) MUTATED      2   74
  DEL PEAK 28(10Q23.31) WILD-TYPE    3  242
                        clus
vv                       DEL PEAK 28(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            74
                        clus
vv                       DEL PEAK 28(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             242
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK 29(11P15.5) MUTATION ANALYSIS
D65V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(11P15.5) MUTATED    51  43
  DEL PEAK 29(11P15.5) WILD-TYPE 195 126
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                            94                            321 
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                            43                            126 
$`DEL PEAK 29(11P15.5) MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-BR-4183 TCGA-BR-4184 
       47.05        21.99        27.35        26.93         6.61         6.97 
TCGA-BR-4191 TCGA-BR-4255 TCGA-BR-4279 TCGA-BR-6564 TCGA-BR-7703 TCGA-BR-7704 
       18.35         4.08         9.57        26.10        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-8080 TCGA-BR-8297 TCGA-BR-8369 
       33.63        39.78        28.73         9.60         7.40        14.04 
TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
        1.48         0.72         0.53        13.02        13.15        13.35 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-A48A TCGA-CG-4304 TCGA-CG-4443 
       12.76        12.59         7.17        12.43        27.02        29.98 
TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-5717 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 
       19.07        18.97         6.97        12.03        15.02         4.01 
TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       69.04        12.66        20.91        20.55        18.84        18.54 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A74A 
       10.26        15.22        15.98        21.14        14.27        19.96 
TCGA-EQ-5647 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-8211 TCGA-HF-7133 TCGA-HJ-7597 
        0.62        72.23        11.38        13.58        63.06        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-A4GD TCGA-HU-A4H0 TCGA-HU-A4H5 TCGA-IN-8462 
        5.92        18.15        22.75         2.10        23.80        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
        3.39        18.38        13.35        19.53         6.44         6.74 
TCGA-IP-7968 TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-RD-A7C1 TCGA-RD-A8MW 
        2.53        37.64        45.67        18.21        16.67        37.91 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        8.94        35.61        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       18.48        37.41        37.22         7.73        22.19        17.85 
TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A925 
       13.35        14.33        21.83         9.73        55.56         4.54 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA68 
       21.04        42.54        18.41        43.66 

$`DEL PEAK 29(11P15.5) WILD-TYPE`
TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       22.98        79.07        16.24         0.23        20.15         9.86 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       58.03        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 
        9.44         4.64         7.43        30.90         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 
       17.29        13.68        19.33        39.12         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 
       30.90        31.20        44.94        21.90         9.21        35.84 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       18.15        15.32         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 
       37.25        14.43        11.44         0.69        29.59        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
       15.58         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33         4.31         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU 
       34.13        13.87         7.53         6.08        34.98        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 
       28.57        12.89         8.98        14.17        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       32.52        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5803 
       21.44        16.14         5.13        13.41        13.18        11.21 
TCGA-CD-5804 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.10        12.53        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4462 
        8.05        54.08         4.01        14.01        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 
        9.01         7.07        12.00        30.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 
        0.99         6.02         0.99       105.07        28.96        65.10 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 
       21.07         7.99        25.71        19.13        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       13.35        17.19        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 
       15.65         8.38         4.34         7.13         7.99        14.47 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       59.54         5.03         0.56         5.52         6.21        77.29 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       52.21        30.51         1.51        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       22.68        24.20         3.25        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        0.26        12.95        29.00        23.84        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RJ TCGA-IN-A6RS 
       15.68        33.40        36.36         3.45        12.46        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 
        6.51        10.62        11.70        15.75        13.51         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZF 
       63.62        36.95         3.72        19.73        14.04         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
        5.13       122.30        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8E2 
       57.44        16.87        19.04         5.79         0.92        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       21.73        38.14        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
        2.50        12.79         2.70         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       15.65        29.59        64.57        73.41        39.45        11.70 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       61.22        18.74        20.81        32.88         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
       60.85         9.50         9.04         2.01        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA69 TCGA-VQ-AA6A 
        5.72        66.81         2.66        11.24        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       32.94        17.13        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        17.26         0.79 

  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                          0.53                           0.00 
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                         72.23                         122.30 
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                         18.00                          14.17 
[1] "0.5 - 72.2 (18.0)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D65V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 29(11P15.5) MUTATED         1        3        9       11         6
  DEL PEAK 29(11P15.5) WILD-TYPE       1       13       32       21        34
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 29(11P15.5) MUTATED           8         0         23         11
  DEL PEAK 29(11P15.5) WILD-TYPE        48         3         58         52
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 29(11P15.5) MUTATED            9        9
  DEL PEAK 29(11P15.5) WILD-TYPE         30       35
D65V3, multiclass
            clus
vv           DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                              3                             13
  STAGE IB                              9                             32
  STAGE II                             11                             21
  STAGE IIA                             6                             34
  STAGE IIB                             8                             48
  STAGE III                             0                              3
  STAGE IIIA                           23                             58
  STAGE IIIB                           11                             52
  STAGE IIIC                            9                             30
  STAGE IV                              9                             35
[1] 11  2
[1] TRUE
[1] "dimension of 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     5  31  40  18
  DEL PEAK 29(11P15.5) WILD-TYPE  18  62 156 101
D65V4, multiclass
    clus
vv   DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  T1                            5                             18
  T2                           31                             62
  T3                           40                            156
  T4                           18                            101
[1] 4 2
[1] TRUE
[1] "dimension of 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    24  30  21  20
  DEL PEAK 29(11P15.5) WILD-TYPE 106  89  65  68
D65V5, multiclass
    clus
vv   DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  N0                           24                            106
  N1                           30                             89
  N2                           21                             65
  N3                           20                             68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V6, binary
                                cls
clus                               0   1
  DEL PEAK 29(11P15.5) MUTATED    86   7
  DEL PEAK 29(11P15.5) WILD-TYPE 303  23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(11P15.5) MUTATED     86    7
  DEL PEAK 29(11P15.5) WILD-TYPE  303   23
   clus
vv  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  0                           86                            303
  1                            7                             23
[1] 2 2
[1] FALSE
D65V7, binary
                                cls
clus                               0   1
  DEL PEAK 29(11P15.5) MUTATED    31  66
  DEL PEAK 29(11P15.5) WILD-TYPE 127 217
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(11P15.5) MUTATED     31   66
  DEL PEAK 29(11P15.5) WILD-TYPE  127  217
        clus
vv       DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  FEMALE                           31                            127
  MALE                             66                            217
[1] 2 2
[1] FALSE
D65V8, binary
                                cls
clus                               0   1
  DEL PEAK 29(11P15.5) MUTATED    66  22
  DEL PEAK 29(11P15.5) WILD-TYPE 256  54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(11P15.5) MUTATED     66   22
  DEL PEAK 29(11P15.5) WILD-TYPE  256   54
     clus
vv    DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  NO                            66                            256
  YES                           22                             54
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 29(11P15.5) MUTATED                                          3
  DEL PEAK 29(11P15.5) WILD-TYPE                                       10
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 29(11P15.5) MUTATED                                       9
  DEL PEAK 29(11P15.5) WILD-TYPE                                    63
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 29(11P15.5) MUTATED                                                       31
  DEL PEAK 29(11P15.5) WILD-TYPE                                                    132
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 29(11P15.5) MUTATED                                                   5
  DEL PEAK 29(11P15.5) WILD-TYPE                                                16
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 29(11P15.5) MUTATED                                                                  21
  DEL PEAK 29(11P15.5) WILD-TYPE                                                                61
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 29(11P15.5) MUTATED                                                    5
  DEL PEAK 29(11P15.5) WILD-TYPE                                                  3
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 29(11P15.5) MUTATED                                                 23
  DEL PEAK 29(11P15.5) WILD-TYPE                                               56
D65V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 29(11P15.5) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        9
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      31
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           21
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            23
                                                                   clus
vv                                                                  DEL PEAK 29(11P15.5) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         63
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       132
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             16
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             61
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 29(11P15.5) MUTATED    74   3   7   8
  DEL PEAK 29(11P15.5) WILD-TYPE 275  15  12  17
D65V10, multiclass
    clus
vv   DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  R0                           74                            275
  R1                            3                             15
  R2                            7                             12
  RX                            8                             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"
D65V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 29(11P15.5) MUTATED      17                         4
  DEL PEAK 29(11P15.5) WILD-TYPE    71                         8
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 29(11P15.5) MUTATED                                           0
  DEL PEAK 29(11P15.5) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 29(11P15.5) MUTATED      63
  DEL PEAK 29(11P15.5) WILD-TYPE   215
D65V12, multiclass
                                           clus
vv                                          DEL PEAK 29(11P15.5) MUTATED
  ASIAN                                                               17
  BLACK OR AFRICAN AMERICAN                                            4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               63
                                           clus
vv                                          DEL PEAK 29(11P15.5) WILD-TYPE
  ASIAN                                                                 71
  BLACK OR AFRICAN AMERICAN                                              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V13, binary
                                cls
clus                               0   1
  DEL PEAK 29(11P15.5) MUTATED     1  61
  DEL PEAK 29(11P15.5) WILD-TYPE   4 255
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(11P15.5) MUTATED      1   61
  DEL PEAK 29(11P15.5) WILD-TYPE    4  255
                        clus
vv                       DEL PEAK 29(11P15.5) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           61
                        clus
vv                       DEL PEAK 29(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            255
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK 30(11Q23.2) MUTATION ANALYSIS
D66V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(11Q23.2) MUTATED    51  44
  DEL PEAK 30(11Q23.2) WILD-TYPE 195 125
  DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE 
                            95                            320 
  DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE 
                            44                            125 
$`DEL PEAK 30(11Q23.2) MUTATED`
TCGA-FP-A8CX TCGA-VQ-A8PU TCGA-3M-AB46 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4267 
        0.23        27.35        58.03         6.97        18.35         6.18 
TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6564 TCGA-BR-6709 TCGA-BR-7722 TCGA-BR-8058 
        9.57        17.29        26.10        12.16        15.32        37.25 
TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8297 TCGA-BR-8365 TCGA-BR-8486 
       11.44         9.60         2.66         7.40        17.52        20.22 
TCGA-BR-8687 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PF 
        8.22        34.98         1.48         0.72        13.51         1.15 
TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5804 TCGA-CD-8527 
       21.44        13.02        13.15        13.35        12.10         7.17 
TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-A48A TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4437 
       12.30        11.64        12.43         3.02        27.02         8.05 
TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 
       29.98        12.03        36.00         1.02        12.03        15.02 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-8575 
       12.66        20.91        18.54        10.26        15.98        18.21 
TCGA-D7-A4YT TCGA-D7-A6EZ TCGA-D7-A74A TCGA-EQ-5647 TCGA-FP-7916 TCGA-FP-8099 
       14.27        20.32        19.96         0.62        14.07        17.06 
TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8249 
       13.58         0.56        63.06        52.21        26.47        28.96 
TCGA-HU-8610 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4H0 TCGA-HU-A4H4 
        0.76         3.25        22.75        11.77         2.10        23.84 
TCGA-HU-A4H6 TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-AB1X TCGA-IP-7968 TCGA-MX-A666 
       21.17         6.44        10.62        13.51         2.53        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A8N1 TCGA-RD-A8N6 
       45.67        18.21         6.08         9.24       115.69         8.94 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8P5 TCGA-VQ-A8PJ TCGA-VQ-A8PK 
        0.92        48.79        13.25         7.73         2.70        17.85 
TCGA-VQ-A8PS TCGA-VQ-A91A TCGA-VQ-A91Q TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A92D 
       13.35        39.45        20.81        55.56         9.04        66.81 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA6F TCGA-VQ-AA6K 
       21.04        42.54        11.24        54.12        12.43 

$`DEL PEAK 30(11Q23.2) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G 
       47.05        21.99        22.98        79.07        16.24        20.15 
TCGA-MX-A663 TCGA-VQ-A94U TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        9.86        26.93        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
        9.47         9.44         6.61         4.64         7.43        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4280 TCGA-BR-6452 
        4.08         4.08         9.34         9.67         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 
       15.95        13.87        13.68        19.33        39.12         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 
       35.24        35.84        33.63        39.78        18.15        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 
        3.45         9.07        29.56        33.21        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 
       29.59        32.25         8.05         0.56        29.42        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
        2.20        15.58         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       22.19         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T 
       31.96        32.58         9.86        20.88        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       13.87         7.53         6.08        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.65        20.42        16.14         5.13        13.41 
TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 
       13.18        11.21        12.76        12.59        12.53        12.33 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.39        12.59        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        6.31        12.30        11.31        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       11.77        12.62        20.02        15.95         1.02         7.99 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 
       54.08         4.01        14.01        19.07         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5720 
       18.97         7.07        12.00        30.97         6.97         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        6.02         0.99       105.07        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 
       69.04        21.07         7.99        25.71        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 
       18.84        18.61        17.85        13.35        17.19        15.22 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU 
       19.50        17.19        14.66        21.14        20.91        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        11.44        22.29        15.65         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF 
        3.48        19.53        22.29        59.54         5.03         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        6.21        77.29        30.51         1.51         5.92        24.39 
TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 
       18.15        22.32        22.82        21.07        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.26        22.68        24.20        25.81        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       12.95        29.00        23.80        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU 
       13.35        19.53         6.74        12.59         6.51        11.70 
TCGA-IN-AB1V TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG 
       15.75         5.56        63.62        37.64        36.95         3.72 
TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT 
       19.73         8.52        74.53         4.60        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 
        5.13        16.67       122.30        37.91        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44        35.61        16.87        19.04         5.79 
TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        5.46        13.02        18.48        43.36        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       38.14        37.22        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       22.19         2.50        12.79         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D 
       15.65        29.59        64.57        14.33        73.41        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       21.83        61.22        18.74        32.88         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
       60.85         9.50         9.73         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
        6.58         5.72         2.66        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        17.13        26.04        16.14        27.55 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

  DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE 
                          0.23                           0.00 
  DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE 
                        115.69                         122.30 
  DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE 
                        13.350                         15.715 
[1] "0.2 - 115.7 (13.3)" "0.0 - 122.3 (15.7)"
[1] "hr=" "1.3"
D66V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 30(11Q23.2) MUTATED         0        6        7       10         9
  DEL PEAK 30(11Q23.2) WILD-TYPE       2       10       34       22        31
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 30(11Q23.2) MUTATED           9         1         18         12
  DEL PEAK 30(11Q23.2) WILD-TYPE        47         2         63         51
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 30(11Q23.2) MUTATED           10       12
  DEL PEAK 30(11Q23.2) WILD-TYPE         29       32
D66V3, multiclass
            clus
vv           DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              6                             10
  STAGE IB                              7                             34
  STAGE II                             10                             22
  STAGE IIA                             9                             31
  STAGE IIB                             9                             47
  STAGE III                             1                              2
  STAGE IIIA                           18                             63
  STAGE IIIB                           12                             51
  STAGE IIIC                           10                             29
  STAGE IV                             12                             32
[1] 11  2
[1] TRUE
[1] "dimension of 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(11Q23.2) MUTATED     7  23  44  24
  DEL PEAK 30(11Q23.2) WILD-TYPE  16  70 152  95
D66V4, multiclass
    clus
vv   DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE
  T1                            7                             16
  T2                           23                             70
  T3                           44                            152
  T4                           24                             95
[1] 4 2
[1] TRUE
[1] "dimension of 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(11Q23.2) MUTATED    26  24  26  20
  DEL PEAK 30(11Q23.2) WILD-TYPE 104  95  60  68
D66V5, multiclass
    clus
vv   DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE
  N0                           26                            104
  N1                           24                             95
  N2                           26                             60
  N3                           20                             68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V6, binary
                                cls
clus                               0   1
  DEL PEAK 30(11Q23.2) MUTATED    80   9
  DEL PEAK 30(11Q23.2) WILD-TYPE 309  21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11Q23.2) MUTATED     80    9
  DEL PEAK 30(11Q23.2) WILD-TYPE  309   21
   clus
vv  DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE
  0                           80                            309
  1                            9                             21
[1] 2 2
[1] FALSE
D66V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(11Q23.2) MUTATED    32  67
  DEL PEAK 30(11Q23.2) WILD-TYPE 126 216
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11Q23.2) MUTATED     32   67
  DEL PEAK 30(11Q23.2) WILD-TYPE  126  216
        clus
vv       DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE
  FEMALE                           32                            126
  MALE                             67                            216
[1] 2 2
[1] FALSE
D66V8, binary
                                cls
clus                               0   1
  DEL PEAK 30(11Q23.2) MUTATED    69  18
  DEL PEAK 30(11Q23.2) WILD-TYPE 253  58
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11Q23.2) MUTATED     69   18
  DEL PEAK 30(11Q23.2) WILD-TYPE  253   58
     clus
vv    DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE
  NO                            69                            253
  YES                           18                             58
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 30(11Q23.2) MUTATED                                          3
  DEL PEAK 30(11Q23.2) WILD-TYPE                                       10
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 30(11Q23.2) MUTATED                                      10
  DEL PEAK 30(11Q23.2) WILD-TYPE                                    62
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 30(11Q23.2) MUTATED                                                       36
  DEL PEAK 30(11Q23.2) WILD-TYPE                                                    127
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 30(11Q23.2) MUTATED                                                   6
  DEL PEAK 30(11Q23.2) WILD-TYPE                                                15
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 30(11Q23.2) MUTATED                                                                  20
  DEL PEAK 30(11Q23.2) WILD-TYPE                                                                62
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 30(11Q23.2) MUTATED                                                    2
  DEL PEAK 30(11Q23.2) WILD-TYPE                                                  6
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 30(11Q23.2) MUTATED                                                 22
  DEL PEAK 30(11Q23.2) WILD-TYPE                                               57
D66V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 30(11Q23.2) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       10
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      36
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            6
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           20
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            22
                                                                   clus
vv                                                                  DEL PEAK 30(11Q23.2) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         62
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       127
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             15
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 30(11Q23.2) MUTATED    72   7   5   5
  DEL PEAK 30(11Q23.2) WILD-TYPE 277  11  14  20
D66V10, multiclass
    clus
vv   DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE
  R0                           72                            277
  R1                            7                             11
  R2                            5                             14
  RX                            5                             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"
D66V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 30(11Q23.2) MUTATED      19                         2
  DEL PEAK 30(11Q23.2) WILD-TYPE    69                        10
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 30(11Q23.2) MUTATED                                           0
  DEL PEAK 30(11Q23.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 30(11Q23.2) MUTATED      61
  DEL PEAK 30(11Q23.2) WILD-TYPE   217
D66V12, multiclass
                                           clus
vv                                          DEL PEAK 30(11Q23.2) MUTATED
  ASIAN                                                               19
  BLACK OR AFRICAN AMERICAN                                            2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               61
                                           clus
vv                                          DEL PEAK 30(11Q23.2) WILD-TYPE
  ASIAN                                                                 69
  BLACK OR AFRICAN AMERICAN                                             10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V13, binary
                                cls
clus                               0   1
  DEL PEAK 30(11Q23.2) MUTATED     2  67
  DEL PEAK 30(11Q23.2) WILD-TYPE   3 249
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11Q23.2) MUTATED      2   67
  DEL PEAK 30(11Q23.2) WILD-TYPE    3  249
                        clus
vv                       DEL PEAK 30(11Q23.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           67
                        clus
vv                       DEL PEAK 30(11Q23.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            249
[1] 2 2
[1] FALSE

Clustering(67) Variable = DEL PEAK 31(12P13.1) MUTATION ANALYSIS
D67V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(12P13.1) MUTATED    36  38
  DEL PEAK 31(12P13.1) WILD-TYPE 210 131
  DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE 
                            74                            341 
  DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE 
                            38                            131 
$`DEL PEAK 31(12P13.1) MUTATED`
TCGA-3M-AB46 TCGA-BR-4183 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-6456 
       58.03         6.61         4.08         9.67         6.18        17.29 
TCGA-BR-6458 TCGA-BR-6709 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7901 TCGA-BR-8060 
       19.33        12.16        35.24        33.63         3.45        11.44 
TCGA-BR-8289 TCGA-BR-8362 TCGA-BR-8369 TCGA-BR-8483 TCGA-BR-8678 TCGA-BR-8683 
        2.66        13.08        14.04         5.39        24.79         9.86 
TCGA-BR-A4CQ TCGA-CD-5800 TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8535 TCGA-CD-A486 
       34.98        13.15        12.76         7.17        12.82         6.31 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4441 
       11.31        12.43        12.20         3.02         7.99        14.01 
TCGA-CG-4477 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-6519 TCGA-D7-6528 TCGA-D7-6817 
       30.97        15.02        69.04        20.55        15.22        12.79 
TCGA-D7-6822 TCGA-D7-A4YT TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
       12.33        14.27        19.96         0.62         7.99        72.23 
TCGA-HU-8245 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL 
       18.15        23.84        23.80         3.39        18.38        13.35 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A93J TCGA-MX-A666 TCGA-R5-A7O7 TCGA-RD-A8MW 
       11.70         2.53        36.95        14.04        45.67        37.91 
TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8P3 TCGA-VQ-A8PJ TCGA-VQ-A8PM 
       35.61         5.46        13.02        37.22         2.70         1.87 
TCGA-VQ-A8PY TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Z 
       14.33        18.74         1.71        42.64         9.50        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-AA6D 
        9.04         2.01         5.72        66.81        21.04        17.13 
TCGA-VQ-AA6I TCGA-ZQ-A9CR 
       16.14         0.79 

$`DEL PEAK 31(12P13.1) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-B7-5816 TCGA-B7-5818 
       20.15         9.86        27.35        26.93        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4279 
        7.43        18.35        30.90         4.08         9.34         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        6.61        34.68        15.95        13.87        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        36.16        35.84        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       28.73         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       29.42        19.96         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
        4.31         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
       25.05         3.72        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       26.73        31.96        32.58        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       34.13        13.87         7.53         6.08         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
       28.34         0.66        32.52        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 
       13.02        13.18        13.35        11.21        12.10        12.59 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
       12.53        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48C TCGA-CD-A4MG 
       15.39        12.07        12.43        12.30        11.61         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        12.62        20.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
        8.05        54.08         4.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        12.00         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 
       12.03        28.96        65.10         4.01        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
       25.71        12.66        20.91        19.13        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
       18.61        17.85        13.35        17.19        10.26        15.98 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       12.36        11.31        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV 
       18.21        14.66        21.14        20.91        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.13        14.47        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       18.81        12.46        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 
        6.51        10.62        15.75        13.51         5.56        63.62 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       37.64         3.72        19.73        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
       16.67       122.30        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       48.79        13.25        18.48        43.36        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       38.14         7.73        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PP 
       22.19         2.50        12.79        17.85         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        13.35        29.59        64.57        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91W 
       11.70        21.83        61.22        20.81        32.88        60.85 
TCGA-VQ-A91Y TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A94P TCGA-VQ-A94R 
        9.73        55.43         4.54         6.58         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        27.55        12.43        17.26 

  DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE 
                          0.62                           0.00 
  DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE 
                         72.23                         122.30 
  DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE 
                        13.115                         15.750 
[1] "0.6 - 72.2 (13.1)"  "0.0 - 122.3 (15.8)"
[1] "hr=" "1.5"
D67V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 31(12P13.1) MUTATED         1        1       11        6         7
  DEL PEAK 31(12P13.1) WILD-TYPE       1       15       30       26        33
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 31(12P13.1) MUTATED           7         0         18          9
  DEL PEAK 31(12P13.1) WILD-TYPE        49         3         63         54
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 31(12P13.1) MUTATED            3       11
  DEL PEAK 31(12P13.1) WILD-TYPE         36       33
D67V3, multiclass
            clus
vv           DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                              1                             15
  STAGE IB                             11                             30
  STAGE II                              6                             26
  STAGE IIA                             7                             33
  STAGE IIB                             7                             49
  STAGE III                             0                              3
  STAGE IIIA                           18                             63
  STAGE IIIB                            9                             54
  STAGE IIIC                            3                             36
  STAGE IV                             11                             33
[1] 11  2
[1] TRUE
[1] "dimension of 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(12P13.1) MUTATED     1  25  34  15
  DEL PEAK 31(12P13.1) WILD-TYPE  22  68 162 104
D67V4, multiclass
    clus
vv   DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE
  T1                            1                             22
  T2                           25                             68
  T3                           34                            162
  T4                           15                            104
[1] 4 2
[1] TRUE
[1] "dimension of 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(12P13.1) MUTATED    22  22  14  16
  DEL PEAK 31(12P13.1) WILD-TYPE 108  97  72  72
D67V5, multiclass
    clus
vv   DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE
  N0                           22                            108
  N1                           22                             97
  N2                           14                             72
  N3                           16                             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V6, binary
                                cls
clus                               0   1
  DEL PEAK 31(12P13.1) MUTATED    65   6
  DEL PEAK 31(12P13.1) WILD-TYPE 324  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(12P13.1) MUTATED     65    6
  DEL PEAK 31(12P13.1) WILD-TYPE  324   24
   clus
vv  DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE
  0                           65                            324
  1                            6                             24
[1] 2 2
[1] FALSE
D67V7, binary
                                cls
clus                               0   1
  DEL PEAK 31(12P13.1) MUTATED    28  49
  DEL PEAK 31(12P13.1) WILD-TYPE 130 234
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(12P13.1) MUTATED     28   49
  DEL PEAK 31(12P13.1) WILD-TYPE  130  234
        clus
vv       DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE
  FEMALE                           28                            130
  MALE                             49                            234
[1] 2 2
[1] FALSE
D67V8, binary
                                cls
clus                               0   1
  DEL PEAK 31(12P13.1) MUTATED    57  16
  DEL PEAK 31(12P13.1) WILD-TYPE 265  60
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(12P13.1) MUTATED     57   16
  DEL PEAK 31(12P13.1) WILD-TYPE  265   60
     clus
vv    DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE
  NO                            57                            265
  YES                           16                             60
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 31(12P13.1) MUTATED                                          2
  DEL PEAK 31(12P13.1) WILD-TYPE                                       11
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 31(12P13.1) MUTATED                                       4
  DEL PEAK 31(12P13.1) WILD-TYPE                                    68
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 31(12P13.1) MUTATED                                                       32
  DEL PEAK 31(12P13.1) WILD-TYPE                                                    131
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 31(12P13.1) MUTATED                                                   0
  DEL PEAK 31(12P13.1) WILD-TYPE                                                21
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 31(12P13.1) MUTATED                                                                  15
  DEL PEAK 31(12P13.1) WILD-TYPE                                                                67
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 31(12P13.1) MUTATED                                                    4
  DEL PEAK 31(12P13.1) WILD-TYPE                                                  4
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 31(12P13.1) MUTATED                                                 20
  DEL PEAK 31(12P13.1) WILD-TYPE                                               59
D67V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 31(12P13.1) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      32
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           15
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            20
                                                                   clus
vv                                                                  DEL PEAK 31(12P13.1) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       131
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 31(12P13.1) MUTATED    58   2   4   5
  DEL PEAK 31(12P13.1) WILD-TYPE 291  16  15  20
D67V10, multiclass
    clus
vv   DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE
  R0                           58                            291
  R1                            2                             16
  R2                            4                             15
  RX                            5                             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"
D67V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 31(12P13.1) MUTATED      14                         3
  DEL PEAK 31(12P13.1) WILD-TYPE    74                         9
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 31(12P13.1) MUTATED                                           0
  DEL PEAK 31(12P13.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 31(12P13.1) MUTATED      47
  DEL PEAK 31(12P13.1) WILD-TYPE   231
D67V12, multiclass
                                           clus
vv                                          DEL PEAK 31(12P13.1) MUTATED
  ASIAN                                                               14
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               47
                                           clus
vv                                          DEL PEAK 31(12P13.1) WILD-TYPE
  ASIAN                                                                 74
  BLACK OR AFRICAN AMERICAN                                              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V13, binary
                                cls
clus                               0   1
  DEL PEAK 31(12P13.1) MUTATED     2  48
  DEL PEAK 31(12P13.1) WILD-TYPE   3 268
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(12P13.1) MUTATED      2   48
  DEL PEAK 31(12P13.1) WILD-TYPE    3  268
                        clus
vv                       DEL PEAK 31(12P13.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           48
                        clus
vv                       DEL PEAK 31(12P13.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            268
[1] 2 2
[1] FALSE

Clustering(68) Variable = DEL PEAK 32(12Q12) MUTATION ANALYSIS
D68V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 32(12Q12) MUTATED    31  27
  DEL PEAK 32(12Q12) WILD-TYPE 215 142
  DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE 
                          58                          357 
  DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE 
                          27                          142 
$`DEL PEAK 32(12Q12) MUTATED`
TCGA-VQ-A8PU TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-7703 TCGA-BR-7704 
       27.35         9.67         6.18        17.29        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8483 
       33.63        18.15         3.45        11.44        29.42         5.39 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A4J6 TCGA-BR-A4PF TCGA-BR-A4QI 
       32.58         9.86         8.22         0.66         1.15        21.44 
TCGA-CD-5798 TCGA-CD-5802 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4300 
       13.41        13.35        11.31        12.43        12.20        20.02 
TCGA-CG-4436 TCGA-CG-5725 TCGA-D7-6519 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-A4YY 
        7.99        15.02        20.55        13.35        15.22        13.78 
TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-A72C TCGA-FP-8211 TCGA-HU-A4GH 
       15.65         0.62         7.99        11.38        13.58        11.77 
TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-IN-7806 TCGA-KB-A93H TCGA-KB-A93J TCGA-R5-A7O7 
       12.95        23.80        36.36        37.64        36.95        45.67 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8PK TCGA-VQ-A8PS 
       35.61         5.79         5.46        13.02        17.85        13.35 
TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-AA64 
       20.81        42.64        55.56         9.04        21.04        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       43.66        16.14        12.43         0.79 

$`DEL PEAK 32(12Q12) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
       20.15         9.86        26.93        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        9.34         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 
       30.90        31.20        44.94        21.90         9.21        35.84 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       39.78        15.32        28.73         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56         2.66        19.96         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       31.96        20.88        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53        28.34        32.52 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM 
       13.51         0.46        20.65        20.42        16.14         5.13 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 
       13.02        13.15        13.18        11.21        12.10        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        6.31        12.30        11.61         6.58        11.77        12.62 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         1.02         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        12.00        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 
        7.99        25.71        12.66        20.91        19.13        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
       18.54        18.61        17.85        17.19        10.26        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44         5.92        36.43        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 
       11.24        11.31        11.44        20.32        22.29         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        4.34        19.96         7.13        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        5.03         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       18.15        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 
        6.51         6.58        20.25         0.26         2.10        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 
       23.84        21.17        14.07        15.68        33.40         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG 
       15.75        13.51         2.53         5.56        63.62         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       19.73        14.04        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT 
       57.44         8.94        16.87        19.04         0.92        48.79 
TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.25        18.48        43.36        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       37.22         7.73        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO 
       22.19         2.50        12.79         2.70         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       23.41        15.65        29.59        64.57        14.33        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S 
       39.45        11.70        21.83        61.22        18.74        32.88 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 
        1.71        60.85         9.50         9.73         2.01        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R 
        4.54         6.58         5.72        66.81         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       11.24        28.41        38.93        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-ZA-A8F6 
       26.04        27.55        17.26 

  DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE 
                        0.62                         0.00 
  DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE 
                       55.56                       122.30 
  DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE 
                       13.68                        15.32 
[1] "0.6 - 55.6 (13.7)"  "0.0 - 122.3 (15.3)"
[1] "hr=" "1.2"
D68V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 32(12Q12) MUTATED         0        2        6        6         7
  DEL PEAK 32(12Q12) WILD-TYPE       2       14       35       26        33
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 32(12Q12) MUTATED           8         0          8          8
  DEL PEAK 32(12Q12) WILD-TYPE        48         3         73         55
                              vv
clus                           STAGE IIIC STAGE IV
  DEL PEAK 32(12Q12) MUTATED            6        6
  DEL PEAK 32(12Q12) WILD-TYPE         33       38
D68V3, multiclass
            clus
vv           DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE
  STAGE I                             0                            2
  STAGE IA                            2                           14
  STAGE IB                            6                           35
  STAGE II                            6                           26
  STAGE IIA                           7                           33
  STAGE IIB                           8                           48
  STAGE III                           0                            3
  STAGE IIIA                          8                           73
  STAGE IIIB                          8                           55
  STAGE IIIC                          6                           33
  STAGE IV                            6                           38
[1] 11  2
[1] TRUE
[1] "dimension of 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(12Q12) MUTATED     2  11  31  14
  DEL PEAK 32(12Q12) WILD-TYPE  21  82 165 105
D68V4, multiclass
    clus
vv   DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE
  T1                          2                           21
  T2                         11                           82
  T3                         31                          165
  T4                         14                          105
[1] 4 2
[1] TRUE
[1] "dimension of 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(12Q12) MUTATED    20  15  11  12
  DEL PEAK 32(12Q12) WILD-TYPE 110 104  75  76
D68V5, multiclass
    clus
vv   DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE
  N0                         20                          110
  N1                         15                          104
  N2                         11                           75
  N3                         12                           76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V6, binary
                              cls
clus                             0   1
  DEL PEAK 32(12Q12) MUTATED    53   3
  DEL PEAK 32(12Q12) WILD-TYPE 336  27
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(12Q12) MUTATED     53    3
  DEL PEAK 32(12Q12) WILD-TYPE  336   27
   clus
vv  DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE
  0                         53                          336
  1                          3                           27
[1] 2 2
[1] FALSE
D68V7, binary
                              cls
clus                             0   1
  DEL PEAK 32(12Q12) MUTATED    19  40
  DEL PEAK 32(12Q12) WILD-TYPE 139 243
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(12Q12) MUTATED     19   40
  DEL PEAK 32(12Q12) WILD-TYPE  139  243
        clus
vv       DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE
  FEMALE                         19                          139
  MALE                           40                          243
[1] 2 2
[1] FALSE
D68V8, binary
                              cls
clus                             0   1
  DEL PEAK 32(12Q12) MUTATED    42  15
  DEL PEAK 32(12Q12) WILD-TYPE 280  61
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(12Q12) MUTATED     42   15
  DEL PEAK 32(12Q12) WILD-TYPE  280   61
     clus
vv    DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE
  NO                          42                          280
  YES                         15                           61
[1] 2 2
[1] FALSE
                              vv
clus                           STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 32(12Q12) MUTATED                                          2
  DEL PEAK 32(12Q12) WILD-TYPE                                       11
                              vv
clus                           STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 32(12Q12) MUTATED                                       7
  DEL PEAK 32(12Q12) WILD-TYPE                                    65
                              vv
clus                           STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 32(12Q12) MUTATED                                                       20
  DEL PEAK 32(12Q12) WILD-TYPE                                                    143
                              vv
clus                           STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 32(12Q12) MUTATED                                                   3
  DEL PEAK 32(12Q12) WILD-TYPE                                                18
                              vv
clus                           STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 32(12Q12) MUTATED                                                                  10
  DEL PEAK 32(12Q12) WILD-TYPE                                                                72
                              vv
clus                           STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 32(12Q12) MUTATED                                                    2
  DEL PEAK 32(12Q12) WILD-TYPE                                                  6
                              vv
clus                           STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 32(12Q12) MUTATED                                                 15
  DEL PEAK 32(12Q12) WILD-TYPE                                               64
D68V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 32(12Q12) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                   2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                      7
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                    20
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         10
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                         2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                          15
                                                                   clus
vv                                                                  DEL PEAK 32(12Q12) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     143
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           72
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            64
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 32(12Q12) MUTATED    45   3   2   2
  DEL PEAK 32(12Q12) WILD-TYPE 304  15  17  23
D68V10, multiclass
    clus
vv   DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE
  R0                         45                          304
  R1                          3                           15
  R2                          2                           17
  RX                          2                           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"
D68V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 32(12Q12) MUTATED      13                         2
  DEL PEAK 32(12Q12) WILD-TYPE    75                        10
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 32(12Q12) MUTATED                                           0    37
  DEL PEAK 32(12Q12) WILD-TYPE                                         1   241
D68V12, multiclass
                                           clus
vv                                          DEL PEAK 32(12Q12) MUTATED
  ASIAN                                                             13
  BLACK OR AFRICAN AMERICAN                                          2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          0
  WHITE                                                             37
                                           clus
vv                                          DEL PEAK 32(12Q12) WILD-TYPE
  ASIAN                                                               75
  BLACK OR AFRICAN AMERICAN                                           10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V13, binary
                              cls
clus                             0   1
  DEL PEAK 32(12Q12) MUTATED     1  38
  DEL PEAK 32(12Q12) WILD-TYPE   4 278
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(12Q12) MUTATED      1   38
  DEL PEAK 32(12Q12) WILD-TYPE    4  278
                        clus
vv                       DEL PEAK 32(12Q12) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         38
                        clus
vv                       DEL PEAK 32(12Q12) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          278
[1] 2 2
[1] FALSE

Clustering(69) Variable = DEL PEAK 33(13Q12.11) MUTATION ANALYSIS
D69V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 33(13Q12.11) MUTATED    29  29
  DEL PEAK 33(13Q12.11) WILD-TYPE 217 140
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                             58                             357 
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                             29                             140 
$`DEL PEAK 33(13Q12.11) MUTATED`
TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-3M-AB46 TCGA-B7-A5TI TCGA-BR-4184 
       47.05        22.98        79.07        58.03        19.56         6.97 
TCGA-BR-4255 TCGA-BR-6456 TCGA-BR-6564 TCGA-BR-6709 TCGA-BR-7715 TCGA-BR-7716 
        4.08        17.29        26.10        12.16        33.63        39.78 
TCGA-BR-7959 TCGA-BR-8289 TCGA-BR-8297 TCGA-BR-8683 TCGA-BR-A4CS TCGA-BR-A4IY 
       33.21         2.66         7.40         9.86         1.48        12.89 
TCGA-BR-A4J6 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-A486 TCGA-CG-4466 TCGA-CG-5724 
        0.66        12.53         7.17         6.31        18.97        12.03 
TCGA-CG-5725 TCGA-D7-5579 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6818 TCGA-D7-8575 
       15.02        20.91        13.35        10.26        12.36        18.21 
TCGA-D7-A4YU TCGA-D7-A6F2 TCGA-FP-7916 TCGA-HF-7133 TCGA-HU-8243 TCGA-HU-A4GC 
       16.44        15.65        14.07        63.06         5.92         3.25 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-IN-8462 TCGA-IN-8663 
       25.81        11.77         6.58        12.95        18.81         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IN-AB1X TCGA-KB-A93J TCGA-RD-A7BS 
       12.46        13.35         6.74        13.51        36.95        11.05 
TCGA-RD-A8N1 TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8P5 TCGA-VQ-A8PM TCGA-VQ-A91A 
      115.69        13.25        13.02         7.73         1.87        39.45 
TCGA-VQ-A91Q TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-AA6G 
       20.81         4.54        66.81        26.04 

$`DEL PEAK 33(13Q12.11) WILD-TYPE`
TCGA-CG-4460 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU 
       21.99        16.24         0.23        20.15         9.86        27.35 
TCGA-VQ-A94U TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.93        26.70        11.70        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 
       15.95        13.87        13.68        19.33        39.12         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       35.24        35.84        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        9.07        29.56        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       19.96         2.20        15.58         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 
        7.53        26.73        24.79        31.96        32.58        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       34.98        27.55        28.57         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
        0.53        28.34        32.52        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.76        12.59        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 
       11.64        15.39        12.07        12.82        12.43        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 
       19.07        12.03         0.00         9.01         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
        0.99       105.07        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 
       21.07         7.99        25.71        12.66        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6528 
       18.84        18.54        18.61        17.85        17.19        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       15.98        12.79        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19        14.66        21.14        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 
       11.31        11.44        20.32        22.29         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 
       21.27        11.38         3.48        19.53        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 
       77.29        52.21        30.51        26.47         1.51        24.39 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       18.15        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD 
       24.30         5.59        24.26        22.68        24.20        22.75 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RI 
       14.07        15.68        33.40        36.36         3.45        18.38 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
       19.53         6.44        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG 
       15.75         2.53         5.56        63.62        37.64         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        6.08         4.60         9.24         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
      122.30        37.91        40.64       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
        8.94        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       48.79         5.46        18.48        43.36        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       38.14        37.22        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PO 
       22.19         2.50        12.79         2.70        17.85         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY 
       23.41        15.65        13.35        29.59        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S 
       73.41        11.70        21.83        61.22        18.74        32.88 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
        1.71        42.64        60.85         9.50         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O 
        9.04         2.01        55.43         6.58         5.72        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
        2.66        42.54        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        17.13        54.12        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        17.26         0.79 

  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                           0.66                            0.00 
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                         115.69                          122.30 
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                          13.30                           15.58 
[1] "0.7 - 115.7 (13.3)" "0.0 - 122.3 (15.6)"
[1] "hr=" "1.3"
D69V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 33(13Q12.11) MUTATED         0        2        8        4         8
  DEL PEAK 33(13Q12.11) WILD-TYPE       2       14       33       28        32
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 33(13Q12.11) MUTATED           7         0         14          7
  DEL PEAK 33(13Q12.11) WILD-TYPE        49         3         67         56
                                 vv
clus                              STAGE IIIC STAGE IV
  DEL PEAK 33(13Q12.11) MUTATED            5        6
  DEL PEAK 33(13Q12.11) WILD-TYPE         34       38
D69V3, multiclass
            clus
vv           DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  STAGE I                                0                               2
  STAGE IA                               2                              14
  STAGE IB                               8                              33
  STAGE II                               4                              28
  STAGE IIA                              8                              32
  STAGE IIB                              7                              49
  STAGE III                              0                               3
  STAGE IIIA                            14                              67
  STAGE IIIB                             7                              56
  STAGE IIIC                             5                              34
  STAGE IV                               6                              38
[1] 11  2
[1] TRUE
[1] "dimension of 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     2  19  29  12
  DEL PEAK 33(13Q12.11) WILD-TYPE  21  74 167 107
D69V4, multiclass
    clus
vv   DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  T1                             2                              21
  T2                            19                              74
  T3                            29                             167
  T4                            12                             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"
                                 vv
clus                               N0  N1  N2  N3
  DEL PEAK 33(13Q12.11) MUTATED    20  16  10  16
  DEL PEAK 33(13Q12.11) WILD-TYPE 110 103  76  72
D69V5, multiclass
    clus
vv   DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  N0                            20                             110
  N1                            16                             103
  N2                            10                              76
  N3                            16                              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V6, binary
                                 cls
clus                                0   1
  DEL PEAK 33(13Q12.11) MUTATED    56   3
  DEL PEAK 33(13Q12.11) WILD-TYPE 333  27
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q12.11) MUTATED     56    3
  DEL PEAK 33(13Q12.11) WILD-TYPE  333   27
   clus
vv  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  0                            56                             333
  1                             3                              27
[1] 2 2
[1] FALSE
D69V7, binary
                                 cls
clus                                0   1
  DEL PEAK 33(13Q12.11) MUTATED    14  49
  DEL PEAK 33(13Q12.11) WILD-TYPE 144 234
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q12.11) MUTATED     14   49
  DEL PEAK 33(13Q12.11) WILD-TYPE  144  234
        clus
vv       DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  FEMALE                            14                             144
  MALE                              49                             234
[1] 2 2
[1] FALSE
D69V8, binary
                                 cls
clus                                0   1
  DEL PEAK 33(13Q12.11) MUTATED    48  12
  DEL PEAK 33(13Q12.11) WILD-TYPE 274  64
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q12.11) MUTATED     48   12
  DEL PEAK 33(13Q12.11) WILD-TYPE  274   64
     clus
vv    DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  NO                             48                             274
  YES                            12                              64
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 33(13Q12.11) MUTATED                                          2
  DEL PEAK 33(13Q12.11) WILD-TYPE                                       11
                                 vv
clus                              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 33(13Q12.11) MUTATED                                      13
  DEL PEAK 33(13Q12.11) WILD-TYPE                                    59
                                 vv
clus                              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 33(13Q12.11) MUTATED                                                       22
  DEL PEAK 33(13Q12.11) WILD-TYPE                                                    141
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 33(13Q12.11) MUTATED                                                   4
  DEL PEAK 33(13Q12.11) WILD-TYPE                                                17
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 33(13Q12.11) MUTATED                                                                   8
  DEL PEAK 33(13Q12.11) WILD-TYPE                                                                74
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 33(13Q12.11) MUTATED                                                    1
  DEL PEAK 33(13Q12.11) WILD-TYPE                                                  7
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 33(13Q12.11) MUTATED                                                 12
  DEL PEAK 33(13Q12.11) WILD-TYPE                                               67
D69V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 33(13Q12.11) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        13
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       22
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             8
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             12
                                                                   clus
vv                                                                  DEL PEAK 33(13Q12.11) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                       11
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                          59
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                        141
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                              17
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                              74
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                              7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                               67
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 33(13Q12.11) MUTATED    48   4   3   4
  DEL PEAK 33(13Q12.11) WILD-TYPE 301  14  16  21
D69V10, multiclass
    clus
vv   DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  R0                            48                             301
  R1                             4                              14
  R2                             3                              16
  RX                             4                              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"
D69V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 33(13Q12.11) MUTATED      12                         1
  DEL PEAK 33(13Q12.11) WILD-TYPE    76                        11
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 33(13Q12.11) MUTATED                                           0
  DEL PEAK 33(13Q12.11) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 33(13Q12.11) MUTATED      41
  DEL PEAK 33(13Q12.11) WILD-TYPE   237
D69V12, multiclass
                                           clus
vv                                          DEL PEAK 33(13Q12.11) MUTATED
  ASIAN                                                                12
  BLACK OR AFRICAN AMERICAN                                             1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                41
                                           clus
vv                                          DEL PEAK 33(13Q12.11) WILD-TYPE
  ASIAN                                                                  76
  BLACK OR AFRICAN AMERICAN                                              11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V13, binary
                                 cls
clus                                0   1
  DEL PEAK 33(13Q12.11) MUTATED     1  44
  DEL PEAK 33(13Q12.11) WILD-TYPE   4 272
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q12.11) MUTATED      1   44
  DEL PEAK 33(13Q12.11) WILD-TYPE    4  272
                        clus
vv                       DEL PEAK 33(13Q12.11) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            44
                        clus
vv                       DEL PEAK 33(13Q12.11) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             272
[1] 2 2
[1] FALSE

Clustering(70) Variable = DEL PEAK 34(14Q23.3) MUTATION ANALYSIS
D70V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 34(14Q23.3) MUTATED    74  57
  DEL PEAK 34(14Q23.3) WILD-TYPE 172 112
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                           131                            284 
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                            57                            112 
$`DEL PEAK 34(14Q23.3) MUTATED`
TCGA-EQ-A4SO TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-A5TI TCGA-B7-A5TJ 
       16.24        27.35        26.93        58.03        19.56        11.01 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4279 TCGA-BR-6456 
        9.44         6.61         4.08         9.67         9.57        17.29 
TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6803 TCGA-BR-7704 TCGA-BR-7715 
       19.33        26.10         9.17        31.20        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8286 
       39.78        28.73        33.21        37.25        11.44        29.42 
TCGA-BR-8289 TCGA-BR-8361 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8484 
        2.66        31.10        14.79         7.36         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8589 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-A452 TCGA-BR-A4CQ 
        9.21        27.12        24.79        20.88         7.53        34.98 
TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD 
        1.48         0.72         0.66        32.52         0.46        20.65 
TCGA-BR-A4PF TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8533 
        1.15        13.18        11.21        12.76         7.17        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 
       12.07        12.82        11.31        12.20        20.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4466 TCGA-CG-4477 
        8.05        54.08         4.01        14.01        18.97        30.97 
TCGA-CG-5725 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 
       15.02        20.55        18.84        18.54        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-8576 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6EY 
       10.26        15.98        14.66        16.44        11.31        11.44 
TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 
       22.29         7.99        11.38        14.07        17.06         0.56 
TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4G3 TCGA-HU-A4GC TCGA-HU-A4GH 
       26.47        18.15        28.96         5.59         3.25        11.77 
TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-A6RL 
        8.98         2.10        23.80        33.40        36.36        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 
       19.53         6.44         6.74        11.70         2.53         5.56 
TCGA-KB-A93H TCGA-MX-A666 TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 
       37.64        14.04        16.67       122.30        37.91       115.69 
TCGA-RD-A8N6 TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        8.94         0.92         5.46        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       43.36        37.22         7.73        46.26        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91N 
       17.85        13.35        64.57        14.33        73.41        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R 
       20.81        55.56         9.04        66.81        21.04        42.54 
TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-ZQ-A9CR 
       18.41        38.93        32.94        26.04         0.79 

$`DEL PEAK 34(14Q23.3) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        22.98        79.07         0.23        20.15 
TCGA-MX-A663 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 
        9.86        26.70        11.70         9.47         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 
        7.43        18.35        30.90         4.08         9.34         6.18 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        6.61        34.68        15.95        13.87        13.68        39.12 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       40.21        30.90        44.94        21.90         9.21        36.16 
TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       35.84        18.15        15.32         3.45         9.07        29.56 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        0.56        19.96         2.20        15.58         7.40         6.18 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8382 
        4.31        14.04         3.32        11.80        31.27        25.05 
TCGA-BR-8384 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
        3.72        20.22         1.12        12.79         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        31.96        32.58         9.86 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU 
        8.22        10.68        34.13        13.87         6.08        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57        12.89         8.98        14.17         0.53        28.34 
TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       13.51        20.42        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8526 
       13.02        13.15        13.35        12.10        12.59        12.53 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 
       12.33        12.30        12.39        12.59        11.64        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI 
        6.31        12.30        12.43        11.61         6.58        11.77 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4443 
       12.62         3.02        27.02        15.95         1.02        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 
       19.07        12.03         0.00         9.01         7.07        12.00 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       18.61        17.85        15.22        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 
       14.76        26.43        11.24        20.32        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 
        4.34        19.96         7.13         0.62        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
       21.27         3.48        19.53        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       13.58         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 
       30.51         1.51         5.92        24.39        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       21.07         0.76        24.30        24.26        22.68        24.20 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT 
       22.75        25.81        21.37        29.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.58        20.25         0.26        12.95        29.00        23.84 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       21.17        14.07        15.68         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V 
       18.38        12.46        12.59         6.51        10.62        15.75 
TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 
       13.51        63.62        36.95         3.72        19.73        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
       11.05         8.61         5.13        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT 
       57.44        35.61        16.87        19.04         5.79        48.79 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       21.73        37.41        38.14        30.97        34.29        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       22.19         2.50         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S 
       29.59        39.45        11.70        21.83        61.22        32.88 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A923 
        1.71        42.64        60.85         9.50         9.73         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94T 
       55.43         4.54         6.58         5.72         2.66        11.24 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J 
       43.66        28.41        17.13        54.12        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                          0.46                           0.00 
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                        122.30                         116.38 
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                         15.39                          14.45 
[1] "0.5 - 122.3 (15.4)" "0.0 - 116.4 (14.4)"
[1] "hr=" "1.1"
D70V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 34(14Q23.3) MUTATED         0        2       13       11        16
  DEL PEAK 34(14Q23.3) WILD-TYPE       2       14       28       21        24
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 34(14Q23.3) MUTATED          16         0         31         22
  DEL PEAK 34(14Q23.3) WILD-TYPE        40         3         50         41
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 34(14Q23.3) MUTATED           10        8
  DEL PEAK 34(14Q23.3) WILD-TYPE         29       36
D70V3, multiclass
            clus
vv           DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              2                             14
  STAGE IB                             13                             28
  STAGE II                             11                             21
  STAGE IIA                            16                             24
  STAGE IIB                            16                             40
  STAGE III                             0                              3
  STAGE IIIA                           31                             50
  STAGE IIIB                           22                             41
  STAGE IIIC                           10                             29
  STAGE IV                              8                             36
[1] 11  2
[1] TRUE
[1] "dimension of 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(14Q23.3) MUTATED     4  29  63  36
  DEL PEAK 34(14Q23.3) WILD-TYPE  19  64 133  83
D70V4, multiclass
    clus
vv   DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  T1                            4                             19
  T2                           29                             64
  T3                           63                            133
  T4                           36                             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"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 34(14Q23.3) MUTATED   38 35 35 21
  DEL PEAK 34(14Q23.3) WILD-TYPE 92 84 51 67
D70V5, multiclass
    clus
vv   DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  N0                           38                             92
  N1                           35                             84
  N2                           35                             51
  N3                           21                             67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V6, binary
                                cls
clus                               0   1
  DEL PEAK 34(14Q23.3) MUTATED   121   4
  DEL PEAK 34(14Q23.3) WILD-TYPE 268  26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q23.3) MUTATED    121    4
  DEL PEAK 34(14Q23.3) WILD-TYPE  268   26
   clus
vv  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  0                          121                            268
  1                            4                             26
[1] 2 2
[1] FALSE
D70V7, binary
                                cls
clus                               0   1
  DEL PEAK 34(14Q23.3) MUTATED    44  92
  DEL PEAK 34(14Q23.3) WILD-TYPE 114 191
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q23.3) MUTATED     44   92
  DEL PEAK 34(14Q23.3) WILD-TYPE  114  191
        clus
vv       DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  FEMALE                           44                            114
  MALE                             92                            191
[1] 2 2
[1] FALSE
D70V8, binary
                                cls
clus                               0   1
  DEL PEAK 34(14Q23.3) MUTATED    99  26
  DEL PEAK 34(14Q23.3) WILD-TYPE 223  50
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q23.3) MUTATED     99   26
  DEL PEAK 34(14Q23.3) WILD-TYPE  223   50
     clus
vv    DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  NO                            99                            223
  YES                           26                             50
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 34(14Q23.3) MUTATED                                          5
  DEL PEAK 34(14Q23.3) WILD-TYPE                                        8
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 34(14Q23.3) MUTATED                                      15
  DEL PEAK 34(14Q23.3) WILD-TYPE                                    57
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 34(14Q23.3) MUTATED                                                       48
  DEL PEAK 34(14Q23.3) WILD-TYPE                                                    115
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 34(14Q23.3) MUTATED                                                   2
  DEL PEAK 34(14Q23.3) WILD-TYPE                                                19
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 34(14Q23.3) MUTATED                                                                  34
  DEL PEAK 34(14Q23.3) WILD-TYPE                                                                48
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 34(14Q23.3) MUTATED                                                    3
  DEL PEAK 34(14Q23.3) WILD-TYPE                                                  5
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 34(14Q23.3) MUTATED                                                 28
  DEL PEAK 34(14Q23.3) WILD-TYPE                                               51
D70V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 34(14Q23.3) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       15
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      48
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           34
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            28
                                                                   clus
vv                                                                  DEL PEAK 34(14Q23.3) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         57
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       115
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             48
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              51
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 34(14Q23.3) MUTATED   114   2   3   7
  DEL PEAK 34(14Q23.3) WILD-TYPE 235  16  16  18
D70V10, multiclass
    clus
vv   DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  R0                          114                            235
  R1                            2                             16
  R2                            3                             16
  RX                            7                             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"
D70V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 34(14Q23.3) MUTATED      26                         3
  DEL PEAK 34(14Q23.3) WILD-TYPE    62                         9
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 34(14Q23.3) MUTATED                                           0
  DEL PEAK 34(14Q23.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 34(14Q23.3) MUTATED      91
  DEL PEAK 34(14Q23.3) WILD-TYPE   187
D70V12, multiclass
                                           clus
vv                                          DEL PEAK 34(14Q23.3) MUTATED
  ASIAN                                                               26
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               91
                                           clus
vv                                          DEL PEAK 34(14Q23.3) WILD-TYPE
  ASIAN                                                                 62
  BLACK OR AFRICAN AMERICAN                                              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                187
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V13, binary
                                cls
clus                               0   1
  DEL PEAK 34(14Q23.3) MUTATED     1  94
  DEL PEAK 34(14Q23.3) WILD-TYPE   4 222
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q23.3) MUTATED      1   94
  DEL PEAK 34(14Q23.3) WILD-TYPE    4  222
                        clus
vv                       DEL PEAK 34(14Q23.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           94
                        clus
vv                       DEL PEAK 34(14Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            222
[1] 2 2
[1] FALSE

Clustering(71) Variable = DEL PEAK 35(14Q32.32) MUTATION ANALYSIS
D71V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 35(14Q32.32) MUTATED    76  53
  DEL PEAK 35(14Q32.32) WILD-TYPE 170 116
  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                            129                             286 
  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                             53                             116 
$`DEL PEAK 35(14Q32.32) MUTATED`
TCGA-CG-4444 TCGA-EQ-A4SO TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-B7-A5TI TCGA-B7-A5TJ 
       47.05        16.24        27.35        26.93        19.56        11.01 
TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4279 TCGA-BR-6456 
        6.61        18.35         4.08         9.67         9.57        17.29 
TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-6803 TCGA-BR-7704 
       19.33        26.10         9.17        12.16        31.20        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8080 
       33.63        39.78        33.21        37.25        11.44         9.60 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8361 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 
       29.42         2.66        31.10        14.79         7.36         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8589 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-8690 
       25.18         9.21        27.12        24.79        20.88        10.68 
TCGA-BR-A452 TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J7 
        7.53         1.48        12.89         0.72         0.66        32.52 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 
        0.46        20.65         1.15        13.18        11.21        12.76 
TCGA-CD-8527 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A48C 
        7.17        15.39        12.07        12.82        11.31        11.61 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4449 
       12.20        20.02         7.99        54.08        29.98        19.07 
TCGA-CG-4477 TCGA-CG-5733 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 
       30.97        21.07        20.55        18.84        18.54        13.35 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YY 
       10.26        15.98        14.66        14.27        16.44        13.78 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-A72C 
       11.31        20.32        22.29        19.96         7.99        11.38 
TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7133 TCGA-HJ-7597 
       14.07        17.06         0.56         6.21        63.06        26.47 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H5 
       18.15        28.96        11.77         8.98         2.10        23.80 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR 
       33.40        36.36        18.81        13.35         6.44         6.74 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A93H TCGA-MX-A666 TCGA-RD-A7C1 TCGA-RD-A8MV 
       11.70         2.53        37.64        14.04        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E2 
       37.91         8.94        35.61         5.46        13.02        43.36 
TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PS TCGA-VQ-A8PX TCGA-VQ-A8PZ 
        7.73        46.26        12.79        13.35        64.57        73.41 
TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91Y TCGA-VQ-A91Z 
       39.45        18.74        20.81        32.88         9.73        55.56 
TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-AA64 TCGA-VQ-AA6A 
        4.54         5.72        66.81        21.04        18.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-ZQ-A9CR 
       32.94        26.04         0.79 

$`DEL PEAK 35(14Q32.32) WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       21.99        22.98        79.07         0.23        20.15         9.86 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 
       58.03        26.70        11.70         9.47         9.44         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 
        4.64         7.43        30.90         4.08         9.34         6.18 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        6.61        34.68        15.95        13.87        13.68        39.12 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       30.90        44.94        21.90         9.21        36.16        35.84 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       14.43         0.69        29.59        32.25         8.05         0.56 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 
       19.96         2.20        15.58         7.40         6.18        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8384 
       14.04         3.32        11.80        31.27        25.05         3.72 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22         1.12        12.79         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 
        7.53        26.73        31.96        32.58         9.86         8.22 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV 
       34.13        13.87         6.08        34.98        27.55        28.57 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4PE 
        8.98        14.17         0.53        28.34        13.51        20.42 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5802 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 
       13.35        12.10        12.59        12.53        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       12.39        12.59        11.64        12.43         6.31        12.30 
TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
       12.43         6.58        11.77        12.62         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 
       15.95         1.02         8.05         4.01        14.01        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        12.00         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6522 
        7.99        25.71        12.66        20.91        19.13        18.61 
TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.85        17.19        15.22        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET 
       21.14        20.91         5.92        36.43        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       11.24        11.44        15.65         8.38         4.34         7.13 
TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        0.62        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-HF-7132 
       22.29        59.54         5.03        13.58         5.52        77.29 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 
       52.21        30.51         1.51         5.92        24.39        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       22.68        24.20         3.25        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        29.00        23.84        21.17        14.07        15.68 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RS 
        3.45         3.39        18.38        12.46        19.53        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 
        6.51        10.62        15.75        13.51         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       36.95         3.72        19.73        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
        5.13        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV 
       16.87        19.04         5.79         0.92        48.79        13.25 
TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       18.48        21.73        37.41        38.14        37.22        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       34.29        16.31        22.19         2.50         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PY 
        1.87         9.27        23.41        15.65        29.59        14.33 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       11.70        21.83        61.22         1.71        42.64        60.85 
TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A94P 
        9.50         9.04         2.01        55.43         6.58         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F 
       42.54        11.24        43.66        28.41        17.13        54.12 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                           0.46                            0.00 
  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                         122.30                          116.38 
  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                          16.24                           14.38 
[1] "0.5 - 122.3 (16.2)" "0.0 - 116.4 (14.4)"
[1] "hr=" "1"  
D71V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 35(14Q32.32) MUTATED         0        3        9       12        14
  DEL PEAK 35(14Q32.32) WILD-TYPE       2       13       32       20        26
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 35(14Q32.32) MUTATED          17         0         31         21
  DEL PEAK 35(14Q32.32) WILD-TYPE        39         3         50         42
                                 vv
clus                              STAGE IIIC STAGE IV
  DEL PEAK 35(14Q32.32) MUTATED           12        7
  DEL PEAK 35(14Q32.32) WILD-TYPE         27       37
D71V3, multiclass
            clus
vv           DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  STAGE I                                0                               2
  STAGE IA                               3                              13
  STAGE IB                               9                              32
  STAGE II                              12                              20
  STAGE IIA                             14                              26
  STAGE IIB                             17                              39
  STAGE III                              0                               3
  STAGE IIIA                            31                              50
  STAGE IIIB                            21                              42
  STAGE IIIC                            12                              27
  STAGE IV                               7                              37
[1] 11  2
[1] TRUE
[1] "dimension of 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(14Q32.32) MUTATED     5  29  62  33
  DEL PEAK 35(14Q32.32) WILD-TYPE  18  64 134  86
D71V4, multiclass
    clus
vv   DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  T1                             5                              18
  T2                            29                              64
  T3                            62                             134
  T4                            33                              86
[1] 4 2
[1] TRUE
[1] "dimension of 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(14Q32.32) MUTATED   35 38 29 26
  DEL PEAK 35(14Q32.32) WILD-TYPE 95 81 57 62
D71V5, multiclass
    clus
vv   DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  N0                            35                              95
  N1                            38                              81
  N2                            29                              57
  N3                            26                              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"
D71V6, binary
                                 cls
clus                                0   1
  DEL PEAK 35(14Q32.32) MUTATED   121   2
  DEL PEAK 35(14Q32.32) WILD-TYPE 268  28
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(14Q32.32) MUTATED    121    2
  DEL PEAK 35(14Q32.32) WILD-TYPE  268   28
   clus
vv  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  0                           121                             268
  1                             2                              28
[1] 2 2
[1] FALSE
D71V7, binary
                                 cls
clus                                0   1
  DEL PEAK 35(14Q32.32) MUTATED    45  88
  DEL PEAK 35(14Q32.32) WILD-TYPE 113 195
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(14Q32.32) MUTATED     45   88
  DEL PEAK 35(14Q32.32) WILD-TYPE  113  195
        clus
vv       DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  FEMALE                            45                             113
  MALE                              88                             195
[1] 2 2
[1] FALSE
D71V8, binary
                                 cls
clus                                0   1
  DEL PEAK 35(14Q32.32) MUTATED    97  27
  DEL PEAK 35(14Q32.32) WILD-TYPE 225  49
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(14Q32.32) MUTATED     97   27
  DEL PEAK 35(14Q32.32) WILD-TYPE  225   49
     clus
vv    DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  NO                             97                             225
  YES                            27                              49
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 35(14Q32.32) MUTATED                                          5
  DEL PEAK 35(14Q32.32) WILD-TYPE                                        8
                                 vv
clus                              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 35(14Q32.32) MUTATED                                      15
  DEL PEAK 35(14Q32.32) WILD-TYPE                                    57
                                 vv
clus                              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 35(14Q32.32) MUTATED                                                       49
  DEL PEAK 35(14Q32.32) WILD-TYPE                                                    114
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 35(14Q32.32) MUTATED                                                   6
  DEL PEAK 35(14Q32.32) WILD-TYPE                                                15
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 35(14Q32.32) MUTATED                                                                  28
  DEL PEAK 35(14Q32.32) WILD-TYPE                                                                54
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 35(14Q32.32) MUTATED                                                    4
  DEL PEAK 35(14Q32.32) WILD-TYPE                                                  4
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 35(14Q32.32) MUTATED                                                 25
  DEL PEAK 35(14Q32.32) WILD-TYPE                                               54
D71V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 35(14Q32.32) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        15
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       49
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             6
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            28
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             25
                                                                   clus
vv                                                                  DEL PEAK 35(14Q32.32) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                          57
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                        114
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                              15
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                              54
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                               54
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 35(14Q32.32) MUTATED   111   3   3   7
  DEL PEAK 35(14Q32.32) WILD-TYPE 238  15  16  18
D71V10, multiclass
    clus
vv   DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  R0                           111                             238
  R1                             3                              15
  R2                             3                              16
  RX                             7                              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"
D71V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 35(14Q32.32) MUTATED      27                         3
  DEL PEAK 35(14Q32.32) WILD-TYPE    61                         9
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 35(14Q32.32) MUTATED                                           0
  DEL PEAK 35(14Q32.32) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 35(14Q32.32) MUTATED      90
  DEL PEAK 35(14Q32.32) WILD-TYPE   188
D71V12, multiclass
                                           clus
vv                                          DEL PEAK 35(14Q32.32) MUTATED
  ASIAN                                                                27
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                90
                                           clus
vv                                          DEL PEAK 35(14Q32.32) WILD-TYPE
  ASIAN                                                                  61
  BLACK OR AFRICAN AMERICAN                                               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 188
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V13, binary
                                 cls
clus                                0   1
  DEL PEAK 35(14Q32.32) MUTATED     0  97
  DEL PEAK 35(14Q32.32) WILD-TYPE   5 219
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(14Q32.32) MUTATED      0   97
  DEL PEAK 35(14Q32.32) WILD-TYPE    5  219
                        clus
vv                       DEL PEAK 35(14Q32.32) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            97
                        clus
vv                       DEL PEAK 35(14Q32.32) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             219
[1] 2 2
[1] FALSE

Clustering(72) Variable = DEL PEAK 36(15Q11.2) MUTATION ANALYSIS
D72V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 36(15Q11.2) MUTATED    70  42
  DEL PEAK 36(15Q11.2) WILD-TYPE 176 127
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                           112                            303 
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                            42                            127 
$`DEL PEAK 36(15Q11.2) MUTATED`
TCGA-CG-4444 TCGA-FP-A8CX TCGA-MX-A663 TCGA-VQ-A94U TCGA-B7-A5TJ TCGA-BR-4257 
       47.05         0.23         9.86        26.93        11.01         9.67 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7901 
       13.68        19.33         9.17        36.16        35.24         3.45 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8686 
       29.42         2.66        14.79         5.39         9.21        20.88 
TCGA-BR-8690 TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-5801 
       10.68        34.98         0.72        20.65        21.44        13.18 
TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 
       12.10        12.59        12.53         7.17        12.30        12.39 
TCGA-CD-8535 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 
       12.82        12.43        11.61        12.20        20.02         7.99 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4466 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 
       54.08         4.01        18.97         1.02        12.03        15.02 
TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6525 
       69.04        12.66        19.13        20.55        18.84        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8575 
       17.19        10.26        15.22        15.98        12.79        18.21 
TCGA-D7-8576 TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-8122 
       14.66        11.31        22.29        15.65        19.96         7.99 
TCGA-F1-6875 TCGA-FP-8211 TCGA-FP-A4BF TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8245 
       72.23        13.58         5.52        63.06        26.47        18.15 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
       28.96        22.82         3.25        25.81        11.77         8.98 
TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RI 
        6.58         2.10        23.84        21.17        33.40        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F7 
       12.46        13.35        10.62        11.70         2.53        63.62 
TCGA-KB-A93J TCGA-R5-A7ZF TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MW 
       36.95         8.52         9.24        11.05        16.67        37.91 
TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
      115.69        35.61         5.79         0.92        48.79         5.46 
TCGA-VQ-A8E7 TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A8PZ TCGA-VQ-A91N TCGA-VQ-A91Q 
       37.41        17.85        13.35        73.41        18.74        20.81 
TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A92D TCGA-VQ-A94R 
        1.71         9.50         9.73        55.56        66.81        42.54 
TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I 
       43.66        32.94        54.12        16.14 

$`DEL PEAK 36(15Q11.2) WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-VQ-A8PU 
       21.99        22.98        79.07        16.24        20.15        27.35 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN 
       58.03        26.70        11.70        19.56         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6563 TCGA-BR-6564 
       34.68        15.95        13.87        17.29        39.12        26.10 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       19.96         2.20        15.58         7.40         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        31.27         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
       25.05         3.72        25.18        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44T 
       24.79        31.96        32.58         9.86         8.22        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       13.87         7.53         6.08         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         8.98        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL 
       32.52        13.51         0.46        20.42         1.15        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13        13.41        13.02        13.15        13.35        11.21 
TCGA-CD-8524 TCGA-CD-8528 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.76        12.33        12.59        11.64        15.39        12.07 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI 
       12.43         6.31        12.30        11.31         6.58        11.77 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       12.62         3.02        27.02        15.95         1.02         8.05 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 
        7.07        12.00        30.97         6.97        36.00         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        6.02         0.99       105.07        28.96        65.10         4.01 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6521 TCGA-D7-6522 
       21.07         7.99        25.71        20.91        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       17.85        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       19.50        17.19        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 
       11.44        20.32         8.38         4.34         7.13         0.62 
TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A9TM 
       22.29        17.06        59.54         5.03         0.56         6.21 
TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       77.29        52.21        30.51         1.51         5.92        24.39 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.32        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
       22.68        24.20        22.75        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
        6.51        20.25         0.26        12.95        29.00        23.80 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       14.07        15.68        36.36         3.45        18.81         3.39 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V 
       19.53         6.44         6.74        12.59         6.51        15.75 
TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
       13.51         5.56        37.64         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BT 
       45.67        18.21        74.53         6.08         4.60         8.61 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
        5.13       122.30        40.64       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        8.94        16.87        19.04        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       43.36        21.73        38.14        37.22         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH 
       34.29        46.26        16.31        22.19         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
        2.70         1.87         9.27        23.41        15.65        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       64.57        14.33        39.45        11.70        21.83        61.22 
TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
       32.88        42.64        60.85         9.04         2.01        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T 
        4.54         6.58         5.72        21.04         2.66        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6J 
       18.41        28.41        38.93        17.13        26.04        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        17.26         0.79 

  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                          0.23                           0.00 
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                        115.69                         122.30 
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                        14.725                         15.320 
[1] "0.2 - 115.7 (14.7)" "0.0 - 122.3 (15.3)"
[1] "hr=" "1.2"
D72V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 36(15Q11.2) MUTATED         1        5       11        8        11
  DEL PEAK 36(15Q11.2) WILD-TYPE       1       11       30       24        29
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 36(15Q11.2) MUTATED          14         0         30         15
  DEL PEAK 36(15Q11.2) WILD-TYPE        42         3         51         48
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 36(15Q11.2) MUTATED            6       12
  DEL PEAK 36(15Q11.2) WILD-TYPE         33       32
D72V3, multiclass
            clus
vv           DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                              5                             11
  STAGE IB                             11                             30
  STAGE II                              8                             24
  STAGE IIA                            11                             29
  STAGE IIB                            14                             42
  STAGE III                             0                              3
  STAGE IIIA                           30                             51
  STAGE IIIB                           15                             48
  STAGE IIIC                            6                             33
  STAGE IV                             12                             32
[1] 11  2
[1] TRUE
[1] "dimension of 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     6  28  61  22
  DEL PEAK 36(15Q11.2) WILD-TYPE  17  65 135  97
D72V4, multiclass
    clus
vv   DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  T1                            6                             17
  T2                           28                             65
  T3                           61                            135
  T4                           22                             97
[1] 4 2
[1] TRUE
[1] "dimension of 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   35 32 27 21
  DEL PEAK 36(15Q11.2) WILD-TYPE 95 87 59 67
D72V5, multiclass
    clus
vv   DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  N0                           35                             95
  N1                           32                             87
  N2                           27                             59
  N3                           21                             67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V6, binary
                                cls
clus                               0   1
  DEL PEAK 36(15Q11.2) MUTATED   107   7
  DEL PEAK 36(15Q11.2) WILD-TYPE 282  23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(15Q11.2) MUTATED    107    7
  DEL PEAK 36(15Q11.2) WILD-TYPE  282   23
   clus
vv  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  0                          107                            282
  1                            7                             23
[1] 2 2
[1] FALSE
D72V7, binary
                                cls
clus                               0   1
  DEL PEAK 36(15Q11.2) MUTATED    42  78
  DEL PEAK 36(15Q11.2) WILD-TYPE 116 205
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(15Q11.2) MUTATED     42   78
  DEL PEAK 36(15Q11.2) WILD-TYPE  116  205
        clus
vv       DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  FEMALE                           42                            116
  MALE                             78                            205
[1] 2 2
[1] FALSE
D72V8, binary
                                cls
clus                               0   1
  DEL PEAK 36(15Q11.2) MUTATED    79  29
  DEL PEAK 36(15Q11.2) WILD-TYPE 243  47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(15Q11.2) MUTATED     79   29
  DEL PEAK 36(15Q11.2) WILD-TYPE  243   47
     clus
vv    DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  NO                            79                            243
  YES                           29                             47
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 36(15Q11.2) MUTATED                                          5
  DEL PEAK 36(15Q11.2) WILD-TYPE                                        8
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 36(15Q11.2) MUTATED                                      15
  DEL PEAK 36(15Q11.2) WILD-TYPE                                    57
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 36(15Q11.2) MUTATED                                                       36
  DEL PEAK 36(15Q11.2) WILD-TYPE                                                    127
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 36(15Q11.2) MUTATED                                                   4
  DEL PEAK 36(15Q11.2) WILD-TYPE                                                17
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 36(15Q11.2) MUTATED                                                                  27
  DEL PEAK 36(15Q11.2) WILD-TYPE                                                                55
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 36(15Q11.2) MUTATED                                                    3
  DEL PEAK 36(15Q11.2) WILD-TYPE                                                  5
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 36(15Q11.2) MUTATED                                                 30
  DEL PEAK 36(15Q11.2) WILD-TYPE                                               49
D72V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 36(15Q11.2) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       15
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      36
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           27
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            30
                                                                   clus
vv                                                                  DEL PEAK 36(15Q11.2) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         57
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       127
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             17
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             55
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              49
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 36(15Q11.2) MUTATED   100   6   3   4
  DEL PEAK 36(15Q11.2) WILD-TYPE 249  12  16  21
D72V10, multiclass
    clus
vv   DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  R0                          100                            249
  R1                            6                             12
  R2                            3                             16
  RX                            4                             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"
D72V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 36(15Q11.2) MUTATED      28                         2
  DEL PEAK 36(15Q11.2) WILD-TYPE    60                        10
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 36(15Q11.2) MUTATED                                           0
  DEL PEAK 36(15Q11.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 36(15Q11.2) MUTATED      73
  DEL PEAK 36(15Q11.2) WILD-TYPE   205
D72V12, multiclass
                                           clus
vv                                          DEL PEAK 36(15Q11.2) MUTATED
  ASIAN                                                               28
  BLACK OR AFRICAN AMERICAN                                            2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               73
                                           clus
vv                                          DEL PEAK 36(15Q11.2) WILD-TYPE
  ASIAN                                                                 60
  BLACK OR AFRICAN AMERICAN                                             10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                205
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V13, binary
                                cls
clus                               0   1
  DEL PEAK 36(15Q11.2) MUTATED     0  85
  DEL PEAK 36(15Q11.2) WILD-TYPE   5 231
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(15Q11.2) MUTATED      0   85
  DEL PEAK 36(15Q11.2) WILD-TYPE    5  231
                        clus
vv                       DEL PEAK 36(15Q11.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           85
                        clus
vv                       DEL PEAK 36(15Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            231
[1] 2 2
[1] FALSE

Clustering(73) Variable = DEL PEAK 37(15Q15.1) MUTATION ANALYSIS
D73V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 37(15Q15.1) MUTATED    68  45
  DEL PEAK 37(15Q15.1) WILD-TYPE 178 124
  DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE 
                           113                            302 
  DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE 
                            45                            124 
$`DEL PEAK 37(15Q15.1) MUTATED`
TCGA-CG-4444 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-MX-A663 TCGA-VQ-A8PU TCGA-3M-AB46 
       47.05        16.24         0.23         9.86        27.35        58.03 
TCGA-B7-A5TJ TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7704 
       11.01         9.67         6.18         9.17        12.16        35.24 
TCGA-BR-7901 TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8373 TCGA-BR-8483 
        3.45         0.69        29.42         2.66        14.79         5.39 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4QI 
       20.88        10.68        34.98         0.72        20.65        21.44 
TCGA-CD-5801 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 
       13.18        12.59        12.53         7.17        12.30        12.39 
TCGA-CD-8535 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 
       12.82        12.43        11.61        12.20        20.02         7.99 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5719 
       54.08         4.01        14.01        18.97        30.97         1.02 
TCGA-CG-5724 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.03        69.04        12.66        19.13        20.55        18.84 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6822 
       13.35        17.19        10.26        15.22        12.79        12.33 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A 
       18.21        14.66        11.31        22.29        15.65        19.96 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7998 TCGA-FP-8211 TCGA-FP-A4BF TCGA-HF-7133 
        7.99        72.23        22.29        13.58         5.52        63.06 
TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4GP 
       26.47        18.15        28.96        22.82        22.75         8.98 
TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        6.58         2.10        12.95        23.84        23.80        21.17 
TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP 
       33.40        18.81        18.38        12.46        13.35         6.44 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-R5-A7ZF TCGA-R5-A805 TCGA-RD-A7BS 
       10.62        11.70         2.53         8.52         9.24        11.05 
TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT 
       16.67        37.91       115.69        35.61         5.79        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A8PZ TCGA-VQ-A91N 
        5.46        18.48        17.85        13.35        73.41        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       20.81         1.71         9.50         9.73        55.56         9.04 
TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6B 
       66.81        42.54        18.41        43.66        32.94 

$`DEL PEAK 37(15Q15.1) WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-KB-A93G TCGA-VQ-A94U TCGA-B7-5816 
       21.99        22.98        79.07        20.15        26.93        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       11.70        19.56         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        9.34         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       17.29        13.68        19.33        39.12        26.10        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        44.94        21.90         9.21        36.16        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 
       33.63        39.78        18.15        15.32        28.73         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 
       29.56        33.21        37.25        14.43        11.44        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 
        9.60        32.25         8.05         0.56        19.96         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        31.27         7.36        25.05         3.72 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U 
       31.96        32.58         9.86         8.22        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        7.53         6.08         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM 
       13.51         0.46        20.42         1.15        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.41        13.02        13.15        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8528 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.76        12.33        12.59        11.64        15.39        12.07 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI 
       12.43         6.31        12.30        11.31         6.58        11.77 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       12.62         3.02        27.02        15.95         1.02         8.05 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
       29.98        19.07        12.03         0.00         9.01         7.07 
TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       12.00         6.97        36.00         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 
      105.07        15.02        28.96        65.10         4.01        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
        7.99        25.71        20.91        18.54        18.61        17.85 
TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       15.98        12.36        11.31        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       17.19        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
       36.43        13.78        14.76        26.43        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 
       20.32         8.38         4.34         7.13         0.62        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 
       21.27        11.38         3.48        19.53        14.07        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 
       59.54         5.03         0.56         6.21        77.29        52.21 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 
       30.51         1.51         5.92        24.39        22.32        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
        3.25        25.81        11.77        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB 
        6.51        20.25         0.26        29.00        14.07        15.68 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS 
       36.36         3.45         3.39        19.53         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
        6.51        15.75        13.51         5.56        63.62        37.64 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV 
       74.53         6.08         4.60         8.61         5.13       122.30 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB 
       40.64       116.38        71.38        57.44         8.94        16.87 
TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       19.04         0.92        13.25        13.02        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       46.26        16.31        22.19         2.50        12.79         2.70 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX 
        1.87         9.27        23.41        15.65        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S 
       14.33        39.45        11.70        21.83        61.22        32.88 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       42.64        60.85         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA69 TCGA-VQ-AA6A 
        5.72        21.04         2.66        11.24        28.41        38.93 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       17.13        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

  DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE 
                          0.23                           0.00 
  DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE 
                        115.69                         122.30 
  DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE 
                        14.010                         15.355 
[1] "0.2 - 115.7 (14.0)" "0.0 - 122.3 (15.4)"
[1] "hr=" "1"  
D73V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 37(15Q15.1) MUTATED         1        3       14        7         8
  DEL PEAK 37(15Q15.1) WILD-TYPE       1       13       27       25        32
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 37(15Q15.1) MUTATED          12         0         33         18
  DEL PEAK 37(15Q15.1) WILD-TYPE        44         3         48         45
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 37(15Q15.1) MUTATED            7       12
  DEL PEAK 37(15Q15.1) WILD-TYPE         32       32
D73V3, multiclass
            clus
vv           DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                              3                             13
  STAGE IB                             14                             27
  STAGE II                              7                             25
  STAGE IIA                             8                             32
  STAGE IIB                            12                             44
  STAGE III                             0                              3
  STAGE IIIA                           33                             48
  STAGE IIIB                           18                             45
  STAGE IIIC                            7                             32
  STAGE IV                             12                             32
[1] 11  2
[1] TRUE
[1] "dimension of 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(15Q15.1) MUTATED     4  32  59  24
  DEL PEAK 37(15Q15.1) WILD-TYPE  19  61 137  95
D73V4, multiclass
    clus
vv   DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE
  T1                            4                             19
  T2                           32                             61
  T3                           59                            137
  T4                           24                             95
[1] 4 2
[1] TRUE
[1] "dimension of 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(15Q15.1) MUTATED   33 32 28 23
  DEL PEAK 37(15Q15.1) WILD-TYPE 97 87 58 65
D73V5, multiclass
    clus
vv   DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE
  N0                           33                             97
  N1                           32                             87
  N2                           28                             58
  N3                           23                             65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V6, binary
                                cls
clus                               0   1
  DEL PEAK 37(15Q15.1) MUTATED   106   6
  DEL PEAK 37(15Q15.1) WILD-TYPE 283  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(15Q15.1) MUTATED    106    6
  DEL PEAK 37(15Q15.1) WILD-TYPE  283   24
   clus
vv  DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE
  0                          106                            283
  1                            6                             24
[1] 2 2
[1] FALSE
D73V7, binary
                                cls
clus                               0   1
  DEL PEAK 37(15Q15.1) MUTATED    42  80
  DEL PEAK 37(15Q15.1) WILD-TYPE 116 203
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(15Q15.1) MUTATED     42   80
  DEL PEAK 37(15Q15.1) WILD-TYPE  116  203
        clus
vv       DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE
  FEMALE                           42                            116
  MALE                             80                            203
[1] 2 2
[1] FALSE
D73V8, binary
                                cls
clus                               0   1
  DEL PEAK 37(15Q15.1) MUTATED    75  32
  DEL PEAK 37(15Q15.1) WILD-TYPE 247  44
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(15Q15.1) MUTATED     75   32
  DEL PEAK 37(15Q15.1) WILD-TYPE  247   44
     clus
vv    DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE
  NO                            75                            247
  YES                           32                             44
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 37(15Q15.1) MUTATED                                          4
  DEL PEAK 37(15Q15.1) WILD-TYPE                                        9
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 37(15Q15.1) MUTATED                                      14
  DEL PEAK 37(15Q15.1) WILD-TYPE                                    58
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 37(15Q15.1) MUTATED                                                       37
  DEL PEAK 37(15Q15.1) WILD-TYPE                                                    126
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 37(15Q15.1) MUTATED                                                   4
  DEL PEAK 37(15Q15.1) WILD-TYPE                                                17
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 37(15Q15.1) MUTATED                                                                  29
  DEL PEAK 37(15Q15.1) WILD-TYPE                                                                53
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 37(15Q15.1) MUTATED                                                    3
  DEL PEAK 37(15Q15.1) WILD-TYPE                                                  5
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 37(15Q15.1) MUTATED                                                 30
  DEL PEAK 37(15Q15.1) WILD-TYPE                                               49
D73V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 37(15Q15.1) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     4
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       14
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      37
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           29
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            30
                                                                   clus
vv                                                                  DEL PEAK 37(15Q15.1) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                       9
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         58
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       126
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             17
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             53
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              49
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 37(15Q15.1) MUTATED    98   7   3   6
  DEL PEAK 37(15Q15.1) WILD-TYPE 251  11  16  19
D73V10, multiclass
    clus
vv   DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE
  R0                           98                            251
  R1                            7                             11
  R2                            3                             16
  RX                            6                             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"
D73V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 37(15Q15.1) MUTATED      27                         3
  DEL PEAK 37(15Q15.1) WILD-TYPE    61                         9
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 37(15Q15.1) MUTATED                                           0
  DEL PEAK 37(15Q15.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 37(15Q15.1) MUTATED      74
  DEL PEAK 37(15Q15.1) WILD-TYPE   204
D73V12, multiclass
                                           clus
vv                                          DEL PEAK 37(15Q15.1) MUTATED
  ASIAN                                                               27
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               74
                                           clus
vv                                          DEL PEAK 37(15Q15.1) WILD-TYPE
  ASIAN                                                                 61
  BLACK OR AFRICAN AMERICAN                                              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                204
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V13, binary
                                cls
clus                               0   1
  DEL PEAK 37(15Q15.1) MUTATED     2  87
  DEL PEAK 37(15Q15.1) WILD-TYPE   3 229
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(15Q15.1) MUTATED      2   87
  DEL PEAK 37(15Q15.1) WILD-TYPE    3  229
                        clus
vv                       DEL PEAK 37(15Q15.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           87
                        clus
vv                       DEL PEAK 37(15Q15.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            229
[1] 2 2
[1] FALSE

Clustering(74) Variable = DEL PEAK 38(16P13.3) MUTATION ANALYSIS
D74V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 38(16P13.3) MUTATED    55  37
  DEL PEAK 38(16P13.3) WILD-TYPE 191 132
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                            92                            323 
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                            37                            132 
$`DEL PEAK 38(16P13.3) MUTATED`
TCGA-CG-4444 TCGA-VQ-A8PU TCGA-BR-4183 TCGA-BR-4255 TCGA-BR-7197 TCGA-BR-7704 
       47.05        27.35         6.61         4.08         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8286 TCGA-BR-8289 
       33.63        39.78         3.45        33.21        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8365 TCGA-BR-8373 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-A452 
       19.96        17.52        14.79        26.73        24.79         7.53 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4PF TCGA-CD-5802 TCGA-CD-5803 
       34.98         1.48         0.72         1.15        13.35        11.21 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A486 
       12.76        12.59        12.53        12.39        12.82         6.31 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4449 TCGA-CG-4455 
       12.30        12.43        11.61        12.20        19.07        12.03 
TCGA-CG-5724 TCGA-D7-5579 TCGA-D7-6528 TCGA-D7-6822 TCGA-D7-A6EX TCGA-D7-A6F0 
       12.03        20.91        15.22        12.33        11.31        22.29 
TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-8211 TCGA-HF-7133 TCGA-HU-8243 
       19.96         7.99        72.23        13.58        63.06         5.92 
TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       18.15        22.82         0.76        22.75        25.81        11.77 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-8663 TCGA-IN-A6RL 
       23.84        23.80        21.17        33.40         3.39        13.35 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A666 
        6.44         6.74        12.59         5.56        37.64        14.04 
TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8N9 TCGA-SW-A7EB 
        6.08         9.24        11.05        16.67        35.61         5.79 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8P5 
       48.79         5.46        13.25        13.02        18.48         7.73 
TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       46.26        22.19        12.79         2.70        17.85         1.87 
TCGA-VQ-A8PX TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-AA68 TCGA-VQ-AA6A 
       64.57        55.56         9.04        21.04        43.66        38.93 
TCGA-VQ-AA6D TCGA-VQ-AA6J 
       17.13        27.55 

$`DEL PEAK 38(16P13.3) WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       21.99        22.98        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        9.86        26.93        58.03        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35        30.90         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        44.94        21.90        36.16        35.84 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
       18.15        15.32        28.73         9.07        29.56        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        8.05         0.56         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 
       31.10        13.08         0.26        22.19         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        31.27         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        7.53        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
       10.68        34.13        13.87         6.08        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         8.98        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI 
       32.52        13.51         0.46        20.65        20.42        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5804 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
       12.10         7.17        12.33        12.30        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI 
       15.39        12.07        12.43        11.31         6.58        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 
       21.07         7.99        25.71        12.66        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 
       10.26        15.98        12.79        12.36        11.31        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 
       14.76        26.43        11.24        11.44        20.32        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-A448 
        8.38         4.34         7.13         0.62        14.47        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       59.54         5.03         0.56         5.52         6.21        77.29 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 
       52.21        30.51        26.47         1.51        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       22.32        21.07        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       24.20         3.25        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       29.00        14.07        15.68        36.36         3.45        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
       18.38        12.46        19.53         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       15.75        13.51         2.53        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
       19.73        45.67        18.21         8.52        74.53         4.60 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        8.61         5.13       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        16.87        19.04 
TCGA-VQ-A8DL TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        0.92        43.36        21.73        37.41        38.14        37.22 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PP 
       30.97        34.29        16.31         2.50         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        13.35        29.59        14.33        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       11.70        21.83        61.22        18.74        20.81        32.88 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A923 
        1.71        42.64        60.85         9.50         9.73         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P 
       55.43         4.54         6.58         5.72        66.81         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F 
       42.54        11.24        18.41        28.41        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        12.43        17.26         0.79 

  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                          0.72                           0.00 
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                         72.23                         122.30 
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                         13.35                          15.58 
[1] "0.7 - 72.2 (13.3)"  "0.0 - 122.3 (15.6)"
[1] "hr=" "1"  
D74V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 38(16P13.3) MUTATED         0        5        7       10        10
  DEL PEAK 38(16P13.3) WILD-TYPE       2       11       34       22        30
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 38(16P13.3) MUTATED          11         1         28          8
  DEL PEAK 38(16P13.3) WILD-TYPE        45         2         53         55
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 38(16P13.3) MUTATED            7        7
  DEL PEAK 38(16P13.3) WILD-TYPE         32       37
D74V3, multiclass
            clus
vv           DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              5                             11
  STAGE IB                              7                             34
  STAGE II                             10                             22
  STAGE IIA                            10                             30
  STAGE IIB                            11                             45
  STAGE III                             1                              2
  STAGE IIIA                           28                             53
  STAGE IIIB                            8                             55
  STAGE IIIC                            7                             32
  STAGE IV                              7                             37
[1] 11  2
[1] TRUE
[1] "dimension of 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     5  18  52  20
  DEL PEAK 38(16P13.3) WILD-TYPE  18  75 144  99
D74V4, multiclass
    clus
vv   DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  T1                            5                             18
  T2                           18                             75
  T3                           52                            144
  T4                           20                             99
[1] 4 2
[1] TRUE
[1] "dimension of 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    28  32  16  17
  DEL PEAK 38(16P13.3) WILD-TYPE 102  87  70  71
D74V5, multiclass
    clus
vv   DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  N0                           28                            102
  N1                           32                             87
  N2                           16                             70
  N3                           17                             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V6, binary
                                cls
clus                               0   1
  DEL PEAK 38(16P13.3) MUTATED    91   4
  DEL PEAK 38(16P13.3) WILD-TYPE 298  26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16P13.3) MUTATED     91    4
  DEL PEAK 38(16P13.3) WILD-TYPE  298   26
   clus
vv  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  0                           91                            298
  1                            4                             26
[1] 2 2
[1] FALSE
D74V7, binary
                                cls
clus                               0   1
  DEL PEAK 38(16P13.3) MUTATED    30  68
  DEL PEAK 38(16P13.3) WILD-TYPE 128 215
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16P13.3) MUTATED     30   68
  DEL PEAK 38(16P13.3) WILD-TYPE  128  215
        clus
vv       DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  FEMALE                           30                            128
  MALE                             68                            215
[1] 2 2
[1] FALSE
D74V8, binary
                                cls
clus                               0   1
  DEL PEAK 38(16P13.3) MUTATED    71  21
  DEL PEAK 38(16P13.3) WILD-TYPE 251  55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16P13.3) MUTATED     71   21
  DEL PEAK 38(16P13.3) WILD-TYPE  251   55
     clus
vv    DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  NO                            71                            251
  YES                           21                             55
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 38(16P13.3) MUTATED                                          3
  DEL PEAK 38(16P13.3) WILD-TYPE                                       10
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 38(16P13.3) MUTATED                                       8
  DEL PEAK 38(16P13.3) WILD-TYPE                                    64
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 38(16P13.3) MUTATED                                                       34
  DEL PEAK 38(16P13.3) WILD-TYPE                                                    129
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 38(16P13.3) MUTATED                                                   7
  DEL PEAK 38(16P13.3) WILD-TYPE                                                14
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 38(16P13.3) MUTATED                                                                  18
  DEL PEAK 38(16P13.3) WILD-TYPE                                                                64
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 38(16P13.3) MUTATED                                                    2
  DEL PEAK 38(16P13.3) WILD-TYPE                                                  6
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 38(16P13.3) MUTATED                                                 26
  DEL PEAK 38(16P13.3) WILD-TYPE                                               53
D74V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 38(16P13.3) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        8
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      34
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            7
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           18
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            26
                                                                   clus
vv                                                                  DEL PEAK 38(16P13.3) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       129
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             14
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              53
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 38(16P13.3) MUTATED    74   5   3   6
  DEL PEAK 38(16P13.3) WILD-TYPE 275  13  16  19
D74V10, multiclass
    clus
vv   DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  R0                           74                            275
  R1                            5                             13
  R2                            3                             16
  RX                            6                             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"
D74V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 38(16P13.3) MUTATED      27                         6
  DEL PEAK 38(16P13.3) WILD-TYPE    61                         6
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 38(16P13.3) MUTATED                                           0
  DEL PEAK 38(16P13.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 38(16P13.3) MUTATED      53
  DEL PEAK 38(16P13.3) WILD-TYPE   225
D74V12, multiclass
                                           clus
vv                                          DEL PEAK 38(16P13.3) MUTATED
  ASIAN                                                               27
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               53
                                           clus
vv                                          DEL PEAK 38(16P13.3) WILD-TYPE
  ASIAN                                                                 61
  BLACK OR AFRICAN AMERICAN                                              6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                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"
D74V13, binary
                                cls
clus                               0   1
  DEL PEAK 38(16P13.3) MUTATED     0  69
  DEL PEAK 38(16P13.3) WILD-TYPE   5 247
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16P13.3) MUTATED      0   69
  DEL PEAK 38(16P13.3) WILD-TYPE    5  247
                        clus
vv                       DEL PEAK 38(16P13.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           69
                        clus
vv                       DEL PEAK 38(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            247
[1] 2 2
[1] FALSE

Clustering(75) Variable = DEL PEAK 39(16Q23.1) MUTATION ANALYSIS
D75V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 39(16Q23.1) MUTATED   104  70
  DEL PEAK 39(16Q23.1) WILD-TYPE 142  99
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                           174                            241 
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                            70                             99 
$`DEL PEAK 39(16Q23.1) MUTATED`
TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 
       47.05        22.98        79.07        16.24        20.15         9.86 
TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       26.93        58.03        26.70        11.70        19.56        11.01 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        9.44         6.61         6.97        18.35         4.08         4.08 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6706 
        9.57         6.61        17.29        19.33        26.10        18.05 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 
       36.16        35.24        33.63        18.15        28.73         3.45 
TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8285 TCGA-BR-8286 
       33.21        11.44         0.69         9.60         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8365 
        2.66        19.96        31.10        13.08         0.26        17.52 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       31.27        14.79        25.18        26.73        24.79        32.58 
TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4PD 
        8.22        13.87         7.53        34.98         0.72        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
       20.42         1.15        21.44        13.15        13.35        11.21 
TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 
       12.76        12.53        12.39        12.07        12.82         6.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       12.43        11.61        12.20        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5723 
       54.08        19.07        12.03         7.07        30.97       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6525 
       12.03        15.02        25.71        12.66        20.91        13.35 
TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-8573 TCGA-D7-8575 
       17.19        15.22        12.79        12.36        19.50        18.21 
TCGA-D7-A4YT TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 
       14.27        36.43        13.78        11.24        11.31        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-F1-6875 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-A4BF 
       15.65         8.38        72.23        14.07        22.29         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 
        6.21        77.29        63.06        30.51         1.51         5.92 
TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4GD 
       18.15        22.82         0.76         5.59        24.26        22.75 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
       11.77         8.98         6.58        20.25         0.26         2.10 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 
       23.84        23.80        21.17        33.40         3.45        18.81 
TCGA-IN-A6RI TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V 
       18.38        19.53         6.44         6.51        11.70        15.75 
TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7ZR TCGA-R5-A805 
       13.51         5.56        63.62        37.64         6.08         9.24 
TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL 
       11.05        16.67         8.94        35.61         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE 
       48.79         5.46        13.02         7.73        46.26        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PP TCGA-VQ-A8PX TCGA-VQ-A8PY 
       12.79        17.85         1.87        23.41        64.57        14.33 
TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X 
       39.45        21.83        61.22        32.88         1.71         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A94R 
        9.73        55.56         9.04         4.54         5.72        42.54 
TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-ZQ-A9CR 
       43.66        38.93        17.13        54.12        26.04         0.79 

$`DEL PEAK 39(16Q23.1) WILD-TYPE`
TCGA-CG-4460 TCGA-FP-A8CX TCGA-VQ-A8PU TCGA-B7-A5TK TCGA-BR-4187 TCGA-BR-4188 
       21.99         0.23        27.35         9.47         4.64         7.43 
TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-6453 
       30.90         9.34         9.67         6.18        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.87        13.68        39.12         9.17        32.78        25.61 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 
       44.94        21.90         9.21        35.84        39.78        15.32 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 
        9.07        29.56        37.25        14.43        29.59        32.25 
TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8364 
        8.05         2.20        15.58         7.40         6.18        22.19 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 
        7.36        25.05         3.72         5.39         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T 
        7.53        31.96         9.86        20.88        10.68        34.13 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 
        0.46        16.14         5.13        13.41        13.02        13.18 
TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 
       12.10        12.59         7.17        12.33        12.30        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG 
       11.64        15.39        12.43        12.30        11.31         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
       11.77        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
        4.01        14.01        29.98         0.00         9.01        18.97 
TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       12.00         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
        0.99        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
        7.99        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       17.85        10.26        15.98        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU 
       16.80        17.19        14.66        21.14        20.91        16.44 
TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 
        5.92        14.76        26.43        11.44        20.32         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 
       19.96         7.13         0.62         7.99        14.47        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       11.38         3.48        19.53        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8249 
       13.58         0.56        52.21        26.47        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       22.32        21.07        24.30        22.68        24.20         3.25 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4H2 
       25.81        21.37        29.98         0.10         6.51        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8663 TCGA-IN-A6RJ 
       29.00        14.07        15.68        36.36         3.39        12.46 
TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IP-7968 TCGA-KB-A93J 
       13.35         6.74        12.59        10.62         2.53        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
       74.53         4.60         8.61         5.13       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB 
       40.64       115.69       116.38        71.38        57.44        16.87 
TCGA-SW-A7EA TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       19.04        13.25        18.48        43.36        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF 
       38.14        37.22        30.97        34.29        16.31         2.50 
TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ 
        2.70         9.27        15.65        13.35        29.59        73.41 
TCGA-VQ-A91D TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A923 
       11.70        18.74        20.81        42.64        60.85         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T 
       55.43         6.58        66.81        21.04         2.66        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       18.41        28.41        32.94        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                          0.26                           0.00 
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                        105.07                         122.30 
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                        14.905                         14.760 
[1] "0.3 - 105.1 (14.9)" "0.0 - 122.3 (14.8)"
[1] "hr=" "1"  
D75V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 39(16Q23.1) MUTATED         1        7       17       17        16
  DEL PEAK 39(16Q23.1) WILD-TYPE       1        9       24       15        24
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 39(16Q23.1) MUTATED          23         2         41         18
  DEL PEAK 39(16Q23.1) WILD-TYPE        33         1         40         45
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 39(16Q23.1) MUTATED           20       12
  DEL PEAK 39(16Q23.1) WILD-TYPE         19       32
D75V3, multiclass
            clus
vv           DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                              7                              9
  STAGE IB                             17                             24
  STAGE II                             17                             15
  STAGE IIA                            16                             24
  STAGE IIB                            23                             33
  STAGE III                             2                              1
  STAGE IIIA                           41                             40
  STAGE IIIB                           18                             45
  STAGE IIIC                           20                             19
  STAGE IV                             12                             32
[1] 11  2
[1] TRUE
[1] "dimension of 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    11  41  82  46
  DEL PEAK 39(16Q23.1) WILD-TYPE  12  52 114  73
D75V4, multiclass
    clus
vv   DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  T1                           11                             12
  T2                           41                             52
  T3                           82                            114
  T4                           46                             73
[1] 4 2
[1] TRUE
[1] "dimension of 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   52 53 31 40
  DEL PEAK 39(16Q23.1) WILD-TYPE 78 66 55 48
D75V5, multiclass
    clus
vv   DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  N0                           52                             78
  N1                           53                             66
  N2                           31                             55
  N3                           40                             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V6, binary
                                cls
clus                               0   1
  DEL PEAK 39(16Q23.1) MUTATED   170   5
  DEL PEAK 39(16Q23.1) WILD-TYPE 219  25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(16Q23.1) MUTATED    170    5
  DEL PEAK 39(16Q23.1) WILD-TYPE  219   25
   clus
vv  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  0                          170                            219
  1                            5                             25
[1] 2 2
[1] FALSE
D75V7, binary
                                cls
clus                               0   1
  DEL PEAK 39(16Q23.1) MUTATED    60 122
  DEL PEAK 39(16Q23.1) WILD-TYPE  98 161
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(16Q23.1) MUTATED     60  122
  DEL PEAK 39(16Q23.1) WILD-TYPE   98  161
        clus
vv       DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  FEMALE                           60                             98
  MALE                            122                            161
[1] 2 2
[1] FALSE
D75V8, binary
                                cls
clus                               0   1
  DEL PEAK 39(16Q23.1) MUTATED   138  34
  DEL PEAK 39(16Q23.1) WILD-TYPE 184  42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(16Q23.1) MUTATED    138   34
  DEL PEAK 39(16Q23.1) WILD-TYPE  184   42
     clus
vv    DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  NO                           138                            184
  YES                           34                             42
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 39(16Q23.1) MUTATED                                          6
  DEL PEAK 39(16Q23.1) WILD-TYPE                                        7
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 39(16Q23.1) MUTATED                                      24
  DEL PEAK 39(16Q23.1) WILD-TYPE                                    48
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 39(16Q23.1) MUTATED                                                       63
  DEL PEAK 39(16Q23.1) WILD-TYPE                                                    100
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 39(16Q23.1) MUTATED                                                  11
  DEL PEAK 39(16Q23.1) WILD-TYPE                                                10
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 39(16Q23.1) MUTATED                                                                  31
  DEL PEAK 39(16Q23.1) WILD-TYPE                                                                51
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 39(16Q23.1) MUTATED                                                    6
  DEL PEAK 39(16Q23.1) WILD-TYPE                                                  2
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 39(16Q23.1) MUTATED                                                 39
  DEL PEAK 39(16Q23.1) WILD-TYPE                                               40
D75V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 39(16Q23.1) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     6
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       24
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      63
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           11
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           31
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            39
                                                                   clus
vv                                                                  DEL PEAK 39(16Q23.1) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         48
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       100
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             10
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             51
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              40
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 39(16Q23.1) MUTATED   145   9   4  10
  DEL PEAK 39(16Q23.1) WILD-TYPE 204   9  15  15
D75V10, multiclass
    clus
vv   DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  R0                          145                            204
  R1                            9                              9
  R2                            4                             15
  RX                           10                             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"
D75V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 39(16Q23.1) MUTATED      37                         4
  DEL PEAK 39(16Q23.1) WILD-TYPE    51                         8
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 39(16Q23.1) MUTATED                                           0
  DEL PEAK 39(16Q23.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 39(16Q23.1) MUTATED     114
  DEL PEAK 39(16Q23.1) WILD-TYPE   164
D75V12, multiclass
                                           clus
vv                                          DEL PEAK 39(16Q23.1) MUTATED
  ASIAN                                                               37
  BLACK OR AFRICAN AMERICAN                                            4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              114
                                           clus
vv                                          DEL PEAK 39(16Q23.1) WILD-TYPE
  ASIAN                                                                 51
  BLACK OR AFRICAN AMERICAN                                              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V13, binary
                                cls
clus                               0   1
  DEL PEAK 39(16Q23.1) MUTATED     2 125
  DEL PEAK 39(16Q23.1) WILD-TYPE   3 191
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(16Q23.1) MUTATED      2  125
  DEL PEAK 39(16Q23.1) WILD-TYPE    3  191
                        clus
vv                       DEL PEAK 39(16Q23.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          125
                        clus
vv                       DEL PEAK 39(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            191
[1] 2 2
[1] FALSE

Clustering(76) Variable = DEL PEAK 40(17P12) MUTATION ANALYSIS
D76V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 40(17P12) MUTATED   104  71
  DEL PEAK 40(17P12) WILD-TYPE 142  98
  DEL PEAK 40(17P12) MUTATED DEL PEAK 40(17P12) WILD-TYPE 
                         175                          240 
  DEL PEAK 40(17P12) MUTATED DEL PEAK 40(17P12) WILD-TYPE 
                          71                           98 
$`DEL PEAK 40(17P12) MUTATED`
TCGA-CG-4444 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-MX-A663 TCGA-VQ-A8PU 
       47.05        79.07        16.24         0.23         9.86        27.35 
TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 
       26.93        58.03        11.70        11.01         9.44         6.61 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6709 
        9.67         6.18        17.29        19.33         9.17        12.16 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8060 
        9.21        35.24        33.63        28.73        33.21        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 
        0.69         9.60        29.42         2.66        19.96        15.58 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8484 
       31.10        13.08        14.04        14.79         5.39        25.18 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 
       24.79        32.58         9.86        10.68        13.87         7.53 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       34.98         1.48         0.72        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 
        1.15        13.02        13.15        12.76        12.59         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 
       12.33        12.30        15.39        12.82         6.31        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.43        11.61        12.20        20.02         3.02        27.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 
        7.99         8.05        54.08         4.01        29.98        19.07 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5725 TCGA-CG-5730 
        7.07        30.97        36.00         1.02        15.02         4.01 
TCGA-CG-5732 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 
       69.04        20.91        20.55        18.84        18.54        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-6822 
       17.19        10.26        15.22        15.98        11.31        12.33 
TCGA-D7-8576 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-8122 
       14.66        16.44        11.31        15.65        19.96         7.99 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 
       72.23        11.38        14.07        17.06        13.58         0.56 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8245 
        6.21        77.29        63.06        26.47         1.51        18.15 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU 
       28.96        22.82        22.75        11.77         8.98         6.58 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
        2.10        12.95        23.80        33.40        36.36        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NU 
        3.39        18.38        13.35         6.44        12.59        11.70 
TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A666 
       15.75         2.53         5.56        37.64        36.95        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 
       45.67        18.21         9.24         8.61        16.67       115.69 
TCGA-RD-A8N6 TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        8.94         0.92         5.46        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       43.36         7.73        46.26        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91N 
        1.87        13.35        64.57        14.33        73.41        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       20.81        42.64         9.50         9.73        55.56         9.04 
TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6B 
        4.54        66.81        11.24        18.41        43.66        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       17.13        54.12        26.04        16.14        27.55        12.43 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK 40(17P12) WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-KB-A93G TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK 
       21.99        22.98        20.15        26.70        19.56         9.47 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        4.08         9.34         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
       13.87        13.68        39.12        26.10        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 
       44.94        21.90        36.16        35.84        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 
       15.32         3.45         9.07        29.56        37.25        14.43 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8295 TCGA-BR-8297 
       29.59        32.25         8.05         0.56         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
        4.31         3.32        11.80        31.27         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        3.72         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        9.34        28.14         6.28         7.53        26.73        31.96 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
       20.88         8.22        34.13         6.08        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         8.98        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       32.52         0.46        21.44        16.14         5.13        13.41 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8526 TCGA-CD-8530 
       13.18        13.35        11.21        12.10        12.53        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A4MG 
       12.59        11.64        12.07        12.43        12.30         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4455 
       11.77        12.62        15.95         1.02        14.01        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5720 
        0.00         9.01        18.97        12.00         6.97         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99       105.07        12.03        28.96        65.10 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6522 
       21.07         7.99        25.71        12.66        19.13        18.61 
TCGA-D7-6524 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       17.85        12.79        12.36        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       17.19        18.21        21.14        20.91        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
       36.43        13.78        14.76        26.43        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 
       20.32        22.29         8.38         4.34         7.13         0.62 
TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 
       14.47        21.27         3.48        19.53        22.29        59.54 
TCGA-FP-8210 TCGA-FP-A4BF TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8243 TCGA-HU-8244 
        5.03         5.52        52.21        30.51         5.92        24.39 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.32        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       22.68        24.20         3.25        25.81        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 
        0.10         6.51        20.25         0.26        29.00        23.84 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-A6RJ TCGA-IN-A6RN 
       21.17        14.07        15.68         3.45        12.46        19.53 
TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-MX-A5UG 
        6.74         6.51        10.62        13.51        63.62         3.72 
TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BS 
       19.73         8.52        74.53         6.08         4.60        11.05 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
        5.13       122.30        37.91        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT 
       57.44        35.61        16.87        19.04         5.79        48.79 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        37.41        38.14        37.22        30.97        34.29 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       16.31        22.19         2.50         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S 
       29.59        39.45        11.70        21.83        61.22        32.88 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
        1.71        60.85         2.01        55.43         6.58         5.72 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-ZA-A8F6 
       21.04         2.66        42.54        28.41        38.93        17.26 

  DEL PEAK 40(17P12) MUTATED DEL PEAK 40(17P12) WILD-TYPE 
                        0.23                         0.00 
  DEL PEAK 40(17P12) MUTATED DEL PEAK 40(17P12) WILD-TYPE 
                      115.69                       122.30 
  DEL PEAK 40(17P12) MUTATED DEL PEAK 40(17P12) WILD-TYPE 
                      14.040                       16.045 
[1] "0.2 - 115.7 (14.0)" "0.0 - 122.3 (16.0)"
[1] "hr=" "1"  
D76V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 40(17P12) MUTATED         1        7       18       16        16
  DEL PEAK 40(17P12) WILD-TYPE       1        9       23       16        24
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 40(17P12) MUTATED          22         0         35         28
  DEL PEAK 40(17P12) WILD-TYPE        34         3         46         35
                              vv
clus                           STAGE IIIC STAGE IV
  DEL PEAK 40(17P12) MUTATED           13       18
  DEL PEAK 40(17P12) WILD-TYPE         26       26
D76V3, multiclass
            clus
vv           DEL PEAK 40(17P12) MUTATED DEL PEAK 40(17P12) WILD-TYPE
  STAGE I                             1                            1
  STAGE IA                            7                            9
  STAGE IB                           18                           23
  STAGE II                           16                           16
  STAGE IIA                          16                           24
  STAGE IIB                          22                           34
  STAGE III                           0                            3
  STAGE IIIA                         35                           46
  STAGE IIIB                         28                           35
  STAGE IIIC                         13                           26
  STAGE IV                           18                           26
[1] 11  2
[1] TRUE
[1] "dimension of 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(17P12) MUTATED     9  45  83  42
  DEL PEAK 40(17P12) WILD-TYPE  14  48 113  77
D76V4, multiclass
    clus
vv   DEL PEAK 40(17P12) MUTATED DEL PEAK 40(17P12) WILD-TYPE
  T1                          9                           14
  T2                         45                           48
  T3                         83                          113
  T4                         42                           77
[1] 4 2
[1] TRUE
[1] "dimension of 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(17P12) MUTATED   55 47 40 34
  DEL PEAK 40(17P12) WILD-TYPE 75 72 46 54
D76V5, multiclass
    clus
vv   DEL PEAK 40(17P12) MUTATED DEL PEAK 40(17P12) WILD-TYPE
  N0                         55                           75
  N1                         47                           72
  N2                         40                           46
  N3                         34                           54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V6, binary
                              cls
clus                             0   1
  DEL PEAK 40(17P12) MUTATED   159   9
  DEL PEAK 40(17P12) WILD-TYPE 230  21
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 40(17P12) MUTATED    159    9
  DEL PEAK 40(17P12) WILD-TYPE  230   21
   clus
vv  DEL PEAK 40(17P12) MUTATED DEL PEAK 40(17P12) WILD-TYPE
  0                        159                          230
  1                          9                           21
[1] 2 2
[1] FALSE
D76V7, binary
                              cls
clus                             0   1
  DEL PEAK 40(17P12) MUTATED    56 125
  DEL PEAK 40(17P12) WILD-TYPE 102 158
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 40(17P12) MUTATED     56  125
  DEL PEAK 40(17P12) WILD-TYPE  102  158
        clus
vv       DEL PEAK 40(17P12) MUTATED DEL PEAK 40(17P12) WILD-TYPE
  FEMALE                         56                          102
  MALE                          125                          158
[1] 2 2
[1] FALSE
D76V8, binary
                              cls
clus                             0   1
  DEL PEAK 40(17P12) MUTATED   125  38
  DEL PEAK 40(17P12) WILD-TYPE 197  38
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 40(17P12) MUTATED    125   38
  DEL PEAK 40(17P12) WILD-TYPE  197   38
     clus
vv    DEL PEAK 40(17P12) MUTATED DEL PEAK 40(17P12) WILD-TYPE
  NO                         125                          197
  YES                         38                           38
[1] 2 2
[1] FALSE
                              vv
clus                           STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 40(17P12) MUTATED                                          8
  DEL PEAK 40(17P12) WILD-TYPE                                        5
                              vv
clus                           STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 40(17P12) MUTATED                                      16
  DEL PEAK 40(17P12) WILD-TYPE                                    56
                              vv
clus                           STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 40(17P12) MUTATED                                                       59
  DEL PEAK 40(17P12) WILD-TYPE                                                    104
                              vv
clus                           STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 40(17P12) MUTATED                                                   9
  DEL PEAK 40(17P12) WILD-TYPE                                                12
                              vv
clus                           STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 40(17P12) MUTATED                                                                  42
  DEL PEAK 40(17P12) WILD-TYPE                                                                40
                              vv
clus                           STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 40(17P12) MUTATED                                                    4
  DEL PEAK 40(17P12) WILD-TYPE                                                  4
                              vv
clus                           STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 40(17P12) MUTATED                                                 42
  DEL PEAK 40(17P12) WILD-TYPE                                               37
D76V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 40(17P12) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                   8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                     16
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                    59
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                          9
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         42
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                          42
                                                                   clus
vv                                                                  DEL PEAK 40(17P12) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       56
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     104
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           12
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           40
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            37
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 40(17P12) MUTATED   144   9   8   5
  DEL PEAK 40(17P12) WILD-TYPE 205   9  11  20
D76V10, multiclass
    clus
vv   DEL PEAK 40(17P12) MUTATED DEL PEAK 40(17P12) WILD-TYPE
  R0                        144                          205
  R1                          9                            9
  R2                          8                           11
  RX                          5                           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"
D76V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 40(17P12) MUTATED      35                         4
  DEL PEAK 40(17P12) WILD-TYPE    53                         8
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 40(17P12) MUTATED                                           1   110
  DEL PEAK 40(17P12) WILD-TYPE                                         0   168
D76V12, multiclass
                                           clus
vv                                          DEL PEAK 40(17P12) MUTATED
  ASIAN                                                             35
  BLACK OR AFRICAN AMERICAN                                          4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                            110
                                           clus
vv                                          DEL PEAK 40(17P12) WILD-TYPE
  ASIAN                                                               53
  BLACK OR AFRICAN AMERICAN                                            8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              168
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V13, binary
                              cls
clus                             0   1
  DEL PEAK 40(17P12) MUTATED     2 117
  DEL PEAK 40(17P12) WILD-TYPE   3 199
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 40(17P12) MUTATED      2  117
  DEL PEAK 40(17P12) WILD-TYPE    3  199
                        clus
vv                       DEL PEAK 40(17P12) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                        117
                        clus
vv                       DEL PEAK 40(17P12) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          199
[1] 2 2
[1] FALSE

Clustering(77) Variable = DEL PEAK 41(17Q24.3) MUTATION ANALYSIS
D77V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 41(17Q24.3) MUTATED    38  32
  DEL PEAK 41(17Q24.3) WILD-TYPE 208 137
  DEL PEAK 41(17Q24.3) MUTATED DEL PEAK 41(17Q24.3) WILD-TYPE 
                            70                            345 
  DEL PEAK 41(17Q24.3) MUTATED DEL PEAK 41(17Q24.3) WILD-TYPE 
                            32                            137 
$`DEL PEAK 41(17Q24.3) MUTATED`
TCGA-CG-4444 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-MX-A663 TCGA-VQ-A94U TCGA-B7-A5TJ 
       47.05        16.24         0.23         9.86        26.93        11.01 
TCGA-BR-4257 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7959 
        9.67        19.33         9.17        35.24        33.63        33.21 
TCGA-BR-8077 TCGA-BR-8291 TCGA-BR-8361 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8485 
        0.69        19.96        31.10        14.79         3.72         9.21 
TCGA-BR-8683 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD 
        9.86        13.87         7.53         0.72        13.51        20.65 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-8524 TCGA-CD-8528 TCGA-CD-8533 TCGA-CD-A489 
        1.15        21.44        12.76        12.33        15.39        11.31 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       11.61        12.20        20.02        54.08         4.01        14.01 
TCGA-CG-4469 TCGA-CG-5730 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-8576 
        7.07         4.01        20.91        17.19        15.22        14.66 
TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A74A TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       16.44        11.31        19.96         5.92        18.15        28.96 
TCGA-HU-A4GP TCGA-HU-A4H2 TCGA-IN-8462 TCGA-IN-8663 TCGA-KB-A93H TCGA-R5-A7O7 
        8.98        12.95        18.81         3.39        37.64        45.67 
TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DU 
        8.61        16.67       115.69         8.94         5.79         5.46 
TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PX TCGA-VQ-A91N TCGA-VQ-A91X TCGA-VQ-A91Y 
       46.26        12.79        64.57        18.74         9.50         9.73 
TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-AA6I TCGA-ZQ-A9CR 
        4.54         5.72        16.14         0.79 

$`DEL PEAK 41(17Q24.3) WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-KB-A93G TCGA-VQ-A8PU TCGA-3M-AB46 
       21.99        22.98        79.07        20.15        27.35        58.03 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        19.56         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.87        17.29        13.68        39.12        26.10 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       36.16        35.84        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        3.45         9.07        29.56        37.25        14.43        11.44 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 
        2.66         2.20        15.58         7.40         6.18        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        31.27         7.36        25.05 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       31.96        32.58        20.88         8.22        10.68        34.13 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        0.46        20.42        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 
       13.15        13.18        13.35        11.21        12.10        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
       12.53         7.17        12.30        12.39        12.59        11.64 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A 
       12.07        12.82        12.43         6.31        12.30        12.43 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        6.58        11.77        12.62         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
        1.02         7.99         8.05        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97        12.00        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        28.96        65.10        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
        7.99        25.71        12.66        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 
       18.54        18.61        17.85        13.35        10.26        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19        18.21        21.14        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.58        20.25         0.26         2.10        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.45        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       19.73        14.04        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
        4.60         9.24        11.05         5.13       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB 
       40.64       116.38        71.38        57.44        35.61        16.87 
TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
       19.04         0.92        48.79        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       43.36        21.73        37.41        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PJ 
       30.97        34.29        16.31        22.19         2.50         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       17.85         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       29.59        14.33        73.41        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       61.22        20.81        32.88         1.71        42.64        60.85 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A92D 
       55.56         9.04         2.01        55.43         6.58        66.81 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       21.04         2.66        42.54        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       28.41        38.93        32.94        17.13        54.12        26.04 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  DEL PEAK 41(17Q24.3) MUTATED DEL PEAK 41(17Q24.3) WILD-TYPE 
                          0.23                           0.00 
  DEL PEAK 41(17Q24.3) MUTATED DEL PEAK 41(17Q24.3) WILD-TYPE 
                        115.69                         122.30 
  DEL PEAK 41(17Q24.3) MUTATED DEL PEAK 41(17Q24.3) WILD-TYPE 
                         13.23                          15.65 
[1] "0.2 - 115.7 (13.2)" "0.0 - 122.3 (15.7)"
[1] "hr=" "1.3"
D77V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 41(17Q24.3) MUTATED         0        1        2        3         7
  DEL PEAK 41(17Q24.3) WILD-TYPE       2       15       39       29        33
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 41(17Q24.3) MUTATED          10         0         18         14
  DEL PEAK 41(17Q24.3) WILD-TYPE        46         3         63         49
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 41(17Q24.3) MUTATED            7        9
  DEL PEAK 41(17Q24.3) WILD-TYPE         32       35
D77V3, multiclass
            clus
vv           DEL PEAK 41(17Q24.3) MUTATED DEL PEAK 41(17Q24.3) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              1                             15
  STAGE IB                              2                             39
  STAGE II                              3                             29
  STAGE IIA                             7                             33
  STAGE IIB                            10                             46
  STAGE III                             0                              3
  STAGE IIIA                           18                             63
  STAGE IIIB                           14                             49
  STAGE IIIC                            7                             32
  STAGE IV                              9                             35
[1] 11  2
[1] TRUE
[1] "dimension of 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(17Q24.3) MUTATED     1  10  37  24
  DEL PEAK 41(17Q24.3) WILD-TYPE  22  83 159  95
D77V4, multiclass
    clus
vv   DEL PEAK 41(17Q24.3) MUTATED DEL PEAK 41(17Q24.3) WILD-TYPE
  T1                            1                             22
  T2                           10                             83
  T3                           37                            159
  T4                           24                             95
[1] 4 2
[1] TRUE
[1] "dimension of 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(17Q24.3) MUTATED    17  16  21  17
  DEL PEAK 41(17Q24.3) WILD-TYPE 113 103  65  71
D77V5, multiclass
    clus
vv   DEL PEAK 41(17Q24.3) MUTATED DEL PEAK 41(17Q24.3) WILD-TYPE
  N0                           17                            113
  N1                           16                            103
  N2                           21                             65
  N3                           17                             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V6, binary
                                cls
clus                               0   1
  DEL PEAK 41(17Q24.3) MUTATED    69   4
  DEL PEAK 41(17Q24.3) WILD-TYPE 320  26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(17Q24.3) MUTATED     69    4
  DEL PEAK 41(17Q24.3) WILD-TYPE  320   26
   clus
vv  DEL PEAK 41(17Q24.3) MUTATED DEL PEAK 41(17Q24.3) WILD-TYPE
  0                           69                            320
  1                            4                             26
[1] 2 2
[1] FALSE
D77V7, binary
                                cls
clus                               0   1
  DEL PEAK 41(17Q24.3) MUTATED    29  47
  DEL PEAK 41(17Q24.3) WILD-TYPE 129 236
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(17Q24.3) MUTATED     29   47
  DEL PEAK 41(17Q24.3) WILD-TYPE  129  236
        clus
vv       DEL PEAK 41(17Q24.3) MUTATED DEL PEAK 41(17Q24.3) WILD-TYPE
  FEMALE                           29                            129
  MALE                             47                            236
[1] 2 2
[1] FALSE
D77V8, binary
                                cls
clus                               0   1
  DEL PEAK 41(17Q24.3) MUTATED    54   7
  DEL PEAK 41(17Q24.3) WILD-TYPE 268  69
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(17Q24.3) MUTATED     54    7
  DEL PEAK 41(17Q24.3) WILD-TYPE  268   69
     clus
vv    DEL PEAK 41(17Q24.3) MUTATED DEL PEAK 41(17Q24.3) WILD-TYPE
  NO                            54                            268
  YES                            7                             69
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 41(17Q24.3) MUTATED                                          3
  DEL PEAK 41(17Q24.3) WILD-TYPE                                       10
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 41(17Q24.3) MUTATED                                       7
  DEL PEAK 41(17Q24.3) WILD-TYPE                                    65
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 41(17Q24.3) MUTATED                                                       25
  DEL PEAK 41(17Q24.3) WILD-TYPE                                                    138
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 41(17Q24.3) MUTATED                                                   3
  DEL PEAK 41(17Q24.3) WILD-TYPE                                                18
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 41(17Q24.3) MUTATED                                                                  15
  DEL PEAK 41(17Q24.3) WILD-TYPE                                                                67
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 41(17Q24.3) MUTATED                                                    2
  DEL PEAK 41(17Q24.3) WILD-TYPE                                                  6
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 41(17Q24.3) MUTATED                                                 20
  DEL PEAK 41(17Q24.3) WILD-TYPE                                               59
D77V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 41(17Q24.3) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        7
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      25
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           15
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            20
                                                                   clus
vv                                                                  DEL PEAK 41(17Q24.3) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       138
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 41(17Q24.3) MUTATED    55   4   6   6
  DEL PEAK 41(17Q24.3) WILD-TYPE 294  14  13  19
D77V10, multiclass
    clus
vv   DEL PEAK 41(17Q24.3) MUTATED DEL PEAK 41(17Q24.3) WILD-TYPE
  R0                           55                            294
  R1                            4                             14
  R2                            6                             13
  RX                            6                             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"
D77V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 41(17Q24.3) MUTATED      15                         0
  DEL PEAK 41(17Q24.3) WILD-TYPE    73                        12
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 41(17Q24.3) MUTATED                                           1
  DEL PEAK 41(17Q24.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 41(17Q24.3) MUTATED      50
  DEL PEAK 41(17Q24.3) WILD-TYPE   228
D77V12, multiclass
                                           clus
vv                                          DEL PEAK 41(17Q24.3) MUTATED
  ASIAN                                                               15
  BLACK OR AFRICAN AMERICAN                                            0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               50
                                           clus
vv                                          DEL PEAK 41(17Q24.3) WILD-TYPE
  ASIAN                                                                 73
  BLACK OR AFRICAN AMERICAN                                             12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                228
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V13, binary
                                cls
clus                               0   1
  DEL PEAK 41(17Q24.3) MUTATED     1  55
  DEL PEAK 41(17Q24.3) WILD-TYPE   4 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(17Q24.3) MUTATED      1   55
  DEL PEAK 41(17Q24.3) WILD-TYPE    4  261
                        clus
vv                       DEL PEAK 41(17Q24.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           55
                        clus
vv                       DEL PEAK 41(17Q24.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            261
[1] 2 2
[1] FALSE

Clustering(78) Variable = DEL PEAK 42(18Q12.2) MUTATION ANALYSIS
D78V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 42(18Q12.2) MUTATED   102  70
  DEL PEAK 42(18Q12.2) WILD-TYPE 144  99
  DEL PEAK 42(18Q12.2) MUTATED DEL PEAK 42(18Q12.2) WILD-TYPE 
                           172                            243 
  DEL PEAK 42(18Q12.2) MUTATED DEL PEAK 42(18Q12.2) WILD-TYPE 
                            70                             99 
$`DEL PEAK 42(18Q12.2) MUTATED`
TCGA-CG-4444 TCGA-CG-4475 TCGA-KB-A93G TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 
       47.05        22.98        20.15        27.35        26.93        58.03 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4255 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6564 
        4.08         6.18         9.57        17.29        13.68        26.10 
TCGA-BR-6709 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       12.16        35.24        33.63        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8364 TCGA-BR-8366 
        9.07        11.44        29.42        19.96        22.19         0.95 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8677 TCGA-BR-8683 
       14.04         3.32        20.22        27.12        26.73         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ 
       20.88         8.22        10.68        13.87         7.53        34.98 
TCGA-BR-A4IY TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5801 
       12.89         0.66        13.51        21.44        13.02        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.35        11.21        12.10        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
        7.17        12.33        12.30        11.64        15.39        12.07 
TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 
        6.31        12.43        11.61        12.20        20.02         3.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4466 
        7.99         8.05        54.08         4.01        19.07        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5730 
        7.07        12.00        30.97         1.02        12.03         4.01 
TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6525 
       69.04        25.71        19.13        20.55        18.54        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6822 TCGA-D7-8573 TCGA-D7-8575 
       17.19        10.26        15.98        12.33        19.50        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EV 
       14.66        21.14        14.27        16.44        36.43        11.24 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 
       20.32        22.29        15.65        19.96         0.62         7.99 
TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8211 
       11.38        19.53        14.07        22.29        17.06        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-7133 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8604 
        0.56         5.52        63.06         5.92        28.96        22.82 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GP 
       21.07        24.30        24.26        22.75        11.77         8.98 
TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-IN-7808 
        6.58         2.10        12.95        23.84        21.17         3.45 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X 
       18.38        13.35         6.74        10.62        11.70        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE 
        2.53         5.56        63.62        37.64        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 
        8.52         6.08         9.24        16.67        37.91       115.69 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       35.61         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PK 
       18.48        43.36         7.73        22.19         2.50        17.85 
TCGA-VQ-A8PS TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
       13.35        42.64         9.50        55.56         9.04         2.01 
TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA6A 
        4.54        66.81        42.54        11.24        18.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       32.94        26.04        12.43         0.79 

$`DEL PEAK 42(18Q12.2) WILD-TYPE`
TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-MX-A663 TCGA-B7-5816 
       21.99        79.07        16.24         0.23         9.86        26.70 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        9.34         9.67         6.61        34.68        15.95        13.87 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       19.89         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 
       21.90         9.21        36.16        35.84        39.78        18.15 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       29.56        33.21        37.25        14.43         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8295 
        9.60        32.25         8.05         0.56         2.66         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       17.52        26.33         4.31        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79         9.34        28.14         6.28         7.53 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4CS 
       24.79        31.96        32.58        34.13         6.08         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       28.34        32.52         0.46        20.65        20.42         1.15 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-8530 TCGA-CD-8531 
       16.14         5.13        13.41        13.15        12.39        12.59 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI 
       12.82        12.43        12.30        11.31         6.58        11.77 
TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 
       12.62        27.02        15.95         1.02        14.01        29.98 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 
       12.03         0.00         9.01         6.97        36.00         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99       105.07        15.02        28.96        65.10 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6522 
       21.07         7.99        12.66        20.91        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 
       17.85        15.22        12.79        12.36        11.31        24.72 
TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 
       16.80        17.19        20.91         5.92        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       26.43        11.31        11.44         8.38         4.34         7.13 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-8209 TCGA-FP-8210 
       14.47        72.23        21.27         3.48        59.54         5.03 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        52.21        30.51        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 
       24.39        18.15        22.32         0.76         5.59        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
       24.20         3.25        25.81        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 
        6.51        20.25         0.26        29.00        23.80        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ 
       15.68        33.40        36.36        18.81         3.39        12.46 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-KB-A93J 
       19.53         6.44        12.59         6.51        15.75        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS 
        3.72        19.73        14.04        74.53         4.60        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
        8.61         5.13       122.30        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DZ TCGA-VQ-A8E3 
       57.44         8.94        16.87        19.04        13.02        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       37.41        38.14        37.22        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       16.31        12.79         2.70         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        29.59        64.57        14.33        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       11.70        21.83        61.22        18.74        20.81        32.88 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
        1.71        60.85         9.73        55.43         6.58         5.72 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F 
       21.04         2.66        43.66        28.41        17.13        54.12 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       16.14        27.55        17.26 

  DEL PEAK 42(18Q12.2) MUTATED DEL PEAK 42(18Q12.2) WILD-TYPE 
                          0.56                           0.00 
  DEL PEAK 42(18Q12.2) MUTATED DEL PEAK 42(18Q12.2) WILD-TYPE 
                        115.69                         122.30 
  DEL PEAK 42(18Q12.2) MUTATED DEL PEAK 42(18Q12.2) WILD-TYPE 
                         13.51                          15.95 
[1] "0.6 - 115.7 (13.5)" "0.0 - 122.3 (15.9)"
[1] "hr=" "1.1"
D78V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 42(18Q12.2) MUTATED         1        4       15       15        18
  DEL PEAK 42(18Q12.2) WILD-TYPE       1       12       26       17        22
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 42(18Q12.2) MUTATED          23         1         37         30
  DEL PEAK 42(18Q12.2) WILD-TYPE        33         2         44         33
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 42(18Q12.2) MUTATED           11       16
  DEL PEAK 42(18Q12.2) WILD-TYPE         28       28
D78V3, multiclass
            clus
vv           DEL PEAK 42(18Q12.2) MUTATED DEL PEAK 42(18Q12.2) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                              4                             12
  STAGE IB                             15                             26
  STAGE II                             15                             17
  STAGE IIA                            18                             22
  STAGE IIB                            23                             33
  STAGE III                             1                              2
  STAGE IIIA                           37                             44
  STAGE IIIB                           30                             33
  STAGE IIIC                           11                             28
  STAGE IV                             16                             28
[1] 11  2
[1] TRUE
[1] "dimension of 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(18Q12.2) MUTATED     6  38 101  33
  DEL PEAK 42(18Q12.2) WILD-TYPE  17  55  95  86
D78V4, multiclass
    clus
vv   DEL PEAK 42(18Q12.2) MUTATED DEL PEAK 42(18Q12.2) WILD-TYPE
  T1                            6                             17
  T2                           38                             55
  T3                          101                             95
  T4                           33                             86
[1] 4 2
[1] TRUE
[1] "dimension of 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(18Q12.2) MUTATED   49 49 39 36
  DEL PEAK 42(18Q12.2) WILD-TYPE 81 70 47 52
D78V5, multiclass
    clus
vv   DEL PEAK 42(18Q12.2) MUTATED DEL PEAK 42(18Q12.2) WILD-TYPE
  N0                           49                             81
  N1                           49                             70
  N2                           39                             47
  N3                           36                             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V6, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q12.2) MUTATED   160  11
  DEL PEAK 42(18Q12.2) WILD-TYPE 229  19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q12.2) MUTATED    160   11
  DEL PEAK 42(18Q12.2) WILD-TYPE  229   19
   clus
vv  DEL PEAK 42(18Q12.2) MUTATED DEL PEAK 42(18Q12.2) WILD-TYPE
  0                          160                            229
  1                           11                             19
[1] 2 2
[1] FALSE
D78V7, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q12.2) MUTATED    60 121
  DEL PEAK 42(18Q12.2) WILD-TYPE  98 162
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q12.2) MUTATED     60  121
  DEL PEAK 42(18Q12.2) WILD-TYPE   98  162
        clus
vv       DEL PEAK 42(18Q12.2) MUTATED DEL PEAK 42(18Q12.2) WILD-TYPE
  FEMALE                           60                             98
  MALE                            121                            162
[1] 2 2
[1] FALSE
D78V8, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q12.2) MUTATED   130  34
  DEL PEAK 42(18Q12.2) WILD-TYPE 192  42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q12.2) MUTATED    130   34
  DEL PEAK 42(18Q12.2) WILD-TYPE  192   42
     clus
vv    DEL PEAK 42(18Q12.2) MUTATED DEL PEAK 42(18Q12.2) WILD-TYPE
  NO                           130                            192
  YES                           34                             42
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 42(18Q12.2) MUTATED                                          4
  DEL PEAK 42(18Q12.2) WILD-TYPE                                        9
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 42(18Q12.2) MUTATED                                      26
  DEL PEAK 42(18Q12.2) WILD-TYPE                                    46
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 42(18Q12.2) MUTATED                                                       61
  DEL PEAK 42(18Q12.2) WILD-TYPE                                                    102
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 42(18Q12.2) MUTATED                                                   6
  DEL PEAK 42(18Q12.2) WILD-TYPE                                                15
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 42(18Q12.2) MUTATED                                                                  39
  DEL PEAK 42(18Q12.2) WILD-TYPE                                                                43
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 42(18Q12.2) MUTATED                                                    2
  DEL PEAK 42(18Q12.2) WILD-TYPE                                                  6
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 42(18Q12.2) MUTATED                                                 41
  DEL PEAK 42(18Q12.2) WILD-TYPE                                               38
D78V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 42(18Q12.2) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     4
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       26
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      61
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            6
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           39
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            41
                                                                   clus
vv                                                                  DEL PEAK 42(18Q12.2) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                       9
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         46
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       102
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             15
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             43
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              38
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 42(18Q12.2) MUTATED   136  10   6   9
  DEL PEAK 42(18Q12.2) WILD-TYPE 213   8  13  16
D78V10, multiclass
    clus
vv   DEL PEAK 42(18Q12.2) MUTATED DEL PEAK 42(18Q12.2) WILD-TYPE
  R0                          136                            213
  R1                           10                              8
  R2                            6                             13
  RX                            9                             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"
D78V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 42(18Q12.2) MUTATED      42                         3
  DEL PEAK 42(18Q12.2) WILD-TYPE    46                         9
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 42(18Q12.2) MUTATED                                           0
  DEL PEAK 42(18Q12.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 42(18Q12.2) MUTATED     109
  DEL PEAK 42(18Q12.2) WILD-TYPE   169
D78V12, multiclass
                                           clus
vv                                          DEL PEAK 42(18Q12.2) MUTATED
  ASIAN                                                               42
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              109
                                           clus
vv                                          DEL PEAK 42(18Q12.2) WILD-TYPE
  ASIAN                                                                 46
  BLACK OR AFRICAN AMERICAN                                              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                169
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V13, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q12.2) MUTATED     3 127
  DEL PEAK 42(18Q12.2) WILD-TYPE   2 189
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q12.2) MUTATED      3  127
  DEL PEAK 42(18Q12.2) WILD-TYPE    2  189
                        clus
vv                       DEL PEAK 42(18Q12.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          127
                        clus
vv                       DEL PEAK 42(18Q12.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            189
[1] 2 2
[1] FALSE

Clustering(79) Variable = DEL PEAK 43(18Q21.2) MUTATION ANALYSIS
D79V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 43(18Q21.2) MUTATED   118  76
  DEL PEAK 43(18Q21.2) WILD-TYPE 128  93
  DEL PEAK 43(18Q21.2) MUTATED DEL PEAK 43(18Q21.2) WILD-TYPE 
                           194                            221 
  DEL PEAK 43(18Q21.2) MUTATED DEL PEAK 43(18Q21.2) WILD-TYPE 
                            76                             93 
$`DEL PEAK 43(18Q21.2) MUTATED`
TCGA-CG-4444 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A8PU 
       47.05        22.98        16.24         0.23        20.15        27.35 
TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       26.93        58.03        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4255 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6456 
        9.44         6.61         4.08         6.18         9.57        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6709 TCGA-BR-7704 TCGA-BR-7715 
       13.68        19.33        26.10        12.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8060 
       39.78        15.32        28.73         3.45         9.07        11.44 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8364 TCGA-BR-8366 
       29.42         2.66        19.96         7.40        22.19         0.95 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 
       14.04         3.32         5.39        20.22         1.12        27.12 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       26.73        31.96         9.86        20.88         8.22        10.68 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J6 
       13.87         7.53        34.98         1.48        12.89         0.66 
TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       13.51        20.42        21.44        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.35        11.21        12.10        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
        7.17        12.33        12.30        11.64        15.39        12.07 
TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4304 
        6.31        12.43        11.61        12.20         3.02        27.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4466 TCGA-CG-4469 
        7.99         8.05        54.08         4.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5730 
       12.00        30.97        36.00         1.02        12.03         4.01 
TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 
       69.04        25.71        20.91        19.13        20.55        18.54 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6822 TCGA-D7-8570 
       13.35        17.19        10.26        15.98        12.33        24.72 
TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU 
       19.50        18.21        14.66        21.14        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A 
       36.43        11.24        20.32        22.29        15.65        19.96 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        0.62         7.99        11.38        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-7133 TCGA-HU-8243 
       17.06        13.58         0.56         5.52        63.06         5.92 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GD 
       28.96        22.82        21.07        24.30        24.26        22.75 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
       11.77         8.98         6.58         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL 
       23.80        21.17         3.45        18.81        18.38        13.35 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 
        6.44         6.74        10.62        11.70        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        5.56        63.62        37.64        45.67        18.21         8.52 
TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N9 
        6.08         9.24        16.67        37.91       115.69        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 
        5.79         0.92        48.79        13.25        18.48        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PK 
       21.73         7.73        16.31        22.19         2.50        17.85 
TCGA-VQ-A8PS TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y 
       13.35        61.22         1.71        42.64         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94R 
       55.56         9.04         2.01         4.54        66.81        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G 
       11.24        18.41        38.93        32.94        17.13        26.04 
TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       12.43         0.79 

$`DEL PEAK 43(18Q21.2) WILD-TYPE`
TCGA-CG-4460 TCGA-CG-5727 TCGA-MX-A663 TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4187 
       21.99        79.07         9.86        26.70         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35        30.90         4.08         9.34         9.67 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6563 TCGA-BR-6565 
        6.61        34.68        15.95        13.87        39.12         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       35.84        18.15        29.56        33.21        37.25        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
        2.20        15.58         6.18        31.10        13.08         0.26 
TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       17.52        26.33         4.31        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8588 
        7.36        25.05         3.72        25.18         9.21        12.79 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8682 
        9.34        28.14         6.28         7.53        24.79        32.58 
TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 
       34.13         6.08        27.55        28.57         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD 
       14.17         0.53        28.34        32.52         0.46        20.65 
TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-8530 TCGA-CD-8531 
        1.15        16.14         5.13        13.41        12.39        12.59 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI 
       12.82        12.43        12.30        11.31         6.58        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 
       12.62        20.02        15.95         1.02        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-5717 TCGA-CG-5720 
       19.07        12.03         0.00         9.01         6.97         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99       105.07        15.02        28.96        65.10 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
       21.07         7.99        12.66        18.84        18.61        17.85 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8572 TCGA-D7-8574 
       15.22        12.79        12.36        11.31        16.80        17.19 
TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX 
       20.91         5.92        13.78        14.76        26.43        11.31 
TCGA-D7-A6EY TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-6875 
       11.44         8.38         4.34         7.13        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A9TM TCGA-HF-7132 
       21.27         3.48        59.54         5.03         6.21        77.29 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
       52.21        30.51        26.47         1.51        24.39        18.15 
TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       22.32         0.76         5.59        22.68        24.20         3.25 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       25.81        21.37        29.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
        0.26        29.00        14.07        15.68        33.40        36.36 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V 
        3.39        12.46        19.53        12.59         6.51        15.75 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZI TCGA-R5-A804 
       36.95         3.72        19.73        14.04        74.53         4.60 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 
       11.05         8.61         5.13       122.30        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DU 
       71.38        57.44         8.94        16.87        19.04         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       13.02        37.41        38.14        37.22        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       46.26        12.79         2.70         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        29.59        64.57        14.33        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91W 
       11.70        21.83        18.74        20.81        32.88        60.85 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-AA68 
       55.43         6.58         5.72        21.04         2.66        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       28.41        54.12        16.14        27.55        17.26 

  DEL PEAK 43(18Q21.2) MUTATED DEL PEAK 43(18Q21.2) WILD-TYPE 
                          0.23                           0.00 
  DEL PEAK 43(18Q21.2) MUTATED DEL PEAK 43(18Q21.2) WILD-TYPE 
                        115.69                         122.30 
  DEL PEAK 43(18Q21.2) MUTATED DEL PEAK 43(18Q21.2) WILD-TYPE 
                         13.63                          15.75 
[1] "0.2 - 115.7 (13.6)" "0.0 - 122.3 (15.8)"
[1] "hr=" "1"  
D79V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 43(18Q21.2) MUTATED         1        4       18       16        20
  DEL PEAK 43(18Q21.2) WILD-TYPE       1       12       23       16        20
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 43(18Q21.2) MUTATED          26         1         41         31
  DEL PEAK 43(18Q21.2) WILD-TYPE        30         2         40         32
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 43(18Q21.2) MUTATED           17       18
  DEL PEAK 43(18Q21.2) WILD-TYPE         22       26
D79V3, multiclass
            clus
vv           DEL PEAK 43(18Q21.2) MUTATED DEL PEAK 43(18Q21.2) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                              4                             12
  STAGE IB                             18                             23
  STAGE II                             16                             16
  STAGE IIA                            20                             20
  STAGE IIB                            26                             30
  STAGE III                             1                              2
  STAGE IIIA                           41                             40
  STAGE IIIB                           31                             32
  STAGE IIIC                           17                             22
  STAGE IV                             18                             26
[1] 11  2
[1] TRUE
[1] "dimension of 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(18Q21.2) MUTATED     7  43 109  42
  DEL PEAK 43(18Q21.2) WILD-TYPE  16  50  87  77
D79V4, multiclass
    clus
vv   DEL PEAK 43(18Q21.2) MUTATED DEL PEAK 43(18Q21.2) WILD-TYPE
  T1                            7                             16
  T2                           43                             50
  T3                          109                             87
  T4                           42                             77
[1] 4 2
[1] TRUE
[1] "dimension of 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(18Q21.2) MUTATED   55 56 40 44
  DEL PEAK 43(18Q21.2) WILD-TYPE 75 63 46 44
D79V5, multiclass
    clus
vv   DEL PEAK 43(18Q21.2) MUTATED DEL PEAK 43(18Q21.2) WILD-TYPE
  N0                           55                             75
  N1                           56                             63
  N2                           40                             46
  N3                           44                             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"
D79V6, binary
                                cls
clus                               0   1
  DEL PEAK 43(18Q21.2) MUTATED   179  13
  DEL PEAK 43(18Q21.2) WILD-TYPE 210  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(18Q21.2) MUTATED    179   13
  DEL PEAK 43(18Q21.2) WILD-TYPE  210   17
   clus
vv  DEL PEAK 43(18Q21.2) MUTATED DEL PEAK 43(18Q21.2) WILD-TYPE
  0                          179                            210
  1                           13                             17
[1] 2 2
[1] FALSE
D79V7, binary
                                cls
clus                               0   1
  DEL PEAK 43(18Q21.2) MUTATED    68 136
  DEL PEAK 43(18Q21.2) WILD-TYPE  90 147
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(18Q21.2) MUTATED     68  136
  DEL PEAK 43(18Q21.2) WILD-TYPE   90  147
        clus
vv       DEL PEAK 43(18Q21.2) MUTATED DEL PEAK 43(18Q21.2) WILD-TYPE
  FEMALE                           68                             90
  MALE                            136                            147
[1] 2 2
[1] FALSE
D79V8, binary
                                cls
clus                               0   1
  DEL PEAK 43(18Q21.2) MUTATED   147  38
  DEL PEAK 43(18Q21.2) WILD-TYPE 175  38
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(18Q21.2) MUTATED    147   38
  DEL PEAK 43(18Q21.2) WILD-TYPE  175   38
     clus
vv    DEL PEAK 43(18Q21.2) MUTATED DEL PEAK 43(18Q21.2) WILD-TYPE
  NO                           147                            175
  YES                           38                             38
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 43(18Q21.2) MUTATED                                          5
  DEL PEAK 43(18Q21.2) WILD-TYPE                                        8
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 43(18Q21.2) MUTATED                                      27
  DEL PEAK 43(18Q21.2) WILD-TYPE                                    45
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 43(18Q21.2) MUTATED                                                       70
  DEL PEAK 43(18Q21.2) WILD-TYPE                                                     93
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 43(18Q21.2) MUTATED                                                   6
  DEL PEAK 43(18Q21.2) WILD-TYPE                                                15
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 43(18Q21.2) MUTATED                                                                  45
  DEL PEAK 43(18Q21.2) WILD-TYPE                                                                37
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 43(18Q21.2) MUTATED                                                    4
  DEL PEAK 43(18Q21.2) WILD-TYPE                                                  4
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 43(18Q21.2) MUTATED                                                 44
  DEL PEAK 43(18Q21.2) WILD-TYPE                                               35
D79V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 43(18Q21.2) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       27
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      70
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            6
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           45
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            44
                                                                   clus
vv                                                                  DEL PEAK 43(18Q21.2) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         45
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                        93
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             15
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             37
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              35
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 43(18Q21.2) MUTATED   156  11   7  10
  DEL PEAK 43(18Q21.2) WILD-TYPE 193   7  12  15
D79V10, multiclass
    clus
vv   DEL PEAK 43(18Q21.2) MUTATED DEL PEAK 43(18Q21.2) WILD-TYPE
  R0                          156                            193
  R1                           11                              7
  R2                            7                             12
  RX                           10                             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"
D79V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 43(18Q21.2) MUTATED      46                         3
  DEL PEAK 43(18Q21.2) WILD-TYPE    42                         9
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 43(18Q21.2) MUTATED                                           0
  DEL PEAK 43(18Q21.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 43(18Q21.2) MUTATED     127
  DEL PEAK 43(18Q21.2) WILD-TYPE   151
D79V12, multiclass
                                           clus
vv                                          DEL PEAK 43(18Q21.2) MUTATED
  ASIAN                                                               46
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              127
                                           clus
vv                                          DEL PEAK 43(18Q21.2) WILD-TYPE
  ASIAN                                                                 42
  BLACK OR AFRICAN AMERICAN                                              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                151
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V13, binary
                                cls
clus                               0   1
  DEL PEAK 43(18Q21.2) MUTATED     3 145
  DEL PEAK 43(18Q21.2) WILD-TYPE   2 171
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(18Q21.2) MUTATED      3  145
  DEL PEAK 43(18Q21.2) WILD-TYPE    2  171
                        clus
vv                       DEL PEAK 43(18Q21.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          145
                        clus
vv                       DEL PEAK 43(18Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            171
[1] 2 2
[1] FALSE

Clustering(80) Variable = DEL PEAK 44(19P13.3) MUTATION ANALYSIS
D80V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 44(19P13.3) MUTATED    88  65
  DEL PEAK 44(19P13.3) WILD-TYPE 158 104
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                           153                            262 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                            65                            104 
$`DEL PEAK 44(19P13.3) MUTATED`
TCGA-CG-4460 TCGA-CG-4475 TCGA-KB-A93G TCGA-VQ-A8PU TCGA-3M-AB46 TCGA-B7-A5TI 
       21.99        22.98        20.15        27.35        58.03        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4257 TCGA-BR-6458 TCGA-BR-6565 
       11.01         9.44         6.61         9.67        19.33         9.17 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 
        9.21        35.24        39.78        28.73         3.45        11.44 
TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8369 
        0.69        29.42         2.66        19.96         2.20        14.04 
TCGA-BR-8373 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8690 TCGA-BR-A4CQ 
       14.79         9.21        20.22        24.79        10.68        34.98 
TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5799 
        1.48        12.89         0.72        20.65         1.15        13.02 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.15        13.35        12.10        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 
        7.17        12.30        12.39        15.39        12.82         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 
       12.30        11.31        12.43        11.61        12.20        20.02 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4466 
        7.99        54.08         4.01        29.98        19.07        18.97 
TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5578 
       36.00        12.03        15.02         4.01        69.04        12.66 
TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       18.84        13.35        10.26        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-8578 TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-8122 
       11.31        19.50        21.14        22.29        15.65         7.99 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A9TM 
       72.23        11.38        14.07        17.06         0.56         6.21 
TCGA-HF-7133 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU 
       63.06         5.92        18.15        11.77         8.98         6.58 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD 
        2.10        12.95        23.84        23.80        21.17        33.40 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RR 
       36.36        18.81         3.39        18.38        13.35         6.74 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       12.59        10.62        11.70         2.53         5.56        63.62 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR 
       37.64        36.95        14.04        45.67        18.21         6.08 
TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB 
        9.24         8.61         5.13        37.91         8.94         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        0.92        48.79         5.46        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       43.36        37.41         7.73        22.19        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y 
       17.85         1.87         1.71        42.64         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A94O 
       55.56         9.04         2.01         4.54         5.72        21.04 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I 
       18.41        43.66        38.93        17.13        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       27.55        12.43         0.79 

$`DEL PEAK 44(19P13.3) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-MX-A663 TCGA-VQ-A94U 
       47.05        79.07        16.24         0.23         9.86        26.93 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         9.47         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 
       18.35        30.90         4.08         4.08         9.34         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.68        39.12        26.10        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 
       44.94        21.90        36.16        35.84        33.63        18.15 
TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       15.32         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8296 
       29.59         9.60        32.25         8.05         0.56        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33         4.31         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       31.27         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU 
        8.22        34.13        13.87         7.53         6.08        27.55 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       28.57         8.98        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL 
       32.52        13.51         0.46        20.42        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8528 TCGA-CD-8531 
        5.13        13.41        13.18        11.21        12.33        12.59 
TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.64        12.07        12.43         6.58        11.77        12.62 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 
        3.02        27.02        15.95         1.02         8.05        14.01 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
       12.03         0.00         9.01         7.07        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.97         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 
       28.96        65.10        21.07         7.99        25.71        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 
       19.13        20.55        18.54        18.61        17.85        17.19 
TCGA-D7-6528 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 
       15.22        12.33        24.72        16.80        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       14.66        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       20.32         8.38         4.34        19.96         7.13         0.62 
TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 
       14.47        21.27         3.48        19.53        22.29        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB 
        5.03        13.58         5.52        77.29        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         1.51        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H8 
        0.10         6.51        20.25         0.26        29.00        14.07 
TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NR 
       15.68         3.45        12.46        19.53         6.44         6.51 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI 
       15.75        13.51         3.72        19.73         8.52        74.53 
TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 
        4.60        11.05        16.67       122.30        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44        35.61        16.87        19.04 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       21.73        38.14        37.22        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       16.31         2.50         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       29.59        64.57        14.33        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91W 
       21.83        61.22        18.74        20.81        32.88        60.85 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
       55.43         6.58        66.81         2.66        42.54        11.24 
TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-ZA-A8F6 
       28.41        32.94        54.12        17.26 

  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                          0.56                           0.00 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                         72.23                         122.30 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                        12.890                         16.555 
[1] "0.6 - 72.2 (12.9)"  "0.0 - 122.3 (16.6)"
[1] "hr=" "1.2"
D80V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 44(19P13.3) MUTATED         1        6       14       14        14
  DEL PEAK 44(19P13.3) WILD-TYPE       1       10       27       18        26
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 44(19P13.3) MUTATED          24         1         31         20
  DEL PEAK 44(19P13.3) WILD-TYPE        32         2         50         43
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 44(19P13.3) MUTATED           13       17
  DEL PEAK 44(19P13.3) WILD-TYPE         26       27
D80V3, multiclass
            clus
vv           DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                              6                             10
  STAGE IB                             14                             27
  STAGE II                             14                             18
  STAGE IIA                            14                             26
  STAGE IIB                            24                             32
  STAGE III                             1                              2
  STAGE IIIA                           31                             50
  STAGE IIIB                           20                             43
  STAGE IIIC                           13                             26
  STAGE IV                             17                             27
[1] 11  2
[1] TRUE
[1] "dimension of 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     8  37  78  35
  DEL PEAK 44(19P13.3) WILD-TYPE  15  56 118  84
D80V4, multiclass
    clus
vv   DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  T1                            8                             15
  T2                           37                             56
  T3                           78                            118
  T4                           35                             84
[1] 4 2
[1] TRUE
[1] "dimension of 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   45 46 29 34
  DEL PEAK 44(19P13.3) WILD-TYPE 85 73 57 54
D80V5, multiclass
    clus
vv   DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  N0                           45                             85
  N1                           46                             73
  N2                           29                             57
  N3                           34                             54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V6, binary
                                cls
clus                               0   1
  DEL PEAK 44(19P13.3) MUTATED   142  10
  DEL PEAK 44(19P13.3) WILD-TYPE 247  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED    142   10
  DEL PEAK 44(19P13.3) WILD-TYPE  247   20
   clus
vv  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  0                          142                            247
  1                           10                             20
[1] 2 2
[1] FALSE
D80V7, binary
                                cls
clus                               0   1
  DEL PEAK 44(19P13.3) MUTATED    48 114
  DEL PEAK 44(19P13.3) WILD-TYPE 110 169
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED     48  114
  DEL PEAK 44(19P13.3) WILD-TYPE  110  169
        clus
vv       DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  FEMALE                           48                            110
  MALE                            114                            169
[1] 2 2
[1] FALSE
D80V8, binary
                                cls
clus                               0   1
  DEL PEAK 44(19P13.3) MUTATED   114  32
  DEL PEAK 44(19P13.3) WILD-TYPE 208  44
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED    114   32
  DEL PEAK 44(19P13.3) WILD-TYPE  208   44
     clus
vv    DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  NO                           114                            208
  YES                           32                             44
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 44(19P13.3) MUTATED                                          4
  DEL PEAK 44(19P13.3) WILD-TYPE                                        9
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 44(19P13.3) MUTATED                                      16
  DEL PEAK 44(19P13.3) WILD-TYPE                                    56
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 44(19P13.3) MUTATED                                                       56
  DEL PEAK 44(19P13.3) WILD-TYPE                                                    107
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 44(19P13.3) MUTATED                                                   5
  DEL PEAK 44(19P13.3) WILD-TYPE                                                16
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 44(19P13.3) MUTATED                                                                  41
  DEL PEAK 44(19P13.3) WILD-TYPE                                                                41
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 44(19P13.3) MUTATED                                                    5
  DEL PEAK 44(19P13.3) WILD-TYPE                                                  3
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 44(19P13.3) MUTATED                                                 34
  DEL PEAK 44(19P13.3) WILD-TYPE                                               45
D80V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 44(19P13.3) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     4
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       16
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      56
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           41
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            34
                                                                   clus
vv                                                                  DEL PEAK 44(19P13.3) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                       9
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         56
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       107
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             16
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             41
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              45
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 44(19P13.3) MUTATED   125   4   9   6
  DEL PEAK 44(19P13.3) WILD-TYPE 224  14  10  19
D80V10, multiclass
    clus
vv   DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  R0                          125                            224
  R1                            4                             14
  R2                            9                             10
  RX                            6                             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"
D80V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 44(19P13.3) MUTATED      37                         6
  DEL PEAK 44(19P13.3) WILD-TYPE    51                         6
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 44(19P13.3) MUTATED                                           1
  DEL PEAK 44(19P13.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 44(19P13.3) MUTATED      93
  DEL PEAK 44(19P13.3) WILD-TYPE   185
D80V12, multiclass
                                           clus
vv                                          DEL PEAK 44(19P13.3) MUTATED
  ASIAN                                                               37
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               93
                                           clus
vv                                          DEL PEAK 44(19P13.3) WILD-TYPE
  ASIAN                                                                 51
  BLACK OR AFRICAN AMERICAN                                              6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                185
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V13, binary
                                cls
clus                               0   1
  DEL PEAK 44(19P13.3) MUTATED     2 104
  DEL PEAK 44(19P13.3) WILD-TYPE   3 212
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED      2  104
  DEL PEAK 44(19P13.3) WILD-TYPE    3  212
                        clus
vv                       DEL PEAK 44(19P13.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          104
                        clus
vv                       DEL PEAK 44(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            212
[1] 2 2
[1] FALSE

Clustering(81) Variable = DEL PEAK 45(19Q13.11) MUTATION ANALYSIS
D81V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 45(19Q13.11) MUTATED    43  30
  DEL PEAK 45(19Q13.11) WILD-TYPE 203 139
  DEL PEAK 45(19Q13.11) MUTATED DEL PEAK 45(19Q13.11) WILD-TYPE 
                             73                             342 
  DEL PEAK 45(19Q13.11) MUTATED DEL PEAK 45(19Q13.11) WILD-TYPE 
                             30                             139 
$`DEL PEAK 45(19Q13.11) MUTATED`
TCGA-VQ-A8PU TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4257 TCGA-BR-7197 
       27.35        11.01         9.44         6.61         9.67         9.21 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 
       35.24        33.63        28.73         3.45        11.44         0.69 
TCGA-BR-8289 TCGA-BR-8369 TCGA-BR-8678 TCGA-BR-A4CS TCGA-BR-A4PF TCGA-CD-5799 
        2.66        14.04        24.79         1.48         1.15        13.02 
TCGA-CD-5800 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A489 
       13.15         7.17        12.30        15.39         6.31        11.31 
TCGA-CG-4300 TCGA-CG-4440 TCGA-CG-4466 TCGA-CG-5724 TCGA-D7-6526 TCGA-D7-6527 
       20.02         4.01        18.97        12.03        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-A4YY TCGA-D7-A6EX 
       15.22        12.79        11.31        19.50        13.78        11.31 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-FP-8099 TCGA-FP-8631 TCGA-HU-8243 
       22.29        15.65         0.62        17.06         0.56         5.92 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4HD 
       11.77         8.98         6.58        12.95        23.84        33.40 
TCGA-IN-A6RI TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A93H TCGA-R5-A7O7 
       18.38        12.59        10.62        11.70        37.64        45.67 
TCGA-RD-A8MW TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8P3 TCGA-VQ-A8PH 
       37.91         5.46        13.02        18.48        37.22        12.79 
TCGA-VQ-A8PK TCGA-VQ-A91N TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 
       17.85        18.74        42.64         9.50        55.56         9.04 
TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-AA6D TCGA-VQ-AA6I TCGA-VQ-AA6J 
        4.54        66.81        21.04        17.13        16.14        27.55 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK 45(19Q13.11) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
       20.15         9.86        26.93        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       19.56         9.47         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 
       31.20        44.94        21.90        36.16        35.84        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       18.15        15.32         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       14.43        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       29.42        19.96         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       31.10        13.08         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33         4.31         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08        34.98        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51         0.46        20.65        20.42        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
        5.13        13.41        13.18        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 
       12.76        12.59        12.53        12.33        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48A 
       11.64        12.07        12.82        12.43        12.30        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 
       11.61         6.58        12.20        11.77        12.62         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6822 
       18.61        17.85        13.35        15.98        12.36        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       24.72        16.80        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 
       20.91        14.27        16.44         5.92        36.43        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 
       26.43        11.24        11.44        20.32         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
       19.96         7.13         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
       11.38         3.48        19.53        14.07        22.29        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        5.03        13.58         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
       52.21        30.51        26.47         1.51        24.39        18.15 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       25.81        21.37        29.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        0.26         2.10        29.00        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ 
       15.68        36.36         3.45        18.81         3.39        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-AB1V 
       13.35        19.53         6.44         6.74         6.51        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       19.73        14.04        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
      122.30        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
        8.94        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       48.79        13.25        43.36        21.73        37.41        38.14 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
        7.73        30.97        34.29        46.26        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.50         2.70         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       13.35        29.59        64.57        14.33        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       11.70        21.83        61.22        20.81        32.88         1.71 
TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
       60.85         9.73         2.01        55.43         6.58         5.72 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
        2.66        42.54        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZA-A8F6 
       38.93        32.94        54.12        26.04        12.43        17.26 

  DEL PEAK 45(19Q13.11) MUTATED DEL PEAK 45(19Q13.11) WILD-TYPE 
                           0.56                            0.00 
  DEL PEAK 45(19Q13.11) MUTATED DEL PEAK 45(19Q13.11) WILD-TYPE 
                          66.81                          122.30 
  DEL PEAK 45(19Q13.11) MUTATED DEL PEAK 45(19Q13.11) WILD-TYPE 
                         12.950                          15.715 
[1] "0.6 - 66.8 (12.9)"  "0.0 - 122.3 (15.7)"
[1] "hr=" "1.2"
D81V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 45(19Q13.11) MUTATED         1        2        6        7         6
  DEL PEAK 45(19Q13.11) WILD-TYPE       1       14       35       25        34
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 45(19Q13.11) MUTATED           9         0         14         14
  DEL PEAK 45(19Q13.11) WILD-TYPE        47         3         67         49
                                 vv
clus                              STAGE IIIC STAGE IV
  DEL PEAK 45(19Q13.11) MUTATED            5        9
  DEL PEAK 45(19Q13.11) WILD-TYPE         34       35
D81V3, multiclass
            clus
vv           DEL PEAK 45(19Q13.11) MUTATED DEL PEAK 45(19Q13.11) WILD-TYPE
  STAGE I                                1                               1
  STAGE IA                               2                              14
  STAGE IB                               6                              35
  STAGE II                               7                              25
  STAGE IIA                              6                              34
  STAGE IIB                              9                              47
  STAGE III                              0                               3
  STAGE IIIA                            14                              67
  STAGE IIIB                            14                              49
  STAGE IIIC                             5                              34
  STAGE IV                               9                              35
[1] 11  2
[1] TRUE
[1] "dimension of 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(19Q13.11) MUTATED     3  14  37  19
  DEL PEAK 45(19Q13.11) WILD-TYPE  20  79 159 100
D81V4, multiclass
    clus
vv   DEL PEAK 45(19Q13.11) MUTATED DEL PEAK 45(19Q13.11) WILD-TYPE
  T1                             3                              20
  T2                            14                              79
  T3                            37                             159
  T4                            19                             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"
                                 vv
clus                               N0  N1  N2  N3
  DEL PEAK 45(19Q13.11) MUTATED    19  17  15  20
  DEL PEAK 45(19Q13.11) WILD-TYPE 111 102  71  68
D81V5, multiclass
    clus
vv   DEL PEAK 45(19Q13.11) MUTATED DEL PEAK 45(19Q13.11) WILD-TYPE
  N0                            19                             111
  N1                            17                             102
  N2                            15                              71
  N3                            20                              68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V6, binary
                                 cls
clus                                0   1
  DEL PEAK 45(19Q13.11) MUTATED    65   7
  DEL PEAK 45(19Q13.11) WILD-TYPE 324  23
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 45(19Q13.11) MUTATED     65    7
  DEL PEAK 45(19Q13.11) WILD-TYPE  324   23
   clus
vv  DEL PEAK 45(19Q13.11) MUTATED DEL PEAK 45(19Q13.11) WILD-TYPE
  0                            65                             324
  1                             7                              23
[1] 2 2
[1] FALSE
D81V7, binary
                                 cls
clus                                0   1
  DEL PEAK 45(19Q13.11) MUTATED    25  50
  DEL PEAK 45(19Q13.11) WILD-TYPE 133 233
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 45(19Q13.11) MUTATED     25   50
  DEL PEAK 45(19Q13.11) WILD-TYPE  133  233
        clus
vv       DEL PEAK 45(19Q13.11) MUTATED DEL PEAK 45(19Q13.11) WILD-TYPE
  FEMALE                            25                             133
  MALE                              50                             233
[1] 2 2
[1] FALSE
D81V8, binary
                                 cls
clus                                0   1
  DEL PEAK 45(19Q13.11) MUTATED    58  11
  DEL PEAK 45(19Q13.11) WILD-TYPE 264  65
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 45(19Q13.11) MUTATED     58   11
  DEL PEAK 45(19Q13.11) WILD-TYPE  264   65
     clus
vv    DEL PEAK 45(19Q13.11) MUTATED DEL PEAK 45(19Q13.11) WILD-TYPE
  NO                             58                             264
  YES                            11                              65
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 45(19Q13.11) MUTATED                                          1
  DEL PEAK 45(19Q13.11) WILD-TYPE                                       12
                                 vv
clus                              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 45(19Q13.11) MUTATED                                       5
  DEL PEAK 45(19Q13.11) WILD-TYPE                                    67
                                 vv
clus                              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 45(19Q13.11) MUTATED                                                       23
  DEL PEAK 45(19Q13.11) WILD-TYPE                                                    140
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 45(19Q13.11) MUTATED                                                   1
  DEL PEAK 45(19Q13.11) WILD-TYPE                                                20
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 45(19Q13.11) MUTATED                                                                  17
  DEL PEAK 45(19Q13.11) WILD-TYPE                                                                65
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 45(19Q13.11) MUTATED                                                    2
  DEL PEAK 45(19Q13.11) WILD-TYPE                                                  6
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 45(19Q13.11) MUTATED                                                 26
  DEL PEAK 45(19Q13.11) WILD-TYPE                                               53
D81V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 45(19Q13.11) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       23
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            17
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             26
                                                                   clus
vv                                                                  DEL PEAK 45(19Q13.11) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                       12
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                        140
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                              6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                               53
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 45(19Q13.11) MUTATED    60   1   5   3
  DEL PEAK 45(19Q13.11) WILD-TYPE 289  17  14  22
D81V10, multiclass
    clus
vv   DEL PEAK 45(19Q13.11) MUTATED DEL PEAK 45(19Q13.11) WILD-TYPE
  R0                            60                             289
  R1                             1                              17
  R2                             5                              14
  RX                             3                              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"
D81V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 45(19Q13.11) MUTATED      15                         4
  DEL PEAK 45(19Q13.11) WILD-TYPE    73                         8
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 45(19Q13.11) MUTATED                                           0
  DEL PEAK 45(19Q13.11) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 45(19Q13.11) MUTATED      47
  DEL PEAK 45(19Q13.11) WILD-TYPE   231
D81V12, multiclass
                                           clus
vv                                          DEL PEAK 45(19Q13.11) MUTATED
  ASIAN                                                                15
  BLACK OR AFRICAN AMERICAN                                             4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                47
                                           clus
vv                                          DEL PEAK 45(19Q13.11) WILD-TYPE
  ASIAN                                                                  73
  BLACK OR AFRICAN AMERICAN                                               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V13, binary
                                 cls
clus                                0   1
  DEL PEAK 45(19Q13.11) MUTATED     1  50
  DEL PEAK 45(19Q13.11) WILD-TYPE   4 266
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 45(19Q13.11) MUTATED      1   50
  DEL PEAK 45(19Q13.11) WILD-TYPE    4  266
                        clus
vv                       DEL PEAK 45(19Q13.11) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            50
                        clus
vv                       DEL PEAK 45(19Q13.11) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             266
[1] 2 2
[1] FALSE

Clustering(82) Variable = DEL PEAK 46(20P12.1) MUTATION ANALYSIS
D82V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 46(20P12.1) MUTATED    18  19
  DEL PEAK 46(20P12.1) WILD-TYPE 228 150
  DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE 
                            37                            378 
  DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE 
                            19                            150 
$`DEL PEAK 46(20P12.1) MUTATED`
TCGA-EQ-A4SO TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6564 TCGA-BR-7723 TCGA-BR-8289 
       16.24         6.18        17.29        26.10        28.73         2.66 
TCGA-BR-A4IY TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-8525 TCGA-CD-A48C TCGA-CG-4301 
       12.89        20.65        21.44        12.59        11.61         3.02 
TCGA-CG-5717 TCGA-CG-5725 TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-8575 
        6.97        15.02        20.55        17.19        10.26        18.21 
TCGA-D7-8576 TCGA-EQ-5647 TCGA-HF-7133 TCGA-HU-8249 TCGA-HU-A4GF TCGA-IN-A6RJ 
       14.66         0.62        63.06        28.96        25.81        12.46 
TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A93J TCGA-RD-A8MW TCGA-SW-A7EA TCGA-VQ-A8DU 
       15.75         2.53        36.95        37.91        19.04         5.46 
TCGA-VQ-A8E0 TCGA-VQ-A8P3 TCGA-VQ-A8PC TCGA-VQ-A8PK TCGA-VQ-A925 TCGA-VQ-AA68 
       18.48        37.22        46.26        17.85         4.54        43.66 
TCGA-VQ-AA6D 
       17.13 

$`DEL PEAK 46(20P12.1) WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        22.98        79.07         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
        9.86        27.35        26.93        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.34         9.67         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 
       13.87        13.68        19.33        39.12         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.56        29.42        19.96         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        31.10        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51         0.46        20.42 
TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 
       13.18        13.35        11.21        12.10        12.76        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        12.00        30.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 
        7.99        25.71        12.66        20.91        19.13        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 
       18.54        18.61        17.85        13.35        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       19.50        17.19        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
        4.34        19.96         7.13         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        18.15        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 
        6.51        10.62        11.70        13.51         5.56        63.62 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       37.64         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 
        8.61         5.13        16.67       122.30        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      116.38        71.38        57.44         8.94        35.61        16.87 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        5.79         0.92        48.79        13.25        13.02        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        37.41        38.14         7.73        30.97        34.29 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM 
       16.31        22.19         2.50        12.79         2.70         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       18.74        20.81        32.88         1.71        42.64        60.85 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
        9.50         9.73        55.56         9.04         2.01        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
        6.58         5.72        66.81        21.04         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       11.24        18.41        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        27.55        12.43        17.26         0.79 

  DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE 
                          0.62                           0.00 
  DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE 
                         63.06                         122.30 
  DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE 
                         17.19                          14.30 
[1] "0.6 - 63.1 (17.2)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.3"
D82V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 46(20P12.1) MUTATED         0        3        4        3         2
  DEL PEAK 46(20P12.1) WILD-TYPE       2       13       37       29        38
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 46(20P12.1) MUTATED           4         0         11          6
  DEL PEAK 46(20P12.1) WILD-TYPE        52         3         70         57
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 46(20P12.1) MUTATED            1        4
  DEL PEAK 46(20P12.1) WILD-TYPE         38       40
D82V3, multiclass
            clus
vv           DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              3                             13
  STAGE IB                              4                             37
  STAGE II                              3                             29
  STAGE IIA                             2                             38
  STAGE IIB                             4                             52
  STAGE III                             0                              3
  STAGE IIIA                           11                             70
  STAGE IIIB                            6                             57
  STAGE IIIC                            1                             38
  STAGE IV                              4                             40
[1] 11  2
[1] TRUE
[1] "dimension of 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(20P12.1) MUTATED     3   9  18   9
  DEL PEAK 46(20P12.1) WILD-TYPE  20  84 178 110
D82V4, multiclass
    clus
vv   DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE
  T1                            3                             20
  T2                            9                             84
  T3                           18                            178
  T4                            9                            110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 46(20P12.1) MUTATED    11  12   9   7
  DEL PEAK 46(20P12.1) WILD-TYPE 119 107  77  81
D82V5, multiclass
    clus
vv   DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE
  N0                           11                            119
  N1                           12                            107
  N2                            9                             77
  N3                            7                             81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V6, binary
                                cls
clus                               0   1
  DEL PEAK 46(20P12.1) MUTATED    33   3
  DEL PEAK 46(20P12.1) WILD-TYPE 356  27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(20P12.1) MUTATED     33    3
  DEL PEAK 46(20P12.1) WILD-TYPE  356   27
   clus
vv  DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE
  0                           33                            356
  1                            3                             27
[1] 2 2
[1] FALSE
D82V7, binary
                                cls
clus                               0   1
  DEL PEAK 46(20P12.1) MUTATED    16  23
  DEL PEAK 46(20P12.1) WILD-TYPE 142 260
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(20P12.1) MUTATED     16   23
  DEL PEAK 46(20P12.1) WILD-TYPE  142  260
        clus
vv       DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE
  FEMALE                           16                            142
  MALE                             23                            260
[1] 2 2
[1] FALSE
D82V8, binary
                                cls
clus                               0   1
  DEL PEAK 46(20P12.1) MUTATED    24  13
  DEL PEAK 46(20P12.1) WILD-TYPE 298  63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(20P12.1) MUTATED     24   13
  DEL PEAK 46(20P12.1) WILD-TYPE  298   63
     clus
vv    DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE
  NO                            24                            298
  YES                           13                             63
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 46(20P12.1) MUTATED                                          1
  DEL PEAK 46(20P12.1) WILD-TYPE                                       12
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 46(20P12.1) MUTATED                                       4
  DEL PEAK 46(20P12.1) WILD-TYPE                                    68
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 46(20P12.1) MUTATED                                                       16
  DEL PEAK 46(20P12.1) WILD-TYPE                                                    147
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 46(20P12.1) MUTATED                                                   2
  DEL PEAK 46(20P12.1) WILD-TYPE                                                19
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 46(20P12.1) MUTATED                                                                   4
  DEL PEAK 46(20P12.1) WILD-TYPE                                                                78
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 46(20P12.1) MUTATED                                                    1
  DEL PEAK 46(20P12.1) WILD-TYPE                                                  7
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 46(20P12.1) MUTATED                                                 10
  DEL PEAK 46(20P12.1) WILD-TYPE                                               69
D82V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 46(20P12.1) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      16
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            10
                                                                   clus
vv                                                                  DEL PEAK 46(20P12.1) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      12
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             78
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              69
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 46(20P12.1) MUTATED    33   1   3   1
  DEL PEAK 46(20P12.1) WILD-TYPE 316  17  16  24
D82V10, multiclass
    clus
vv   DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE
  R0                           33                            316
  R1                            1                             17
  R2                            3                             16
  RX                            1                             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"
D82V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 46(20P12.1) MUTATED       6                         1
  DEL PEAK 46(20P12.1) WILD-TYPE    82                        11
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 46(20P12.1) MUTATED                                           0
  DEL PEAK 46(20P12.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 46(20P12.1) MUTATED      26
  DEL PEAK 46(20P12.1) WILD-TYPE   252
D82V12, multiclass
                                           clus
vv                                          DEL PEAK 46(20P12.1) MUTATED
  ASIAN                                                                6
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               26
                                           clus
vv                                          DEL PEAK 46(20P12.1) WILD-TYPE
  ASIAN                                                                 82
  BLACK OR AFRICAN AMERICAN                                             11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                252
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V13, binary
                                cls
clus                               0   1
  DEL PEAK 46(20P12.1) MUTATED     0  25
  DEL PEAK 46(20P12.1) WILD-TYPE   5 291
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(20P12.1) MUTATED      0   25
  DEL PEAK 46(20P12.1) WILD-TYPE    5  291
                        clus
vv                       DEL PEAK 46(20P12.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           25
                        clus
vv                       DEL PEAK 46(20P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            291
[1] 2 2
[1] FALSE

Clustering(83) Variable = DEL PEAK 47(21Q11.2) MUTATION ANALYSIS
D83V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 47(21Q11.2) MUTATED    99  75
  DEL PEAK 47(21Q11.2) WILD-TYPE 147  94
  DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE 
                           174                            241 
  DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE 
                            75                             94 
$`DEL PEAK 47(21Q11.2) MUTATED`
TCGA-CG-4444 TCGA-CG-4475 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU 
       47.05        22.98         0.23        20.15         9.86        27.35 
TCGA-VQ-A94U TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4255 
       26.93        11.70        11.01         9.44         6.97         4.08 
TCGA-BR-4257 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6803 
        9.67        13.68        19.33        26.10         9.17        31.20 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8060 
       35.24        33.63        39.78        28.73        33.21        11.44 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8291 TCGA-BR-8361 TCGA-BR-8365 
       29.59         9.60         8.05        19.96        31.10        17.52 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        4.31        14.04        14.79         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       20.22        24.79         9.86        20.88         8.22        10.68 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4J9 
        7.53        34.98         1.48         0.72        13.51         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5804 TCGA-CD-8524 
       20.65        20.42         1.15        21.44        12.10        12.76 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 
       12.53         7.17        12.39        12.82        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-4440 
       12.43        11.61        12.20        20.02        54.08         4.01 
TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       12.03        18.97        30.97         6.97        36.00         1.02 
TCGA-CG-5724 TCGA-CG-5728 TCGA-CG-5730 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
       12.03        65.10         4.01        20.91        19.13        20.55 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 
       13.35        17.19        15.98        12.79        11.31        12.33 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-EQ-5647 
       14.66        21.14        16.44        11.31        15.65         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-A4BF TCGA-FP-A9TM 
        7.99        72.23        11.38        19.53         5.52         6.21 
TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G8 
       63.06        26.47         1.51        28.96        22.82        22.68 
TCGA-HU-A4GC TCGA-HU-A4GP TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 
        3.25         8.98         0.26        29.00        23.80        21.17 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       33.40        36.36        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 
       13.35         6.74        10.62        11.70        15.75         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-R5-A7O7 TCGA-R5-A7ZE 
        5.56        63.62        37.64        36.95        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A8MV TCGA-RD-A8MW 
        8.52        74.53         6.08         9.24       122.30        37.91 
TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL 
      115.69        57.44         8.94        35.61         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8P5 
       48.79        13.25        13.02        18.48        21.73         7.73 
TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PP TCGA-VQ-A8PX 
       22.19         2.70        17.85         1.87        23.41        64.57 
TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U 
       14.33        39.45        61.22        18.74        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
       42.64         9.50         9.73        55.56         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
       55.43         4.54        21.04        42.54        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       43.66        32.94        54.12        26.04        12.43         0.79 

$`DEL PEAK 47(21Q11.2) WILD-TYPE`
TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-A5TI 
       21.99        79.07        16.24        58.03        26.70        19.56 
TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.47         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 
       15.95        13.87        17.29        39.12        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 
       44.94        21.90         9.21        36.16        35.84        18.15 
TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 
       15.32         3.45         9.07        29.56        37.25        14.43 
TCGA-BR-8077 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 
        0.69        32.25         0.56        29.42         2.66         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        13.08         0.26        22.19 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 
        0.95        26.33         3.32        11.80        31.27         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.05         3.72         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        31.96        32.58 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       34.13        13.87         6.08        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 
       13.35        11.21        12.59        12.33        12.30        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A4MG 
       11.64        15.39        12.07        12.43         6.31         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        12.62         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 
        7.99         8.05        14.01        29.98        19.07         0.00 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        9.01         7.07        12.00         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
      105.07        15.02        28.96        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       25.71        12.66        18.84        18.54        18.61        17.85 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.26        15.22        12.36        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX 
       17.19        18.21        20.91        14.27         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 
       22.29         8.38         4.34        19.96         7.13        14.47 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       21.27         3.48        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB 
        5.03        13.58         0.56        77.29        52.21        30.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        18.15        22.32        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF 
       24.30         5.59        24.26        24.20        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-HU-A4HB 
       20.25         2.10        12.95        23.84        14.07        15.68 
TCGA-IN-7808 TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1X 
        3.45        19.53         6.44        12.59         6.51        13.51 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT 
        3.72        19.73        14.04         4.60        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB 
        5.13        16.67        40.64       116.38        71.38        16.87 
TCGA-SW-A7EA TCGA-VQ-A8DU TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       19.04         5.46        43.36        37.41        38.14        37.22 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH 
       30.97        34.29        46.26        16.31         2.50        12.79 
TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91D 
        9.27        15.65        13.35        29.59        73.41        11.70 
TCGA-VQ-A91E TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
       21.83        32.88        60.85         6.58         5.72        66.81 
TCGA-VQ-A94P TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6I TCGA-VQ-AA6J 
        2.66        28.41        38.93        17.13        16.14        27.55 
TCGA-ZA-A8F6 
       17.26 

  DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE 
                          0.23                           0.00 
  DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE 
                        122.30                         116.38 
  DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE 
                        14.725                         15.020 
[1] "0.2 - 122.3 (14.7)" "0.0 - 116.4 (15.0)"
[1] "hr=" "1.1"
D83V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 47(21Q11.2) MUTATED         1        6       17       10        17
  DEL PEAK 47(21Q11.2) WILD-TYPE       1       10       24       22        23
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 47(21Q11.2) MUTATED          24         1         40         26
  DEL PEAK 47(21Q11.2) WILD-TYPE        32         2         41         37
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 47(21Q11.2) MUTATED           14       17
  DEL PEAK 47(21Q11.2) WILD-TYPE         25       27
D83V3, multiclass
            clus
vv           DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                              6                             10
  STAGE IB                             17                             24
  STAGE II                             10                             22
  STAGE IIA                            17                             23
  STAGE IIB                            24                             32
  STAGE III                             1                              2
  STAGE IIIA                           40                             41
  STAGE IIIB                           26                             37
  STAGE IIIC                           14                             25
  STAGE IV                             17                             27
[1] 11  2
[1] TRUE
[1] "dimension of 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(21Q11.2) MUTATED     8  38  89  44
  DEL PEAK 47(21Q11.2) WILD-TYPE  15  55 107  75
D83V4, multiclass
    clus
vv   DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE
  T1                            8                             15
  T2                           38                             55
  T3                           89                            107
  T4                           44                             75
[1] 4 2
[1] TRUE
[1] "dimension of 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(21Q11.2) MUTATED   48 54 41 33
  DEL PEAK 47(21Q11.2) WILD-TYPE 82 65 45 55
D83V5, multiclass
    clus
vv   DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE
  N0                           48                             82
  N1                           54                             65
  N2                           41                             45
  N3                           33                             55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V6, binary
                                cls
clus                               0   1
  DEL PEAK 47(21Q11.2) MUTATED   164  10
  DEL PEAK 47(21Q11.2) WILD-TYPE 225  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(21Q11.2) MUTATED    164   10
  DEL PEAK 47(21Q11.2) WILD-TYPE  225   20
   clus
vv  DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE
  0                          164                            225
  1                           10                             20
[1] 2 2
[1] FALSE
D83V7, binary
                                cls
clus                               0   1
  DEL PEAK 47(21Q11.2) MUTATED    70 112
  DEL PEAK 47(21Q11.2) WILD-TYPE  88 171
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(21Q11.2) MUTATED     70  112
  DEL PEAK 47(21Q11.2) WILD-TYPE   88  171
        clus
vv       DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE
  FEMALE                           70                             88
  MALE                            112                            171
[1] 2 2
[1] FALSE
D83V8, binary
                                cls
clus                               0   1
  DEL PEAK 47(21Q11.2) MUTATED   130  37
  DEL PEAK 47(21Q11.2) WILD-TYPE 192  39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(21Q11.2) MUTATED    130   37
  DEL PEAK 47(21Q11.2) WILD-TYPE  192   39
     clus
vv    DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE
  NO                           130                            192
  YES                           37                             39
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 47(21Q11.2) MUTATED                                          8
  DEL PEAK 47(21Q11.2) WILD-TYPE                                        5
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 47(21Q11.2) MUTATED                                      24
  DEL PEAK 47(21Q11.2) WILD-TYPE                                    48
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 47(21Q11.2) MUTATED                                                       60
  DEL PEAK 47(21Q11.2) WILD-TYPE                                                    103
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 47(21Q11.2) MUTATED                                                   9
  DEL PEAK 47(21Q11.2) WILD-TYPE                                                12
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 47(21Q11.2) MUTATED                                                                  40
  DEL PEAK 47(21Q11.2) WILD-TYPE                                                                42
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 47(21Q11.2) MUTATED                                                    1
  DEL PEAK 47(21Q11.2) WILD-TYPE                                                  7
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 47(21Q11.2) MUTATED                                                 39
  DEL PEAK 47(21Q11.2) WILD-TYPE                                               40
D83V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 47(21Q11.2) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                       24
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      60
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            9
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           40
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            39
                                                                   clus
vv                                                                  DEL PEAK 47(21Q11.2) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                       5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         48
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       103
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             12
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             42
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              40
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 47(21Q11.2) MUTATED   146   9   8   6
  DEL PEAK 47(21Q11.2) WILD-TYPE 203   9  11  19
D83V10, multiclass
    clus
vv   DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE
  R0                          146                            203
  R1                            9                              9
  R2                            8                             11
  RX                            6                             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"
D83V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 47(21Q11.2) MUTATED      31                         6
  DEL PEAK 47(21Q11.2) WILD-TYPE    57                         6
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 47(21Q11.2) MUTATED                                           0
  DEL PEAK 47(21Q11.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 47(21Q11.2) MUTATED     115
  DEL PEAK 47(21Q11.2) WILD-TYPE   163
D83V12, multiclass
                                           clus
vv                                          DEL PEAK 47(21Q11.2) MUTATED
  ASIAN                                                               31
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              115
                                           clus
vv                                          DEL PEAK 47(21Q11.2) WILD-TYPE
  ASIAN                                                                 57
  BLACK OR AFRICAN AMERICAN                                              6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                163
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V13, binary
                                cls
clus                               0   1
  DEL PEAK 47(21Q11.2) MUTATED     2 119
  DEL PEAK 47(21Q11.2) WILD-TYPE   3 197
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(21Q11.2) MUTATED      2  119
  DEL PEAK 47(21Q11.2) WILD-TYPE    3  197
                        clus
vv                       DEL PEAK 47(21Q11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          119
                        clus
vv                       DEL PEAK 47(21Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            197
[1] 2 2
[1] FALSE

Clustering(84) Variable = DEL PEAK 48(21Q22.13) MUTATION ANALYSIS
D84V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 48(21Q22.13) MUTATED   113  74
  DEL PEAK 48(21Q22.13) WILD-TYPE 133  95
  DEL PEAK 48(21Q22.13) MUTATED DEL PEAK 48(21Q22.13) WILD-TYPE 
                            187                             228 
  DEL PEAK 48(21Q22.13) MUTATED DEL PEAK 48(21Q22.13) WILD-TYPE 
                             74                              95 
$`DEL PEAK 48(21Q22.13) MUTATED`
TCGA-CG-4444 TCGA-CG-4475 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU 
       47.05        22.98         0.23        20.15         9.86        27.35 
TCGA-VQ-A94U TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4191 
       26.93        11.70        11.01         9.44         6.97        18.35 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 
        4.08         9.67        13.68        19.33        26.10         9.17 
TCGA-BR-6803 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7959 
       31.20        35.24        33.63        39.78        28.73        33.21 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8291 TCGA-BR-8296 
       14.43        11.44         9.60         8.05        19.96        15.58 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8365 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8373 
        7.40        31.10        17.52         4.31        14.04        14.79 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        5.39        25.18         9.21        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY 
       20.88        10.68         7.53        34.98         1.48        12.89 
TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.72        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 
       21.44        12.76        12.53         7.17        12.33        12.39 
TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 
       12.82        11.31        12.43        11.61        12.20        20.02 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 
       54.08         4.01        19.07        12.03        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 
       30.97         6.97         1.02        12.03        15.02        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6525 
        4.01        69.04        20.91        19.13        20.55        13.35 
TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8578 TCGA-D7-A4YT 
       17.19        15.98        12.79        11.31        21.14        14.27 
TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-F1-6875 
       16.44        11.31        15.65        19.96         0.62        72.23 
TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-A9TM TCGA-HF-7133 TCGA-HJ-7597 
       11.38        19.53        17.06         6.21        63.06        26.47 
TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GH 
        1.51        28.96        22.82        22.68         3.25        11.77 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        8.98         6.58         0.26        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       23.80        21.17        36.36        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
       12.46        13.35         6.74         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J 
       15.75         2.53         5.56        63.62        37.64        36.95 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A805 TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 
        9.24        16.67       122.30        37.91       115.69        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PC 
       13.25        13.02        18.48        37.41         7.73        46.26 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PP TCGA-VQ-A8PX TCGA-VQ-A8PY 
       22.19        17.85         1.87        23.41        64.57        14.33 
TCGA-VQ-A91A TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       39.45        61.22        18.74        20.81         1.71        42.64 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A92D 
        9.73        55.56         2.01        55.43         4.54        66.81 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A 
       21.04        42.54        11.24        18.41        43.66        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        17.13        54.12        16.14        27.55        12.43 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK 48(21Q22.13) WILD-TYPE`
TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-A5TI 
       21.99        79.07        16.24        58.03        26.70        19.56 
TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 
        9.47         6.61         4.64         7.43        30.90         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.34         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.87        17.29        39.12        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 
       19.89        12.16         8.98        40.21        30.90        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 
       21.90         9.21        36.16        35.84        18.15        15.32 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 
        3.45         9.07        29.56        37.25         0.69        29.59 
TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8360 
       32.25         0.56        29.42         2.66         2.20         6.18 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8370 
       13.08         0.26        22.19         0.95        26.33         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8486 
       11.80        31.27         7.36        25.05         3.72        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U 
        7.53        26.73        31.96         8.22        34.13        13.87 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
        6.08        27.55        28.57         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       28.34         0.66        32.52        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8525 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.59        12.30        12.59        11.64        15.39        12.07 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43         6.31        12.30         6.58        11.77        12.62 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4472 TCGA-CG-5718 
       14.01        29.98         0.00         9.01        12.00        36.00 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5733 
        0.99         6.02         0.99       105.07        28.96        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
        7.99        25.71        12.66        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 
       17.85        10.26        15.22        12.36        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 
       16.80        19.50        17.19        18.21        14.66        20.91 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       11.44        20.32        22.29         8.38         4.34         7.13 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
        7.99        14.47        21.27         3.48        14.07        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-7132 
       59.54         5.03        13.58         0.56         5.52        77.29 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       52.21        30.51         5.92        24.39        18.15        22.32 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT 
       22.75        25.81        21.37        29.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 
       20.25         2.10        14.07        15.68        33.40         3.45 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-AB1X TCGA-MX-A5UG TCGA-MX-A5UJ 
       19.53         6.44        12.59        13.51         3.72        19.73 
TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8N0 TCGA-RD-A8N2 
        4.60        11.05         8.61         5.13        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-VQ-A8DU TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 
       71.38        16.87         5.46        43.36        21.73        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH 
       37.22        30.97        34.29        16.31         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ 
        2.70         9.27        15.65        13.35        29.59        73.41 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A922 
       11.70        21.83        32.88        60.85         9.50         9.04 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-AA69 TCGA-VQ-AA6G TCGA-ZA-A8F6 
        6.58         5.72         2.66        28.41        26.04        17.26 

  DEL PEAK 48(21Q22.13) MUTATED DEL PEAK 48(21Q22.13) WILD-TYPE 
                           0.23                            0.00 
  DEL PEAK 48(21Q22.13) MUTATED DEL PEAK 48(21Q22.13) WILD-TYPE 
                         122.30                          116.38 
  DEL PEAK 48(21Q22.13) MUTATED DEL PEAK 48(21Q22.13) WILD-TYPE 
                          15.98                           14.07 
[1] "0.2 - 122.3 (16.0)" "0.0 - 116.4 (14.1)"
[1] "hr=" "1.2"
D84V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 48(21Q22.13) MUTATED         1        6       19       10        18
  DEL PEAK 48(21Q22.13) WILD-TYPE       1       10       22       22        22
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 48(21Q22.13) MUTATED          25         2         43         27
  DEL PEAK 48(21Q22.13) WILD-TYPE        31         1         38         36
                                 vv
clus                              STAGE IIIC STAGE IV
  DEL PEAK 48(21Q22.13) MUTATED           16       19
  DEL PEAK 48(21Q22.13) WILD-TYPE         23       25
D84V3, multiclass
            clus
vv           DEL PEAK 48(21Q22.13) MUTATED DEL PEAK 48(21Q22.13) WILD-TYPE
  STAGE I                                1                               1
  STAGE IA                               6                              10
  STAGE IB                              19                              22
  STAGE II                              10                              22
  STAGE IIA                             18                              22
  STAGE IIB                             25                              31
  STAGE III                              2                               1
  STAGE IIIA                            43                              38
  STAGE IIIB                            27                              36
  STAGE IIIC                            16                              23
  STAGE IV                              19                              25
[1] 11  2
[1] TRUE
[1] "dimension of 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(21Q22.13) MUTATED     8  44  90  49
  DEL PEAK 48(21Q22.13) WILD-TYPE  15  49 106  70
D84V4, multiclass
    clus
vv   DEL PEAK 48(21Q22.13) MUTATED DEL PEAK 48(21Q22.13) WILD-TYPE
  T1                             8                              15
  T2                            44                              49
  T3                            90                             106
  T4                            49                              70
[1] 4 2
[1] TRUE
[1] "dimension of 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(21Q22.13) MUTATED   52 56 40 40
  DEL PEAK 48(21Q22.13) WILD-TYPE 78 63 46 48
D84V5, multiclass
    clus
vv   DEL PEAK 48(21Q22.13) MUTATED DEL PEAK 48(21Q22.13) WILD-TYPE
  N0                            52                              78
  N1                            56                              63
  N2                            40                              46
  N3                            40                              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V6, binary
                                 cls
clus                                0   1
  DEL PEAK 48(21Q22.13) MUTATED   177  11
  DEL PEAK 48(21Q22.13) WILD-TYPE 212  19
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 48(21Q22.13) MUTATED    177   11
  DEL PEAK 48(21Q22.13) WILD-TYPE  212   19
   clus
vv  DEL PEAK 48(21Q22.13) MUTATED DEL PEAK 48(21Q22.13) WILD-TYPE
  0                           177                             212
  1                            11                              19
[1] 2 2
[1] FALSE
D84V7, binary
                                 cls
clus                                0   1
  DEL PEAK 48(21Q22.13) MUTATED    71 125
  DEL PEAK 48(21Q22.13) WILD-TYPE  87 158
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 48(21Q22.13) MUTATED     71  125
  DEL PEAK 48(21Q22.13) WILD-TYPE   87  158
        clus
vv       DEL PEAK 48(21Q22.13) MUTATED DEL PEAK 48(21Q22.13) WILD-TYPE
  FEMALE                            71                              87
  MALE                             125                             158
[1] 2 2
[1] FALSE
D84V8, binary
                                 cls
clus                                0   1
  DEL PEAK 48(21Q22.13) MUTATED   140  38
  DEL PEAK 48(21Q22.13) WILD-TYPE 182  38
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 48(21Q22.13) MUTATED    140   38
  DEL PEAK 48(21Q22.13) WILD-TYPE  182   38
     clus
vv    DEL PEAK 48(21Q22.13) MUTATED DEL PEAK 48(21Q22.13) WILD-TYPE
  NO                            140                             182
  YES                            38                              38
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 48(21Q22.13) MUTATED                                          8
  DEL PEAK 48(21Q22.13) WILD-TYPE                                        5
                                 vv
clus                              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 48(21Q22.13) MUTATED                                      27
  DEL PEAK 48(21Q22.13) WILD-TYPE                                    45
                                 vv
clus                              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 48(21Q22.13) MUTATED                                                       64
  DEL PEAK 48(21Q22.13) WILD-TYPE                                                     99
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 48(21Q22.13) MUTATED                                                  11
  DEL PEAK 48(21Q22.13) WILD-TYPE                                                10
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 48(21Q22.13) MUTATED                                                                  42
  DEL PEAK 48(21Q22.13) WILD-TYPE                                                                40
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 48(21Q22.13) MUTATED                                                    1
  DEL PEAK 48(21Q22.13) WILD-TYPE                                                  7
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 48(21Q22.13) MUTATED                                                 42
  DEL PEAK 48(21Q22.13) WILD-TYPE                                               37
D84V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 48(21Q22.13) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        27
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       64
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            11
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            42
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             42
                                                                   clus
vv                                                                  DEL PEAK 48(21Q22.13) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                        5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                          45
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                         99
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                              10
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                              40
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                              7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                               37
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 48(21Q22.13) MUTATED   160   8   7   8
  DEL PEAK 48(21Q22.13) WILD-TYPE 189  10  12  17
D84V10, multiclass
    clus
vv   DEL PEAK 48(21Q22.13) MUTATED DEL PEAK 48(21Q22.13) WILD-TYPE
  R0                           160                             189
  R1                             8                              10
  R2                             7                              12
  RX                             8                              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"
D84V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 48(21Q22.13) MUTATED      35                         7
  DEL PEAK 48(21Q22.13) WILD-TYPE    53                         5
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 48(21Q22.13) MUTATED                                           0
  DEL PEAK 48(21Q22.13) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 48(21Q22.13) MUTATED     123
  DEL PEAK 48(21Q22.13) WILD-TYPE   155
D84V12, multiclass
                                           clus
vv                                          DEL PEAK 48(21Q22.13) MUTATED
  ASIAN                                                                35
  BLACK OR AFRICAN AMERICAN                                             7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               123
                                           clus
vv                                          DEL PEAK 48(21Q22.13) WILD-TYPE
  ASIAN                                                                  53
  BLACK OR AFRICAN AMERICAN                                               5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V13, binary
                                 cls
clus                                0   1
  DEL PEAK 48(21Q22.13) MUTATED     2 129
  DEL PEAK 48(21Q22.13) WILD-TYPE   3 187
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 48(21Q22.13) MUTATED      2  129
  DEL PEAK 48(21Q22.13) WILD-TYPE    3  187
                        clus
vv                       DEL PEAK 48(21Q22.13) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           129
                        clus
vv                       DEL PEAK 48(21Q22.13) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             187
[1] 2 2
[1] FALSE

Clustering(85) Variable = DEL PEAK 49(22Q13.31) MUTATION ANALYSIS
D85V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 49(22Q13.31) MUTATED    90  64
  DEL PEAK 49(22Q13.31) WILD-TYPE 156 105
  DEL PEAK 49(22Q13.31) MUTATED DEL PEAK 49(22Q13.31) WILD-TYPE 
                            154                             261 
  DEL PEAK 49(22Q13.31) MUTATED DEL PEAK 49(22Q13.31) WILD-TYPE 
                             64                             105 
$`DEL PEAK 49(22Q13.31) MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU 
       47.05        21.99        16.24        20.15         9.86        27.35 
TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4191 
       26.93        58.03        11.01         9.44         6.61        18.35 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 
        4.08         9.67         6.18        17.29        19.33        26.10 
TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-8058 TCGA-BR-8059 
        9.17        12.16         9.21        33.63        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       11.44         0.69         9.60         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8369 TCGA-BR-8484 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       31.10        14.04        25.18        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J1 
        9.86         8.22        10.68        34.98        12.89         0.72 
TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 
       32.52        20.65         1.15        21.44        13.02        13.15 
TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-A486 
       12.76        12.53        12.39        15.39        12.07         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4301 
       12.30        11.31        12.43        11.61        12.20         3.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4466 
        8.05        54.08         4.01        14.01        19.07        18.97 
TCGA-CG-4477 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-5579 
       30.97        12.03        15.02        69.04        12.66        20.91 
TCGA-D7-6519 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 
       20.55        13.35        17.19        10.26        15.22        12.79 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8578 
       11.31        12.33        24.72        19.50        18.21        21.14 
TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-FP-7829 
       16.44        11.31        15.65        19.96         0.62        19.53 
TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HU-8243 
       17.06         0.56         5.52         6.21        63.06         5.92 
TCGA-HU-8249 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
       28.96        22.75         8.98         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       23.84        21.17        33.40         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IN-AB1V 
       13.35        19.53         6.44         6.74        11.70        15.75 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93J TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR 
        2.53         5.56        36.95        45.67        18.21         6.08 
TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL 
        8.61        16.67       115.69        35.61         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
       48.79         5.46        13.25        13.02        18.48        43.36 
TCGA-VQ-A8P3 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.22        46.26        22.19        12.79        17.85         1.87 
TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       14.33        39.45        18.74        20.81         1.71        42.64 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94T 
        9.50         9.73         9.04         4.54        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-ZQ-A9CR 
       18.41        38.93        32.94         0.79 

$`DEL PEAK 49(22Q13.31) WILD-TYPE`
TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
       22.98        79.07         0.23        26.70        11.70        19.56 
TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 
        9.47         6.97         4.64         7.43        30.90         4.08 
TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        9.34         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       13.68        39.12        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.24        35.84        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8078 
       28.73         3.45         9.07        29.56        33.21        29.59 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8296 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       15.58        13.08         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33         4.31         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 
        7.36        25.05         3.72         5.39         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
        7.53        31.96        20.88        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 
        6.08         1.48        27.55        28.57         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE 
        0.53        28.34         0.66        13.51         0.46        20.42 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       16.14         5.13        13.41        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 
       12.10        12.59         7.17        12.33        12.30        12.59 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.64        12.82        12.43         6.58        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4443 
       20.02        27.02        15.95         1.02         7.99        29.98 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 
       12.03         0.00         9.01         7.07        12.00         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        21.07         7.99        25.71 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6815 
       19.13        18.84        18.54        18.61        17.85        15.98 
TCGA-D7-6818 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT 
       12.36        16.80        17.19        14.66        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       11.44        20.32        22.29         8.38         4.34         7.13 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-7132 
       14.07        22.29        59.54         5.03        13.58        77.29 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
       52.21        30.51        26.47         1.51        24.39        18.15 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        22.68        24.20         3.25        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       29.00        23.80        14.07        15.68        36.36         3.45 
TCGA-IN-8462 TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1X TCGA-KB-A6F7 
       18.81        12.59         6.51        10.62        13.51        63.62 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZF TCGA-R5-A7ZI 
       37.64         3.72        19.73        14.04         8.52        74.53 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
        4.60         9.24        11.05         5.13       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB 
       40.64       116.38        71.38        57.44         8.94        16.87 
TCGA-SW-A7EA TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       19.04        21.73        37.41        38.14         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP 
       34.29        16.31         2.50         2.70         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91D 
       15.65        13.35        29.59        64.57        73.41        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A923 
       21.83        61.22        32.88        60.85        55.56         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
       55.43         6.58         5.72        21.04         2.66        42.54 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       43.66        28.41        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  DEL PEAK 49(22Q13.31) MUTATED DEL PEAK 49(22Q13.31) WILD-TYPE 
                           0.26                            0.00 
  DEL PEAK 49(22Q13.31) MUTATED DEL PEAK 49(22Q13.31) WILD-TYPE 
                         115.69                          122.30 
  DEL PEAK 49(22Q13.31) MUTATED DEL PEAK 49(22Q13.31) WILD-TYPE 
                          13.35                           15.95 
[1] "0.3 - 115.7 (13.3)" "0.0 - 122.3 (15.9)"
[1] "hr=" "1.1"
D85V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 49(22Q13.31) MUTATED         1        2       16       12        13
  DEL PEAK 49(22Q13.31) WILD-TYPE       1       14       25       20        27
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 49(22Q13.31) MUTATED          19         2         37         26
  DEL PEAK 49(22Q13.31) WILD-TYPE        37         1         44         37
                                 vv
clus                              STAGE IIIC STAGE IV
  DEL PEAK 49(22Q13.31) MUTATED           11       15
  DEL PEAK 49(22Q13.31) WILD-TYPE         28       29
D85V3, multiclass
            clus
vv           DEL PEAK 49(22Q13.31) MUTATED DEL PEAK 49(22Q13.31) WILD-TYPE
  STAGE I                                1                               1
  STAGE IA                               2                              14
  STAGE IB                              16                              25
  STAGE II                              12                              20
  STAGE IIA                             13                              27
  STAGE IIB                             19                              37
  STAGE III                              2                               1
  STAGE IIIA                            37                              44
  STAGE IIIB                            26                              37
  STAGE IIIC                            11                              28
  STAGE IV                              15                              29
[1] 11  2
[1] TRUE
[1] "dimension of 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(22Q13.31) MUTATED     6  36  76  39
  DEL PEAK 49(22Q13.31) WILD-TYPE  17  57 120  80
D85V4, multiclass
    clus
vv   DEL PEAK 49(22Q13.31) MUTATED DEL PEAK 49(22Q13.31) WILD-TYPE
  T1                             6                              17
  T2                            36                              57
  T3                            76                             120
  T4                            39                              80
[1] 4 2
[1] TRUE
[1] "dimension of 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(22Q13.31) MUTATED   42 39 40 33
  DEL PEAK 49(22Q13.31) WILD-TYPE 88 80 46 55
D85V5, multiclass
    clus
vv   DEL PEAK 49(22Q13.31) MUTATED DEL PEAK 49(22Q13.31) WILD-TYPE
  N0                            42                              88
  N1                            39                              80
  N2                            40                              46
  N3                            33                              55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V6, binary
                                 cls
clus                                0   1
  DEL PEAK 49(22Q13.31) MUTATED   147   7
  DEL PEAK 49(22Q13.31) WILD-TYPE 242  23
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 49(22Q13.31) MUTATED    147    7
  DEL PEAK 49(22Q13.31) WILD-TYPE  242   23
   clus
vv  DEL PEAK 49(22Q13.31) MUTATED DEL PEAK 49(22Q13.31) WILD-TYPE
  0                           147                             242
  1                             7                              23
[1] 2 2
[1] FALSE
D85V7, binary
                                 cls
clus                                0   1
  DEL PEAK 49(22Q13.31) MUTATED    52 109
  DEL PEAK 49(22Q13.31) WILD-TYPE 106 174
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 49(22Q13.31) MUTATED     52  109
  DEL PEAK 49(22Q13.31) WILD-TYPE  106  174
        clus
vv       DEL PEAK 49(22Q13.31) MUTATED DEL PEAK 49(22Q13.31) WILD-TYPE
  FEMALE                            52                             106
  MALE                             109                             174
[1] 2 2
[1] FALSE
D85V8, binary
                                 cls
clus                                0   1
  DEL PEAK 49(22Q13.31) MUTATED   116  33
  DEL PEAK 49(22Q13.31) WILD-TYPE 206  43
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 49(22Q13.31) MUTATED    116   33
  DEL PEAK 49(22Q13.31) WILD-TYPE  206   43
     clus
vv    DEL PEAK 49(22Q13.31) MUTATED DEL PEAK 49(22Q13.31) WILD-TYPE
  NO                            116                             206
  YES                            33                              43
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 49(22Q13.31) MUTATED                                          6
  DEL PEAK 49(22Q13.31) WILD-TYPE                                        7
                                 vv
clus                              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 49(22Q13.31) MUTATED                                      19
  DEL PEAK 49(22Q13.31) WILD-TYPE                                    53
                                 vv
clus                              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 49(22Q13.31) MUTATED                                                       56
  DEL PEAK 49(22Q13.31) WILD-TYPE                                                    107
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 49(22Q13.31) MUTATED                                                   9
  DEL PEAK 49(22Q13.31) WILD-TYPE                                                12
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 49(22Q13.31) MUTATED                                                                  27
  DEL PEAK 49(22Q13.31) WILD-TYPE                                                                55
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 49(22Q13.31) MUTATED                                                    2
  DEL PEAK 49(22Q13.31) WILD-TYPE                                                  6
                                 vv
clus                              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 49(22Q13.31) MUTATED                                                 41
  DEL PEAK 49(22Q13.31) WILD-TYPE                                               38
D85V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 49(22Q13.31) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      6
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        19
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       56
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             9
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            27
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             41
                                                                   clus
vv                                                                  DEL PEAK 49(22Q13.31) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                          53
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                        107
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                              12
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                              55
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                              6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                               38
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 49(22Q13.31) MUTATED   124   8   9   8
  DEL PEAK 49(22Q13.31) WILD-TYPE 225  10  10  17
D85V10, multiclass
    clus
vv   DEL PEAK 49(22Q13.31) MUTATED DEL PEAK 49(22Q13.31) WILD-TYPE
  R0                           124                             225
  R1                             8                              10
  R2                             9                              10
  RX                             8                              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"
D85V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 49(22Q13.31) MUTATED      31                         3
  DEL PEAK 49(22Q13.31) WILD-TYPE    57                         9
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 49(22Q13.31) MUTATED                                           1
  DEL PEAK 49(22Q13.31) WILD-TYPE                                         0
                                 vv
clus                              WHITE
  DEL PEAK 49(22Q13.31) MUTATED     102
  DEL PEAK 49(22Q13.31) WILD-TYPE   176
D85V12, multiclass
                                           clus
vv                                          DEL PEAK 49(22Q13.31) MUTATED
  ASIAN                                                                31
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               102
                                           clus
vv                                          DEL PEAK 49(22Q13.31) WILD-TYPE
  ASIAN                                                                  57
  BLACK OR AFRICAN AMERICAN                                               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               0
  WHITE                                                                 176
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V13, binary
                                 cls
clus                                0   1
  DEL PEAK 49(22Q13.31) MUTATED     2 109
  DEL PEAK 49(22Q13.31) WILD-TYPE   3 207
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 49(22Q13.31) MUTATED      2  109
  DEL PEAK 49(22Q13.31) WILD-TYPE    3  207
                        clus
vv                       DEL PEAK 49(22Q13.31) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           109
                        clus
vv                       DEL PEAK 49(22Q13.31) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             207
[1] 2 2
[1] FALSE

Clustering(86) Variable = DEL PEAK 50(XP22.2) MUTATION ANALYSIS
D86V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 50(XP22.2) MUTATED    51  31
  DEL PEAK 50(XP22.2) WILD-TYPE 195 138
  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                           82                           333 
  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                           31                           138 
$`DEL PEAK 50(XP22.2) MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-A5TN 
       47.05        21.99        27.35        26.93        58.03         9.44 
TCGA-BR-4191 TCGA-BR-6458 TCGA-BR-7716 TCGA-BR-8059 TCGA-BR-8289 TCGA-BR-8297 
       18.35        19.33        39.78        14.43         2.66         7.40 
TCGA-BR-8362 TCGA-BR-8369 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8590 TCGA-BR-8680 
       13.08        14.04         9.21        20.22         9.34        31.96 
TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4J6 TCGA-BR-A4PD 
        9.86        10.68        13.87        34.98         0.66        20.65 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8531 
        1.15        21.44        13.02        13.35        12.76        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 
       11.64        15.39        12.07        12.82        12.30        11.31 
TCGA-CD-A4MH TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-5718 TCGA-CG-5725 
       12.20        54.08        14.01        19.07        36.00        15.02 
TCGA-CG-5734 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
        7.99        20.91        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
       12.79        12.33        18.21        11.31        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-FP-8211 TCGA-FP-A4BF TCGA-HU-A4G3 
       15.65        19.96         0.62        13.58         5.52         5.59 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GU TCGA-HU-A4H5 TCGA-IN-7806 TCGA-IN-7808 
       22.75        25.81         6.58        23.80        36.36         3.45 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RP TCGA-KB-A93J TCGA-R5-A7O7 
        3.39        18.38        13.35         6.44        36.95        45.67 
TCGA-RD-A8N6 TCGA-VQ-A8P3 TCGA-VQ-A8PC TCGA-VQ-A8PS TCGA-VQ-A91Y TCGA-VQ-A91Z 
        8.94        37.22        46.26        13.35         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6A 
        9.04         5.72        43.66        38.93 

$`DEL PEAK 50(XP22.2) WILD-TYPE`
TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       22.98        79.07        16.24         0.23        20.15         9.86 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 
       26.70        11.70        19.56        11.01         9.47         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.87        17.29        13.68        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 
        9.21        36.16        35.24        35.84        33.63        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       37.25        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56        29.42        19.96         2.20        15.58 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33         4.31         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8487 
        7.36        25.05         3.72         5.39        25.18         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A452 
       24.79        32.58        20.88         8.22        34.13         7.53 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53        28.34        32.52        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 
        0.46        20.42        16.14         5.13        13.41        13.15 
TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.18        11.21        12.10        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A48A 
       12.33        12.30        12.39        12.43         6.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 
       27.02        15.95         1.02         7.99         8.05         4.01 
TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       29.98        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       12.00        30.97         6.97         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 
       69.04        21.07        25.71        12.66        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6818 
       18.84        18.54        18.61        17.85        13.35        12.36 
TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 
       11.31        24.72        16.80        19.50        17.19        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A747 
       13.78        14.76        26.43        11.24        11.44         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        4.34         7.13         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       59.54         5.03         0.56         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       18.15        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH 
       24.30        24.26        22.68        24.20         3.25        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
        0.26         2.10        12.95        29.00        23.84        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RN 
       14.07        15.68        33.40        18.81        12.46        19.53 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        37.64         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       19.73        14.04        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
       48.79         5.46        13.25        13.02        18.48        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        37.41        38.14         7.73        30.97        34.29 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       16.31        22.19         2.50        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX 
        1.87         9.27        23.41        15.65        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       18.74        20.81        32.88         1.71        42.64        60.85 
TCGA-VQ-A91X TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A92D 
        9.50         2.01        55.43         4.54         6.58        66.81 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 
       21.04         2.66        42.54        11.24        18.41        28.41 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       32.94        17.13        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        17.26         0.79 

  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                         0.62                          0.00 
  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                        58.03                        122.30 
  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                       14.025                        15.580 
[1] "0.6 - 58.0 (14.0)"  "0.0 - 122.3 (15.6)"
[1] "hr=" "1.1"
D86V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 50(XP22.2) MUTATED         1        1        7       10         6
  DEL PEAK 50(XP22.2) WILD-TYPE       1       15       34       22        34
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 50(XP22.2) MUTATED          13         1         21          6
  DEL PEAK 50(XP22.2) WILD-TYPE        43         2         60         57
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 50(XP22.2) MUTATED            8        8
  DEL PEAK 50(XP22.2) WILD-TYPE         31       36
D86V3, multiclass
            clus
vv           DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             1                            15
  STAGE IB                             7                            34
  STAGE II                            10                            22
  STAGE IIA                            6                            34
  STAGE IIB                           13                            43
  STAGE III                            1                             2
  STAGE IIIA                          21                            60
  STAGE IIIB                           6                            57
  STAGE IIIC                           8                            31
  STAGE IV                             8                            36
[1] 11  2
[1] TRUE
[1] "dimension of 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     3  21  38  22
  DEL PEAK 50(XP22.2) WILD-TYPE  20  72 158  97
D86V4, multiclass
    clus
vv   DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  T1                           3                            20
  T2                          21                            72
  T3                          38                           158
  T4                          22                            97
[1] 4 2
[1] TRUE
[1] "dimension of 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    22  27  19  15
  DEL PEAK 50(XP22.2) WILD-TYPE 108  92  67  73
D86V5, multiclass
    clus
vv   DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  N0                          22                           108
  N1                          27                            92
  N2                          19                            67
  N3                          15                            73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V6, binary
                               cls
clus                              0   1
  DEL PEAK 50(XP22.2) MUTATED    76   6
  DEL PEAK 50(XP22.2) WILD-TYPE 313  24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 50(XP22.2) MUTATED     76    6
  DEL PEAK 50(XP22.2) WILD-TYPE  313   24
   clus
vv  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  0                          76                           313
  1                           6                            24
[1] 2 2
[1] FALSE
D86V7, binary
                               cls
clus                              0   1
  DEL PEAK 50(XP22.2) MUTATED    25  60
  DEL PEAK 50(XP22.2) WILD-TYPE 133 223
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 50(XP22.2) MUTATED     25   60
  DEL PEAK 50(XP22.2) WILD-TYPE  133  223
        clus
vv       DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  FEMALE                          25                           133
  MALE                            60                           223
[1] 2 2
[1] FALSE
D86V8, binary
                               cls
clus                              0   1
  DEL PEAK 50(XP22.2) MUTATED    64  16
  DEL PEAK 50(XP22.2) WILD-TYPE 258  60
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 50(XP22.2) MUTATED     64   16
  DEL PEAK 50(XP22.2) WILD-TYPE  258   60
     clus
vv    DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  NO                           64                           258
  YES                          16                            60
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 50(XP22.2) MUTATED                                          3
  DEL PEAK 50(XP22.2) WILD-TYPE                                       10
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 50(XP22.2) MUTATED                                      10
  DEL PEAK 50(XP22.2) WILD-TYPE                                    62
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 50(XP22.2) MUTATED                                                       31
  DEL PEAK 50(XP22.2) WILD-TYPE                                                    132
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 50(XP22.2) MUTATED                                                   2
  DEL PEAK 50(XP22.2) WILD-TYPE                                                19
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 50(XP22.2) MUTATED                                                                  14
  DEL PEAK 50(XP22.2) WILD-TYPE                                                                68
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 50(XP22.2) MUTATED                                                    3
  DEL PEAK 50(XP22.2) WILD-TYPE                                                  5
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 50(XP22.2) MUTATED                                                 22
  DEL PEAK 50(XP22.2) WILD-TYPE                                               57
D86V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 50(XP22.2) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                      10
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     31
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          14
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           22
                                                                   clus
vv                                                                  DEL PEAK 50(XP22.2) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        62
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      132
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 50(XP22.2) MUTATED    68   3   3   2
  DEL PEAK 50(XP22.2) WILD-TYPE 281  15  16  23
D86V10, multiclass
    clus
vv   DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  R0                          68                           281
  R1                           3                            15
  R2                           3                            16
  RX                           2                            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"
D86V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 50(XP22.2) MUTATED      18                         0
  DEL PEAK 50(XP22.2) WILD-TYPE    70                        12
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 50(XP22.2) MUTATED                                           0    58
  DEL PEAK 50(XP22.2) WILD-TYPE                                         1   220
D86V12, multiclass
                                           clus
vv                                          DEL PEAK 50(XP22.2) MUTATED
  ASIAN                                                              18
  BLACK OR AFRICAN AMERICAN                                           0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              58
                                           clus
vv                                          DEL PEAK 50(XP22.2) WILD-TYPE
  ASIAN                                                                70
  BLACK OR AFRICAN AMERICAN                                            12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               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"
D86V13, binary
                               cls
clus                              0   1
  DEL PEAK 50(XP22.2) MUTATED     2  63
  DEL PEAK 50(XP22.2) WILD-TYPE   3 253
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 50(XP22.2) MUTATED      2   63
  DEL PEAK 50(XP22.2) WILD-TYPE    3  253
                        clus
vv                       DEL PEAK 50(XP22.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          63
                        clus
vv                       DEL PEAK 50(XP22.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           253
[1] 2 2
[1] FALSE

Clustering(87) Variable = DEL PEAK 51(XP21.1) MUTATION ANALYSIS
D87V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 51(XP21.1) MUTATED    42  32
  DEL PEAK 51(XP21.1) WILD-TYPE 204 137
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                           74                           341 
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                           32                           137 
$`DEL PEAK 51(XP21.1) MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-A5TI 
       47.05        21.99        27.35        26.93        58.03        19.56 
TCGA-B7-A5TN TCGA-BR-4191 TCGA-BR-6458 TCGA-BR-8059 TCGA-BR-8291 TCGA-BR-8297 
        9.44        18.35        19.33        14.43        19.96         7.40 
TCGA-BR-8362 TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8683 TCGA-BR-A44U TCGA-BR-A452 
       13.08        17.52        14.04         9.86        13.87         7.53 
TCGA-BR-A4CQ TCGA-BR-A4J6 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-8524 
       34.98         0.66        20.65         1.15        21.44        12.76 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-A489 TCGA-CD-A4MH TCGA-CG-4437 
       11.64        15.39        12.07        11.31        12.20         8.05 
TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-5725 TCGA-CG-5734 
       54.08        29.98        19.07         7.07        15.02         7.99 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       20.91        19.13        13.35        15.22        15.98        12.79 
TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A74A 
       12.33        18.21        11.31        20.32        15.65        19.96 
TCGA-EQ-5647 TCGA-FP-8211 TCGA-FP-A4BF TCGA-HU-A4GD TCGA-HU-A4H5 TCGA-IN-7808 
        0.62        13.58         5.52        22.75        23.80         3.45 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-AB1X TCGA-KB-A93H 
        3.39        18.38        13.35         6.44        13.51        37.64 
TCGA-KB-A93J TCGA-R5-A7O7 TCGA-RD-A8N6 TCGA-VQ-A8PC TCGA-VQ-A8PS TCGA-VQ-A8PY 
       36.95        45.67         8.94        46.26        13.35        14.33 
TCGA-VQ-A91N TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A 
       18.74        55.56         9.04        18.41        43.66        38.93 
TCGA-VQ-AA6D TCGA-VQ-AA6J 
       17.13        27.55 

$`DEL PEAK 51(XP21.1) WILD-TYPE`
TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       22.98        79.07        16.24         0.23        20.15         9.86 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 
       26.70        11.70        11.01         9.47         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.87        17.29        13.68        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       37.25        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56        29.42         2.66         2.20        15.58 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 
        6.18        31.10         0.26        22.19         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
        4.31         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 
        7.53        26.73        24.79        31.96        32.58        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
        8.22        10.68        34.13         6.08         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL 
       28.34        32.52        13.51         0.46        20.42        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       11.21        12.10        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       12.30        12.39        12.59        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.30        12.43        11.61         6.58        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
        4.01        14.01        12.03         0.00         9.01        18.97 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99       105.07        12.03        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6519 
        4.01        69.04        21.07        25.71        12.66        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 
       18.84        18.54        18.61        17.85        17.19        10.26 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       12.36        11.31        24.72        16.80        19.50        17.19 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
       36.43        13.78        14.76        26.43        11.24        11.44 
TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 
       22.29         8.38         4.34         7.13         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A9TM 
       22.29        17.06        59.54         5.03         0.56         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        5.92        24.39        18.15        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        29.00        23.84        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RN 
       15.68        33.40        36.36        18.81        12.46        19.53 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        2.53         5.56        63.62         3.72        19.73        14.04 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
       40.64       115.69       116.38        71.38        57.44        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       16.87        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       13.25        13.02        18.48        43.36        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       38.14        37.22         7.73        30.97        34.29        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       22.19         2.50        12.79         2.70        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ 
        9.27        23.41        15.65        29.59        64.57        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S 
       39.45        11.70        21.83        61.22        20.81        32.88 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A923 
        1.71        42.64        60.85         9.50         9.73         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O 
       55.43         4.54         6.58         5.72        66.81        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F 
        2.66        42.54        11.24        28.41        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        12.43        17.26         0.79 

  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                         0.62                          0.00 
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                        58.03                        122.30 
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                        15.52                         14.47 
[1] "0.6 - 58.0 (15.5)"  "0.0 - 122.3 (14.5)"
[1] "hr=" "1.1"
D87V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 51(XP21.1) MUTATED         1        1        6        7         6
  DEL PEAK 51(XP21.1) WILD-TYPE       1       15       35       25        34
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 51(XP21.1) MUTATED          10         1         20          8
  DEL PEAK 51(XP21.1) WILD-TYPE        46         2         61         55
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 51(XP21.1) MUTATED            6        7
  DEL PEAK 51(XP21.1) WILD-TYPE         33       37
D87V3, multiclass
            clus
vv           DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             1                            15
  STAGE IB                             6                            35
  STAGE II                             7                            25
  STAGE IIA                            6                            34
  STAGE IIB                           10                            46
  STAGE III                            1                             2
  STAGE IIIA                          20                            61
  STAGE IIIB                           8                            55
  STAGE IIIC                           6                            33
  STAGE IV                             7                            37
[1] 11  2
[1] TRUE
[1] "dimension of 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     3  18  33  21
  DEL PEAK 51(XP21.1) WILD-TYPE  20  75 163  98
D87V4, multiclass
    clus
vv   DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  T1                           3                            20
  T2                          18                            75
  T3                          33                           163
  T4                          21                            98
[1] 4 2
[1] TRUE
[1] "dimension of 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    20  22  18  14
  DEL PEAK 51(XP21.1) WILD-TYPE 110  97  68  74
D87V5, multiclass
    clus
vv   DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  N0                          20                           110
  N1                          22                            97
  N2                          18                            68
  N3                          14                            74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V6, binary
                               cls
clus                              0   1
  DEL PEAK 51(XP21.1) MUTATED    69   4
  DEL PEAK 51(XP21.1) WILD-TYPE 320  26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XP21.1) MUTATED     69    4
  DEL PEAK 51(XP21.1) WILD-TYPE  320   26
   clus
vv  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  0                          69                           320
  1                           4                            26
[1] 2 2
[1] FALSE
D87V7, binary
                               cls
clus                              0   1
  DEL PEAK 51(XP21.1) MUTATED    23  53
  DEL PEAK 51(XP21.1) WILD-TYPE 135 230
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XP21.1) MUTATED     23   53
  DEL PEAK 51(XP21.1) WILD-TYPE  135  230
        clus
vv       DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  FEMALE                          23                           135
  MALE                            53                           230
[1] 2 2
[1] FALSE
D87V8, binary
                               cls
clus                              0   1
  DEL PEAK 51(XP21.1) MUTATED    56  15
  DEL PEAK 51(XP21.1) WILD-TYPE 266  61
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XP21.1) MUTATED     56   15
  DEL PEAK 51(XP21.1) WILD-TYPE  266   61
     clus
vv    DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  NO                           56                           266
  YES                          15                            61
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 51(XP21.1) MUTATED                                          3
  DEL PEAK 51(XP21.1) WILD-TYPE                                       10
                               vv
clus                            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 51(XP21.1) MUTATED                                      10
  DEL PEAK 51(XP21.1) WILD-TYPE                                    62
                               vv
clus                            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 51(XP21.1) MUTATED                                                       25
  DEL PEAK 51(XP21.1) WILD-TYPE                                                    138
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 51(XP21.1) MUTATED                                                   2
  DEL PEAK 51(XP21.1) WILD-TYPE                                                19
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 51(XP21.1) MUTATED                                                                  14
  DEL PEAK 51(XP21.1) WILD-TYPE                                                                68
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 51(XP21.1) MUTATED                                                    1
  DEL PEAK 51(XP21.1) WILD-TYPE                                                  7
                               vv
clus                            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 51(XP21.1) MUTATED                                                 21
  DEL PEAK 51(XP21.1) WILD-TYPE                                               58
D87V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 51(XP21.1) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                    3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                      10
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                     25
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          14
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                          1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                           21
                                                                   clus
vv                                                                  DEL PEAK 51(XP21.1) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     10
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        62
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      138
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                            7
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                             58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 51(XP21.1) MUTATED    59   5   2   2
  DEL PEAK 51(XP21.1) WILD-TYPE 290  13  17  23
D87V10, multiclass
    clus
vv   DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  R0                          59                           290
  R1                           5                            13
  R2                           2                            17
  RX                           2                            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"
D87V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 51(XP21.1) MUTATED      11                         1
  DEL PEAK 51(XP21.1) WILD-TYPE    77                        11
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 51(XP21.1) MUTATED                                           0    52
  DEL PEAK 51(XP21.1) WILD-TYPE                                         1   226
D87V12, multiclass
                                           clus
vv                                          DEL PEAK 51(XP21.1) MUTATED
  ASIAN                                                              11
  BLACK OR AFRICAN AMERICAN                                           1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              52
                                           clus
vv                                          DEL PEAK 51(XP21.1) WILD-TYPE
  ASIAN                                                                77
  BLACK OR AFRICAN AMERICAN                                            11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               226
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V13, binary
                               cls
clus                              0   1
  DEL PEAK 51(XP21.1) MUTATED     2  50
  DEL PEAK 51(XP21.1) WILD-TYPE   3 266
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XP21.1) MUTATED      2   50
  DEL PEAK 51(XP21.1) WILD-TYPE    3  266
                        clus
vv                       DEL PEAK 51(XP21.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          50
                        clus
vv                       DEL PEAK 51(XP21.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           266
[1] 2 2
[1] FALSE

Clustering(88) Variable = DEL PEAK 52(XQ21.33) MUTATION ANALYSIS
D88V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 52(XQ21.33) MUTATED    35  21
  DEL PEAK 52(XQ21.33) WILD-TYPE 211 148
  DEL PEAK 52(XQ21.33) MUTATED DEL PEAK 52(XQ21.33) WILD-TYPE 
                            56                            359 
  DEL PEAK 52(XQ21.33) MUTATED DEL PEAK 52(XQ21.33) WILD-TYPE 
                            21                            148 
$`DEL PEAK 52(XQ21.33) MUTATED`
TCGA-CG-4444 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-5818 TCGA-B7-A5TI 
       47.05        27.35        26.93        58.03        11.70        19.56 
TCGA-B7-A5TN TCGA-BR-7197 TCGA-BR-7716 TCGA-BR-8058 TCGA-BR-8291 TCGA-BR-8361 
        9.44         9.21        39.78        37.25        19.96        31.10 
TCGA-BR-8365 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ 
       17.52        24.79        31.96        13.87         7.53        34.98 
TCGA-BR-A4CS TCGA-BR-A4J8 TCGA-CD-5800 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8532 
        1.48        13.51        13.15         7.17        12.30        11.64 
TCGA-CD-8534 TCGA-CD-A489 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4443 
       12.07        11.31        20.02         3.02         7.99        29.98 
TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-5725 TCGA-D7-6519 TCGA-D7-6528 TCGA-D7-6822 
       19.07         7.07        15.02        20.55        15.22        12.33 
TCGA-D7-8575 TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A74A TCGA-EQ-8122 TCGA-FP-8211 
       18.21        11.31        20.32        19.96         7.99        13.58 
TCGA-HF-7133 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-A6RI TCGA-IN-A6RR 
       63.06        23.80        33.40        36.36        18.38         6.74 
TCGA-VQ-A8DT TCGA-VQ-A8E0 TCGA-VQ-A8P5 TCGA-VQ-A8PS TCGA-VQ-A91Q TCGA-VQ-A91X 
       48.79        18.48         7.73        13.35        20.81         9.50 
TCGA-VQ-AA6A TCGA-VQ-AA6D 
       38.93        17.13 

$`DEL PEAK 52(XQ21.33) WILD-TYPE`
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       21.99        22.98        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-B7-5816 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 
        9.86        26.70        11.01         9.47         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 
       21.90        36.16        35.24        35.84        33.63        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56        29.42         2.66         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 
        7.40         6.18        13.08         0.26        22.19         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 
       28.14         6.28         7.53        26.73        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU 
       20.88         8.22        10.68        34.13         6.08        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52         0.46        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 
       13.18        13.35        11.21        12.10        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8535 
       12.53        12.33        12.39        12.59        15.39        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
       12.43         6.31        12.30        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.20        11.77        12.62        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4462 
        8.05        54.08         4.01        14.01        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97        12.00        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
       25.71        12.66        20.91        19.13        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
       18.61        17.85        13.35        17.19        10.26        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.79        12.36        11.31        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       17.19        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       11.44        22.29        15.65         8.38         4.34         7.13 
TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB 
        0.56         5.52         6.21        77.29        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
       26.47         1.51         5.92        24.39        18.15        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8462 
       23.84        21.17        14.07        15.68         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS 
        3.39        12.46        13.35        19.53         6.44        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        63.62        37.64        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       57.44         8.94        35.61        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        0.92         5.46        13.25        13.02        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       37.41        38.14        37.22        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       16.31        22.19         2.50        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX 
        1.87         9.27        23.41        15.65        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y 
       18.74        32.88         1.71        42.64        60.85         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       55.56         9.04         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
        5.72        66.81        21.04         2.66        42.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        43.66        28.41        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        27.55        12.43        17.26         0.79 

  DEL PEAK 52(XQ21.33) MUTATED DEL PEAK 52(XQ21.33) WILD-TYPE 
                          1.48                           0.00 
  DEL PEAK 52(XQ21.33) MUTATED DEL PEAK 52(XQ21.33) WILD-TYPE 
                         63.06                         122.30 
  DEL PEAK 52(XQ21.33) MUTATED DEL PEAK 52(XQ21.33) WILD-TYPE 
                        17.865                         14.430 
[1] "1.5 - 63.1 (17.9)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.2"
D88V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 52(XQ21.33) MUTATED         1        1        8        6         3
  DEL PEAK 52(XQ21.33) WILD-TYPE       1       15       33       26        37
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 52(XQ21.33) MUTATED           7         0         13          6
  DEL PEAK 52(XQ21.33) WILD-TYPE        49         3         68         57
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 52(XQ21.33) MUTATED            4        6
  DEL PEAK 52(XQ21.33) WILD-TYPE         35       38
D88V3, multiclass
            clus
vv           DEL PEAK 52(XQ21.33) MUTATED DEL PEAK 52(XQ21.33) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                              1                             15
  STAGE IB                              8                             33
  STAGE II                              6                             26
  STAGE IIA                             3                             37
  STAGE IIB                             7                             49
  STAGE III                             0                              3
  STAGE IIIA                           13                             68
  STAGE IIIB                            6                             57
  STAGE IIIC                            4                             35
  STAGE IV                              6                             38
[1] 11  2
[1] TRUE
[1] "dimension of 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(XQ21.33) MUTATED     2  14  27  14
  DEL PEAK 52(XQ21.33) WILD-TYPE  21  79 169 105
D88V4, multiclass
    clus
vv   DEL PEAK 52(XQ21.33) MUTATED DEL PEAK 52(XQ21.33) WILD-TYPE
  T1                            2                             21
  T2                           14                             79
  T3                           27                            169
  T4                           14                            105
[1] 4 2
[1] TRUE
[1] "dimension of 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(XQ21.33) MUTATED    19  15  12   9
  DEL PEAK 52(XQ21.33) WILD-TYPE 111 104  74  79
D88V5, multiclass
    clus
vv   DEL PEAK 52(XQ21.33) MUTATED DEL PEAK 52(XQ21.33) WILD-TYPE
  N0                           19                            111
  N1                           15                            104
  N2                           12                             74
  N3                            9                             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"
D88V6, binary
                                cls
clus                               0   1
  DEL PEAK 52(XQ21.33) MUTATED    51   3
  DEL PEAK 52(XQ21.33) WILD-TYPE 338  27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 52(XQ21.33) MUTATED     51    3
  DEL PEAK 52(XQ21.33) WILD-TYPE  338   27
   clus
vv  DEL PEAK 52(XQ21.33) MUTATED DEL PEAK 52(XQ21.33) WILD-TYPE
  0                           51                            338
  1                            3                             27
[1] 2 2
[1] FALSE
D88V7, binary
                                cls
clus                               0   1
  DEL PEAK 52(XQ21.33) MUTATED    16  41
  DEL PEAK 52(XQ21.33) WILD-TYPE 142 242
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 52(XQ21.33) MUTATED     16   41
  DEL PEAK 52(XQ21.33) WILD-TYPE  142  242
        clus
vv       DEL PEAK 52(XQ21.33) MUTATED DEL PEAK 52(XQ21.33) WILD-TYPE
  FEMALE                           16                            142
  MALE                             41                            242
[1] 2 2
[1] FALSE
D88V8, binary
                                cls
clus                               0   1
  DEL PEAK 52(XQ21.33) MUTATED    37  15
  DEL PEAK 52(XQ21.33) WILD-TYPE 285  61
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 52(XQ21.33) MUTATED     37   15
  DEL PEAK 52(XQ21.33) WILD-TYPE  285   61
     clus
vv    DEL PEAK 52(XQ21.33) MUTATED DEL PEAK 52(XQ21.33) WILD-TYPE
  NO                            37                            285
  YES                           15                             61
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEL PEAK 52(XQ21.33) MUTATED                                          1
  DEL PEAK 52(XQ21.33) WILD-TYPE                                       12
                                vv
clus                             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEL PEAK 52(XQ21.33) MUTATED                                       8
  DEL PEAK 52(XQ21.33) WILD-TYPE                                    64
                                vv
clus                             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 52(XQ21.33) MUTATED                                                       19
  DEL PEAK 52(XQ21.33) WILD-TYPE                                                    144
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEL PEAK 52(XQ21.33) MUTATED                                                   3
  DEL PEAK 52(XQ21.33) WILD-TYPE                                                18
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 52(XQ21.33) MUTATED                                                                  12
  DEL PEAK 52(XQ21.33) WILD-TYPE                                                                70
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEL PEAK 52(XQ21.33) MUTATED                                                    2
  DEL PEAK 52(XQ21.33) WILD-TYPE                                                  6
                                vv
clus                             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEL PEAK 52(XQ21.33) MUTATED                                                 12
  DEL PEAK 52(XQ21.33) WILD-TYPE                                               67
D88V9, multiclass
                                                                   clus
vv                                                                  DEL PEAK 52(XQ21.33) MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                        8
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                      19
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                            3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           12
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                            12
                                                                   clus
vv                                                                  DEL PEAK 52(XQ21.33) WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                                      12
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                                         64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                                       144
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                             18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             70
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                             6
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                              67
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 52(XQ21.33) MUTATED    47   3   1   1
  DEL PEAK 52(XQ21.33) WILD-TYPE 302  15  18  24
D88V10, multiclass
    clus
vv   DEL PEAK 52(XQ21.33) MUTATED DEL PEAK 52(XQ21.33) WILD-TYPE
  R0                           47                            302
  R1                            3                             15
  R2                            1                             18
  RX                            1                             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"
D88V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 52(XQ21.33) MUTATED      10                         1
  DEL PEAK 52(XQ21.33) WILD-TYPE    78                        11
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 52(XQ21.33) MUTATED                                           0
  DEL PEAK 52(XQ21.33) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 52(XQ21.33) MUTATED      34
  DEL PEAK 52(XQ21.33) WILD-TYPE   244
D88V12, multiclass
                                           clus
vv                                          DEL PEAK 52(XQ21.33) MUTATED
  ASIAN                                                               10
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               34
                                           clus
vv                                          DEL PEAK 52(XQ21.33) WILD-TYPE
  ASIAN                                                                 78
  BLACK OR AFRICAN AMERICAN                                             11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                244
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V13, binary
                                cls
clus                               0   1
  DEL PEAK 52(XQ21.33) MUTATED     1  37
  DEL PEAK 52(XQ21.33) WILD-TYPE   4 279
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 52(XQ21.33) MUTATED      1   37
  DEL PEAK 52(XQ21.33) WILD-TYPE    4  279
                        clus
vv                       DEL PEAK 52(XQ21.33) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           37
                        clus
vv                       DEL PEAK 52(XQ21.33) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            279
[1] 2 2
[1] FALSE
