[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/15090008/STAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/STAD-TP/15098840/transformed.cor.cli.txt"

nPatients in clinical file=438, in cluster file=441, common to both=436
[1]  89 436
[1] "AMP PEAK  1(1P36.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                            64                            372 
  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                            64                            372 
[1] "AMP PEAK  2(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          158                           278 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          158                           278 
[1] "AMP PEAK  3(1Q42.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                          149                           287 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                          149                           287 
[1] "AMP PEAK  4(3Q26.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                          163                           273 
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                          163                           273 
[1] "AMP PEAK  5(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                           128                            308 
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                           128                            308 
[1] "AMP PEAK  6(5P13.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE 
                          124                           312 
  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE 
                          124                           312 
[1] "AMP PEAK  7(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE 
                          121                           315 
  AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE 
                          121                           315 
[1] "AMP PEAK  8(6Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE 
                         86                         350 
  AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE 
                         86                         350 
[1] "AMP PEAK  9(6Q21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE 
                         81                         355 
  AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE 
                         81                         355 
[1] "AMP PEAK 10(7P22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                          228                           208 
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                          228                           208 
[1] "AMP PEAK 11(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                          213                           223 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                          213                           223 
[1] "AMP PEAK 12(7Q21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                          203                           233 
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                          203                           233 
[1] "AMP PEAK 13(7Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE 
                          201                           235 
  AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE 
                          201                           235 
[1] "AMP PEAK 14(8P23.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE 
                          175                           261 
  AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE 
                          175                           261 
[1] "AMP PEAK 15(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                           305                            131 
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                           305                            131 
[1] "AMP PEAK 16(9P24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE 
                           64                           372 
  AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE 
                           64                           372 
[1] "AMP PEAK 17(9P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE 
                           89                           347 
  AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE 
                           89                           347 
[1] "AMP PEAK 18(9Q34.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE 
                          121                           315 
  AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE 
                          121                           315 
[1] "AMP PEAK 19(10P11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE 
                            118                             318 
  AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE 
                            118                             318 
[1] "AMP PEAK 20(10Q22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE 
                            88                            348 
  AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE 
                            88                            348 
[1] "AMP PEAK 21(10Q26.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE 
                             88                             348 
  AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE 
                             88                             348 
[1] "AMP PEAK 22(11P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE 
                          87                          349 
  AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE 
                          87                          349 
[1] "AMP PEAK 23(11P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE 
                            91                            345 
  AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE 
                            91                            345 
[1] "AMP PEAK 24(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE 
                           115                            321 
  AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE 
                           115                            321 
[1] "AMP PEAK 25(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE 
                           127                            309 
  AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE 
                           127                            309 
[1] "AMP PEAK 26(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE 
                         108                          328 
  AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE 
                         108                          328 
[1] "AMP PEAK 27(13Q12.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE 
                           168                            268 
  AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE 
                           168                            268 
[1] "AMP PEAK 28(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE 
                           179                            257 
  AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE 
                           179                            257 
[1] "AMP PEAK 29(15Q26.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(15Q26.1) MUTATED AMP PEAK 29(15Q26.1) WILD-TYPE 
                           111                            325 
  AMP PEAK 29(15Q26.1) MUTATED AMP PEAK 29(15Q26.1) WILD-TYPE 
                           111                            325 
[1] "AMP PEAK 30(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE 
                         145                          291 
  AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE 
                         145                          291 
[1] "AMP PEAK 31(18Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 31(18Q11.2) MUTATED AMP PEAK 31(18Q11.2) WILD-TYPE 
                           137                            299 
  AMP PEAK 31(18Q11.2) MUTATED AMP PEAK 31(18Q11.2) WILD-TYPE 
                           137                            299 
[1] "AMP PEAK 32(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 32(19P13.2) MUTATED AMP PEAK 32(19P13.2) WILD-TYPE 
                            46                            390 
  AMP PEAK 32(19P13.2) MUTATED AMP PEAK 32(19P13.2) WILD-TYPE 
                            46                            390 
[1] "AMP PEAK 33(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE 
                         129                          307 
  AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE 
                         129                          307 
[1] "AMP PEAK 34(19Q13.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE 
                            109                             327 
  AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE 
                            109                             327 
[1] "AMP PEAK 35(20Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE 
                           290                            146 
  AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE 
                           290                            146 
[1] "AMP PEAK 36(XQ27.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE 
                           83                           353 
  AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE 
                           83                           353 
[1] "DEL PEAK  1(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           133                            303 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           133                            303 
[1] "DEL PEAK  2(1P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           94                           342 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           94                           342 
[1] "DEL PEAK  3(1Q44) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         30                         406 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         30                         406 
[1] "DEL PEAK  4(1Q44) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE 
                         26                         410 
  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE 
                         26                         410 
[1] "DEL PEAK  5(2Q32.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE 
                           62                           374 
  DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE 
                           62                           374 
[1] "DEL PEAK  6(2Q33.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(2Q33.3) MUTATED DEL PEAK  6(2Q33.3) WILD-TYPE 
                           49                           387 
  DEL PEAK  6(2Q33.3) MUTATED DEL PEAK  6(2Q33.3) WILD-TYPE 
                           49                           387 
[1] "DEL PEAK  7(2Q37.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(2Q37.2) MUTATED DEL PEAK  7(2Q37.2) WILD-TYPE 
                           72                           364 
  DEL PEAK  7(2Q37.2) MUTATED DEL PEAK  7(2Q37.2) WILD-TYPE 
                           72                           364 
[1] "DEL PEAK  8(3P26.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3P26.1) MUTATED DEL PEAK  8(3P26.1) WILD-TYPE 
                          140                           296 
  DEL PEAK  8(3P26.1) MUTATED DEL PEAK  8(3P26.1) WILD-TYPE 
                          140                           296 
[1] "DEL PEAK  9(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                          156                           280 
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                          156                           280 
[1] "DEL PEAK 10(3Q26.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                            47                            389 
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                            47                            389 
[1] "DEL PEAK 11(4P16.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE 
                          167                           269 
  DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE 
                          167                           269 
[1] "DEL PEAK 12(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                          190                           246 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                          190                           246 
[1] "DEL PEAK 13(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                          197                           239 
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                          197                           239 
[1] "DEL PEAK 14(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                          166                           270 
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                          166                           270 
[1] "DEL PEAK 15(5Q23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE 
                          156                           280 
  DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE 
                          156                           280 
[1] "DEL PEAK 16(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                          113                           323 
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                          113                           323 
[1] "DEL PEAK 17(6Q14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE 
                           88                           348 
  DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE 
                           88                           348 
[1] "DEL PEAK 18(6Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE 
                           77                           359 
  DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE 
                           77                           359 
[1] "DEL PEAK 19(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                        101                         335 
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                        101                         335 
[1] "DEL PEAK 20(7Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                           70                           366 
  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                           70                           366 
[1] "DEL PEAK 21(7Q36.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                           97                           339 
  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                           97                           339 
[1] "DEL PEAK 22(8P23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(8P23.3) MUTATED DEL PEAK 22(8P23.3) WILD-TYPE 
                          123                           313 
  DEL PEAK 22(8P23.3) MUTATED DEL PEAK 22(8P23.3) WILD-TYPE 
                          123                           313 
[1] "DEL PEAK 23(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                        191                         245 
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                        191                         245 
[1] "DEL PEAK 24(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                          189                           247 
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                          189                           247 
[1] "DEL PEAK 25(9Q21.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                           113                            323 
  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                           113                            323 
[1] "DEL PEAK 26(10P12.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(10P12.31) MUTATED DEL PEAK 26(10P12.31) WILD-TYPE 
                             66                             370 
  DEL PEAK 26(10P12.31) MUTATED DEL PEAK 26(10P12.31) WILD-TYPE 
                             66                             370 
[1] "DEL PEAK 27(10Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE 
                            78                            358 
  DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE 
                            78                            358 
[1] "DEL PEAK 28(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                            114                             322 
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                            114                             322 
[1] "DEL PEAK 29(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                            97                            339 
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                            97                            339 
[1] "DEL PEAK 30(11Q23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE 
                            97                            339 
  DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE 
                            97                            339 
[1] "DEL PEAK 31(12P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE 
                            74                            362 
  DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE 
                            74                            362 
[1] "DEL PEAK 32(12Q12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE 
                          58                          378 
  DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE 
                          58                          378 
[1] "DEL PEAK 33(13Q12.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                             61                             375 
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                             61                             375 
[1] "DEL PEAK 34(14Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                           134                            302 
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                           134                            302 
[1] "DEL PEAK 35(14Q32.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                            131                             305 
  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                            131                             305 
[1] "DEL PEAK 36(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                           119                            317 
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                           119                            317 
[1] "DEL PEAK 37(15Q15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE 
                           121                            315 
  DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE 
                           121                            315 
[1] "DEL PEAK 38(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                            92                            344 
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                            92                            344 
[1] "DEL PEAK 39(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                           180                            256 
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                           180                            256 
[1] "DEL PEAK 40(17P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(17P13.3) MUTATED DEL PEAK 40(17P13.3) WILD-TYPE 
                           172                            264 
  DEL PEAK 40(17P13.3) MUTATED DEL PEAK 40(17P13.3) WILD-TYPE 
                           172                            264 
[1] "DEL PEAK 41(17P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(17P12) MUTATED DEL PEAK 41(17P12) WILD-TYPE 
                         177                          259 
  DEL PEAK 41(17P12) MUTATED DEL PEAK 41(17P12) WILD-TYPE 
                         177                          259 
[1] "DEL PEAK 42(17Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(17Q24.3) MUTATED DEL PEAK 42(17Q24.3) WILD-TYPE 
                            76                            360 
  DEL PEAK 42(17Q24.3) MUTATED DEL PEAK 42(17Q24.3) WILD-TYPE 
                            76                            360 
[1] "DEL PEAK 43(18Q12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(18Q12.2) MUTATED DEL PEAK 43(18Q12.2) WILD-TYPE 
                           180                            256 
  DEL PEAK 43(18Q12.2) MUTATED DEL PEAK 43(18Q12.2) WILD-TYPE 
                           180                            256 
[1] "DEL PEAK 44(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(18Q21.2) MUTATED DEL PEAK 44(18Q21.2) WILD-TYPE 
                           203                            233 
  DEL PEAK 44(18Q21.2) MUTATED DEL PEAK 44(18Q21.2) WILD-TYPE 
                           203                            233 
[1] "DEL PEAK 45(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE 
                           158                            278 
  DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE 
                           158                            278 
[1] "DEL PEAK 46(19Q13.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 46(19Q13.11) MUTATED DEL PEAK 46(19Q13.11) WILD-TYPE 
                             75                             361 
  DEL PEAK 46(19Q13.11) MUTATED DEL PEAK 46(19Q13.11) WILD-TYPE 
                             75                             361 
[1] "DEL PEAK 47(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                            38                            398 
  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                            38                            398 
[1] "DEL PEAK 48(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE 
                           181                            255 
  DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE 
                           181                            255 
[1] "DEL PEAK 49(21Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 49(21Q22.3) MUTATED DEL PEAK 49(21Q22.3) WILD-TYPE 
                           191                            245 
  DEL PEAK 49(21Q22.3) MUTATED DEL PEAK 49(21Q22.3) WILD-TYPE 
                           191                            245 
[1] "DEL PEAK 50(22Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 50(22Q13.31) MUTATED DEL PEAK 50(22Q13.31) WILD-TYPE 
                            158                             278 
  DEL PEAK 50(22Q13.31) MUTATED DEL PEAK 50(22Q13.31) WILD-TYPE 
                            158                             278 
[1] "DEL PEAK 51(XP22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 51(XP22.2) MUTATED DEL PEAK 51(XP22.2) WILD-TYPE 
                           82                           354 
  DEL PEAK 51(XP22.2) MUTATED DEL PEAK 51(XP22.2) WILD-TYPE 
                           82                           354 
[1] "DEL PEAK 52(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 52(XP21.1) MUTATED DEL PEAK 52(XP21.1) WILD-TYPE 
                           71                           365 
  DEL PEAK 52(XP21.1) MUTATED DEL PEAK 52(XP21.1) WILD-TYPE 
                           71                           365 
[1] "DEL PEAK 53(XQ21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 53(XQ21.33) MUTATED DEL PEAK 53(XQ21.33) WILD-TYPE 
                            55                            381 
  DEL PEAK 53(XQ21.33) MUTATED DEL PEAK 53(XQ21.33) WILD-TYPE 
                            55                            381 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "RADIATION_THERAPY"                     
[14] "HISTOLOGICAL_TYPE"                     
[15] "RADIATIONS_RADIATION_REGIMENINDICATION"
[16] "COMPLETENESS_OF_RESECTION"             
[17] "NUMBER_OF_LYMPH_NODES"                 
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCH_NUMBER"                          

Input Data has 20 rows and 436 columns.

[1] "Batch" "20"   
[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=137,	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=247,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	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:'DCC_UPLOAD_DATE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'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 13:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH_NUMBER':	nDistinctValues=23,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[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 436 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"                        
 [2] "NEOPLASM_DISEASESTAGE"                 
 [3] "PATHOLOGY_T_STAGE"                     
 [4] "PATHOLOGY_N_STAGE"                     
 [5] "PATHOLOGY_M_STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL_TYPE"                     
 [8] "RADIATIONS_RADIATION_REGIMENINDICATION"
 [9] "COMPLETENESS_OF_RESECTION"             
[10] "NUMBER_OF_LYMPH_NODES"                 
[11] "RACE"                                  
[12] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=54, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, 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 
 22  90 195 119 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 22  90 195 119 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
 22  90 195 119 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 22  90 195 119 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
129 118  84  89 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
129 118  84  89 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
129 118  84  89 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
129 118  84  89 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=7, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS_OF_RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=34, 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    35  25
  AMP PEAK  1(1P36.22) WILD-TYPE 219 125
  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                            60                            344 
  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                            25                            125 
$`AMP PEAK  1(1P36.22) MUTATED`
TCGA-BR-4183 TCGA-BR-7197 TCGA-BR-7901 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8484 
        6.61         9.21         3.45        12.95         2.66        25.18 
TCGA-BR-8588 TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-CD-5799 TCGA-CD-5802 
       12.79        22.26         0.72        13.51         3.25         0.30 
TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4475 
       12.43        12.20        29.98        47.05        19.07        22.98 
TCGA-CG-5718 TCGA-CG-5732 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-A4YU 
       36.00        69.04        18.54        10.26        15.22        16.44 
TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-FP-7829 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-A4GH 
       11.24         2.96        19.53        18.08        26.47        11.77 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RI 
        8.98         6.25        27.42        21.21         3.45        18.38 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IP-7968 TCGA-R5-A805 
        1.41         6.44         6.74         1.81         2.53         9.24 
TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-VQ-A8DU TCGA-VQ-A8E0 
        8.61        16.67        37.91       115.69         5.46        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PX TCGA-VQ-A91U 
       35.24        22.19        17.85         1.87        64.57         1.71 
TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6D 
        4.54        64.18        42.54        18.41        32.94        17.13 

$`AMP PEAK  1(1P36.22) WILD-TYPE`
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-4191 TCGA-BR-4201 TCGA-BR-4267 
        6.97         4.64         7.43        18.35        30.90         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        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 
       30.90        31.20        32.94        12.82        24.76        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       12.43         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        0.56        16.31         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 
       19.50        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        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 
       14.79         0.26        15.85         3.72         5.39         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22         1.12        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08         1.48        13.41        13.51        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        12.82         0.66        19.36         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 
        2.83        13.15        13.18         0.07         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.13         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.31        11.61         6.58         0.10        12.62        20.02 
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-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       54.08         4.01        14.01        12.03        21.99         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-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 
       15.02        28.96        79.07        65.10         4.01        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        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-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        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-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        11.44         9.76        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
        7.40         7.13         0.62         7.99        16.24        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-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A8CX TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
        0.23         1.51         5.92        14.27        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
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        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL 
        8.88         8.81        18.81         3.39         5.36         5.19 
TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X 
       13.08        12.59         6.51         5.56         7.82        13.51 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        60.56        20.15        37.64         3.72        19.73 
TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
        9.86        45.67        18.21         8.52        61.25         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 
       34.45        27.88        32.48         7.73        28.96        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-A8PU TCGA-VQ-A8PY 
       23.41        15.65        13.35        26.24        27.35        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       65.16        36.69        11.70        11.93        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       20.81        22.68        36.16         7.36         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
       52.24         9.04         2.01        55.43         6.58         5.72 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA69 
       21.04         2.66        11.24        22.09        40.08        28.41 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       29.98        54.12        26.04        16.14        21.11        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                           0.3                            0.0 
  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 
                        14.365                         12.790 
[1] "0.3 - 115.7 (14.4)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1"  
D1V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  1(1P36.22) MUTATED         1        4        5        7         3
  AMP PEAK  1(1P36.22) WILD-TYPE       2       10       36       24        35
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  1(1P36.22) MUTATED           7         1         13         10
  AMP PEAK  1(1P36.22) WILD-TYPE        48         3         72         52
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK  1(1P36.22) MUTATED            6        5
  AMP PEAK  1(1P36.22) WILD-TYPE         35       41
D1V3, multiclass
            clus
vv           AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  STAGE I                               1                              2
  STAGE IA                              4                             10
  STAGE IB                              5                             36
  STAGE II                              7                             24
  STAGE IIA                             3                             35
  STAGE IIB                             7                             48
  STAGE III                             1                              3
  STAGE IIIA                           13                             72
  STAGE IIIB                           10                             52
  STAGE IIIC                            6                             35
  STAGE IV                              5                             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
  AMP PEAK  1(1P36.22) MUTATED     6  14  31  12
  AMP PEAK  1(1P36.22) WILD-TYPE  16  76 164 107
D1V4, multiclass
    clus
vv   AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  T1                            6                             16
  T2                           14                             76
  T3                           31                            164
  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    16  18  14  15
  AMP PEAK  1(1P36.22) WILD-TYPE 113 100  70  74
D1V5, multiclass
    clus
vv   AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  N0                           16                            113
  N1                           18                            100
  N2                           14                             70
  N3                           15                             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"
D1V6, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.22) MUTATED    59   2
  AMP PEAK  1(1P36.22) WILD-TYPE 328  28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.22) MUTATED     59    2
  AMP PEAK  1(1P36.22) WILD-TYPE  328   28
   clus
vv  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  0                           59                            328
  1                            2                             28
[1] 2 2
[1] FALSE
D1V7, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.22) MUTATED    13  51
  AMP PEAK  1(1P36.22) WILD-TYPE 145 227
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.22) MUTATED     13   51
  AMP PEAK  1(1P36.22) WILD-TYPE  145  227
        clus
vv       AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  FEMALE                           13                            145
  MALE                             51                            227
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  1(1P36.22) MUTATED                                       9
  AMP PEAK  1(1P36.22) WILD-TYPE                                    62
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  1(1P36.22) MUTATED                                                       22
  AMP PEAK  1(1P36.22) WILD-TYPE                                                    140
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  1(1P36.22) MUTATED                                                                  16
  AMP PEAK  1(1P36.22) WILD-TYPE                                                                65
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  1(1P36.22) MUTATED                                                 10
  AMP PEAK  1(1P36.22) WILD-TYPE                                               68
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK  1(1P36.22) MUTATED                                                          3
  AMP PEAK  1(1P36.22) WILD-TYPE                                                       18
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK  1(1P36.22) MUTATED                                                           1
  AMP PEAK  1(1P36.22) WILD-TYPE                                                         7
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK  1(1P36.22) MUTATED                                          2
  AMP PEAK  1(1P36.22) WILD-TYPE                                       11
D1V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  1(1P36.22) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      22
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           16
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
                                                                   clus
vv                                                                  AMP PEAK  1(1P36.22) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       140
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             65
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              68
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      11
[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"
D1V9, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.22) MUTATED     0  64
  AMP PEAK  1(1P36.22) WILD-TYPE   6 366
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.22) MUTATED      0   64
  AMP PEAK  1(1P36.22) WILD-TYPE    6  366
     clus
vv    AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  NO                             0                              6
  YES                           64                            366
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  1(1P36.22) MUTATED    51   2   2   3
  AMP PEAK  1(1P36.22) WILD-TYPE 296  16  17  22
D1V10, multiclass
    clus
vv   AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  R0                           51                            296
  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                        10
                                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      40
  AMP PEAK  1(1P36.22) WILD-TYPE   234
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                                                               40
                                           clus
vv                                          AMP PEAK  1(1P36.22) WILD-TYPE
  ASIAN                                                                 76
  BLACK OR AFRICAN AMERICAN                                             10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V13, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.22) MUTATED     0  42
  AMP PEAK  1(1P36.22) WILD-TYPE   4 271
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.22) MUTATED      0   42
  AMP PEAK  1(1P36.22) WILD-TYPE    4  271
                        clus
vv                       AMP PEAK  1(1P36.22) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           42
                        clus
vv                       AMP PEAK  1(1P36.22) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            271
[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    89  53
  AMP PEAK  2(1Q21.3) WILD-TYPE 165  97
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          142                           262 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           53                            97 
$`AMP PEAK  2(1Q21.3) MUTATED`
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6705 
       11.01         9.44         6.61        17.29        19.33        25.61 
TCGA-BR-7197 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8286 
        9.21        18.15        28.73         3.45        11.44        12.95 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8381 
        2.66         2.20         6.18        14.04        14.79         0.26 
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-8680 TCGA-BR-8687 TCGA-BR-A4J1 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4PD 
       15.81         8.22         0.72        12.82        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-8524 TCGA-CD-8526 
       20.42         1.15        13.64        13.15         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 
        0.10         0.13         0.16         0.13         0.13         3.42 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4436 
        9.34        12.43        11.61         6.58        12.20         7.99 
TCGA-CG-4438 TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       54.08        47.05        21.99        18.97         7.07        12.00 
TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5730 TCGA-D7-5579 TCGA-D7-6519 
       22.98        36.00        12.03         4.01        11.93        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        10.55 
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         2.96        15.65         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-8211 TCGA-FP-8631 
       16.24        72.23         3.48        14.07        13.58         0.56 
TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
        5.52        18.08        26.47         5.92        14.27        12.59 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GT 
        3.25        22.75        25.81        11.77         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RI 
        6.25        12.95        12.30        27.42         3.45        18.38 
TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU TCGA-KB-A6F7 
        5.19         1.41         6.44         6.74         1.81        60.56 
TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N1 
       18.21         6.08         8.61        16.67       122.30       115.69 
TCGA-RD-A8N6 TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        8.94        48.79         5.46        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PX TCGA-VQ-A8PY 
       35.24        21.73         2.70        17.85        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       65.16        36.69        18.74        20.81         1.71        36.16 
TCGA-VQ-A91Y TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U 
        9.73         4.54        64.18        42.54        11.24        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6K 
       18.41        40.08        32.94        12.43 

$`AMP PEAK  2(1Q21.3) WILD-TYPE`
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-4267 TCGA-BR-4279 TCGA-BR-4280 
        7.43        18.35        30.90         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-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        9.17        32.78        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 
       21.11        30.90        31.20        32.94        12.82        24.76 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7851 
       35.24        23.93        15.42        28.01        15.32        12.43 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 
       12.26         9.60        20.55         8.05         0.56        16.31 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40        19.50        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 
       19.17        15.85         3.72        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
       15.68        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        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        19.36         0.46        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        5.13         2.83         3.25        13.18         0.30         0.07 
TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A489 
        0.07         0.07         0.10         0.10         0.10        11.31 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        1.02         8.05         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 
       12.03         0.00         9.01        30.97         6.97         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-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10        69.04        21.07         7.99        12.36 
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        15.16        13.78        14.76        13.71 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.44         9.76         8.38         4.34         7.40         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-A8CX TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8602 
       59.54         5.03         0.23         1.51        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GX 
       11.84        24.20        21.37        29.98         0.10        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        0.26         2.10        19.36        23.84         9.67         8.88 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN 
        8.81        21.21        18.81         3.39         5.36        13.08 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
       12.59         6.51         5.56         7.82        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        5.56        20.15        37.64         3.72        19.73         9.86 
TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       45.67         8.52        61.25         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        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       27.88        32.48         7.73        28.96        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-A8PU TCGA-VQ-A91D 
       23.41        15.65        13.35        26.24        27.35        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z 
       11.93        61.22        22.68         7.36         9.50        52.24 
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-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
        2.66        28.41        29.98        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        21.11        10.62         0.79 

  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                         0.07                          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 
                        12.69                         13.08 
[1] "0.1 - 122.3 (12.7)" "0.0 - 116.4 (13.1)"
[1] "hr=" "1"  
D2V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  2(1Q21.3) MUTATED         2        6       16        9        14
  AMP PEAK  2(1Q21.3) WILD-TYPE       1        8       25       22        24
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  2(1Q21.3) MUTATED          20         2         32         20
  AMP PEAK  2(1Q21.3) WILD-TYPE        35         2         53         42
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK  2(1Q21.3) MUTATED           12       18
  AMP PEAK  2(1Q21.3) WILD-TYPE         29       28
D2V3, multiclass
            clus
vv           AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  STAGE I                              2                             1
  STAGE IA                             6                             8
  STAGE IB                            16                            25
  STAGE II                             9                            22
  STAGE IIA                           14                            24
  STAGE IIB                           20                            35
  STAGE III                            2                             2
  STAGE IIIA                          32                            53
  STAGE IIIB                          20                            42
  STAGE IIIC                          12                            29
  STAGE IV                            18                            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  2(1Q21.3) MUTATED    10  34  75  36
  AMP PEAK  2(1Q21.3) WILD-TYPE  12  56 120  83
D2V4, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  T1                          10                            12
  T2                          34                            56
  T3                          75                           120
  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   49 35 30 34
  AMP PEAK  2(1Q21.3) WILD-TYPE 80 83 54 55
D2V5, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  N0                          49                            80
  N1                          35                            83
  N2                          30                            54
  N3                          34                            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"
D2V6, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED   139  10
  AMP PEAK  2(1Q21.3) WILD-TYPE 248  20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED    139   10
  AMP PEAK  2(1Q21.3) WILD-TYPE  248   20
   clus
vv  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  0                         139                           248
  1                          10                            20
[1] 2 2
[1] FALSE
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED    57 101
  AMP PEAK  2(1Q21.3) WILD-TYPE 101 177
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     57  101
  AMP PEAK  2(1Q21.3) WILD-TYPE  101  177
        clus
vv       AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  FEMALE                          57                           101
  MALE                           101                           177
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  2(1Q21.3) MUTATED                                      16
  AMP PEAK  2(1Q21.3) WILD-TYPE                                    55
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  2(1Q21.3) MUTATED                                                       59
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                    103
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  2(1Q21.3) MUTATED                                                                  32
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                                49
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  2(1Q21.3) MUTATED                                                 33
  AMP PEAK  2(1Q21.3) WILD-TYPE                                               45
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK  2(1Q21.3) MUTATED                                                          6
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                       15
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK  2(1Q21.3) MUTATED                                                           4
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                         4
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK  2(1Q21.3) MUTATED                                          6
  AMP PEAK  2(1Q21.3) WILD-TYPE                                        7
D2V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  2(1Q21.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      16
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     59
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          32
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           33
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    6
                                                                   clus
vv                                                                  AMP PEAK  2(1Q21.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        55
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      103
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            49
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             45
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      7
[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"
D2V9, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED     5 153
  AMP PEAK  2(1Q21.3) WILD-TYPE   1 277
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED      5  153
  AMP PEAK  2(1Q21.3) WILD-TYPE    1  277
     clus
vv    AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  NO                            5                             1
  YES                         153                           277
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  2(1Q21.3) MUTATED   118  10   9   9
  AMP PEAK  2(1Q21.3) WILD-TYPE 229   8  10  16
D2V10, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  R0                         118                           229
  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                         6
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  2(1Q21.3) MUTATED                                           1    93
  AMP PEAK  2(1Q21.3) WILD-TYPE                                         0   181
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                                                              93
                                           clus
vv                                          AMP PEAK  2(1Q21.3) WILD-TYPE
  ASIAN                                                                53
  BLACK OR AFRICAN AMERICAN                                             6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               181
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V13, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED     0 114
  AMP PEAK  2(1Q21.3) WILD-TYPE   4 199
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED      0  114
  AMP PEAK  2(1Q21.3) WILD-TYPE    4  199
                        clus
vv                       AMP PEAK  2(1Q21.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                         114
                        clus
vv                       AMP PEAK  2(1Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           199
[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  53
  AMP PEAK  3(1Q42.3) WILD-TYPE 170  97
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                          137                           267 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                           53                            97 
$`AMP PEAK  3(1Q42.3) MUTATED`
TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4267 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6705 
       11.01         6.61         6.18        19.33         9.17        25.61 
TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-8059 
        9.21        15.42        28.01        18.15        28.73        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 
       11.44         0.69         9.60        12.95         2.66         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8369 TCGA-BR-8381 TCGA-BR-8483 
        7.40         6.18        19.50        14.04         0.26         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8680 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8687 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4J5 TCGA-BR-A4J8 
        8.22         7.53        22.26         0.72        12.82        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-CD-5800 TCGA-CD-8524 TCGA-CD-8525 
        0.46        20.42         1.15        13.15         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48C 
        0.10         0.16         0.13         3.42         9.34        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-4460 
        6.58        12.20         7.99        54.08        19.07        21.99 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5719 TCGA-CG-5730 TCGA-D7-5578 
       18.97         7.07        12.00         1.02         4.01        12.66 
TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6817 
       11.93        18.84        18.54        17.19        10.26        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-A4YU 
       10.55        11.31        12.33        24.72        19.50        16.44 
TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 
       11.31         2.96         0.62         7.99        16.24        72.23 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HJ-7597 
        3.48        14.07         0.56         5.52        18.08        26.47 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4GC 
        5.92        14.27        12.59        14.17         0.76         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4H2 
       22.75        25.81        11.77         0.10         6.51        12.95 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
       27.42         3.45         5.19        13.08         1.41         6.44 
TCGA-IN-AB1V TCGA-KB-A6F7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A8MV TCGA-RD-A8N1 
        7.82        60.56        18.21         6.08       122.30       115.69 
TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
       35.61        48.79         5.46        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PY 
       35.24         7.73        12.79         2.70        17.85        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91Y 
       65.16        36.69        18.74        20.81        22.68         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R 
       52.24         9.04         4.54        64.18        21.04        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6K 
       11.24        18.41        32.94        17.13        12.43 

$`AMP PEAK  3(1Q42.3) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 
       26.70        11.70        19.56         9.47         9.44         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 
        4.64         7.43        18.35        30.90         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-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       26.10        32.78        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 
       21.11        30.90        31.20        32.94        12.82        24.76 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       35.24        23.93        15.32        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       12.76        18.71        17.49        12.26        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        0.56        16.31        15.58        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-8382 TCGA-BR-8384 TCGA-BR-8589 TCGA-BR-8590 
       19.17        14.79        15.85         3.72        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 
        9.86        15.68        10.68        12.56        13.87         6.08 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        1.48        13.41        13.51        12.89         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-BR-A4QL 
        0.53         0.66        19.36        20.65        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        5.13         2.83         3.25        13.18         0.30         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.07         0.07         0.13         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
        0.10        11.31        12.43         0.10        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-4444 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        47.05        12.03         0.00         9.01 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 
       22.98        30.97         6.97        36.00         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        0.99       105.07        12.03        15.02        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 
       65.10        69.04        21.07         7.99        12.36        19.13 
TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 
       20.55        18.61        17.85        13.35        15.22        15.98 
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-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.24        11.44         9.76        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 
        7.40         7.13        14.47        21.27        11.38        19.53 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A8CX 
       22.29        17.06        59.54         5.03        13.58         0.23 
TCGA-HU-8238 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 
        1.51        11.41        12.10        10.62        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       12.30        11.84        24.20        21.37        29.98         8.98 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.25        10.19         0.26         2.10        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 
       12.30         9.67         8.88         8.81        21.21        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
        3.39        18.38         5.36         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93G 
        5.56         1.81        13.51         2.53         5.56        20.15 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZF 
       37.64         3.72        19.73         9.86        45.67         8.52 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
       61.25         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       16.67        37.91        40.64       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8E3 
        8.94        16.87        19.04         5.79         0.92        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       34.45        27.88        32.48        28.96        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       16.31        22.19         2.50         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91D 
       15.65        13.35        26.24        27.35        64.57        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       11.93        61.22         1.71        36.16         7.36         9.50 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94U 
        2.01        55.43         6.58         5.72         2.66        22.09 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       40.08        28.41        29.98        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11        10.62         0.79 

  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                         0.07                          0.00 
  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 
                        12.59                         13.35 
[1] "0.1 - 122.3 (12.6)" "0.0 - 116.4 (13.3)"
[1] "hr=" "1.1"
D3V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  3(1Q42.3) MUTATED         1        7       13       10        13
  AMP PEAK  3(1Q42.3) WILD-TYPE       2        7       28       21        25
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  3(1Q42.3) MUTATED          13         3         30         22
  AMP PEAK  3(1Q42.3) WILD-TYPE        42         1         55         40
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK  3(1Q42.3) MUTATED           15       16
  AMP PEAK  3(1Q42.3) WILD-TYPE         26       30
D3V3, multiclass
            clus
vv           AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  STAGE I                              1                             2
  STAGE IA                             7                             7
  STAGE IB                            13                            28
  STAGE II                            10                            21
  STAGE IIA                           13                            25
  STAGE IIB                           13                            42
  STAGE III                            3                             1
  STAGE IIIA                          30                            55
  STAGE IIIB                          22                            40
  STAGE IIIC                          15                            26
  STAGE IV                            16                            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  3(1Q42.3) MUTATED    10  26  67  43
  AMP PEAK  3(1Q42.3) WILD-TYPE  12  64 128  76
D3V4, multiclass
    clus
vv   AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  T1                          10                            12
  T2                          26                            64
  T3                          67                           128
  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   45 33 31 32
  AMP PEAK  3(1Q42.3) WILD-TYPE 84 85 53 57
D3V5, multiclass
    clus
vv   AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  N0                          45                            84
  N1                          33                            85
  N2                          31                            53
  N3                          32                            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 255  21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED    132    9
  AMP PEAK  3(1Q42.3) WILD-TYPE  255   21
   clus
vv  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  0                         132                           255
  1                           9                            21
[1] 2 2
[1] FALSE
D3V7, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q42.3) MUTATED    52  97
  AMP PEAK  3(1Q42.3) WILD-TYPE 106 181
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED     52   97
  AMP PEAK  3(1Q42.3) WILD-TYPE  106  181
        clus
vv       AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  FEMALE                          52                           106
  MALE                            97                           181
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  3(1Q42.3) MUTATED                                      12
  AMP PEAK  3(1Q42.3) WILD-TYPE                                    59
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  3(1Q42.3) MUTATED                                                       53
  AMP PEAK  3(1Q42.3) WILD-TYPE                                                    109
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  3(1Q42.3) MUTATED                                                                  29
  AMP PEAK  3(1Q42.3) WILD-TYPE                                                                52
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  3(1Q42.3) MUTATED                                                 39
  AMP PEAK  3(1Q42.3) WILD-TYPE                                               39
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK  3(1Q42.3) MUTATED                                                          7
  AMP PEAK  3(1Q42.3) WILD-TYPE                                                       14
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK  3(1Q42.3) MUTATED                                                           3
  AMP PEAK  3(1Q42.3) WILD-TYPE                                                         5
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK  3(1Q42.3) MUTATED                                          5
  AMP PEAK  3(1Q42.3) WILD-TYPE                                        8
D3V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  3(1Q42.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     53
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          29
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           39
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    5
                                                                   clus
vv                                                                  AMP PEAK  3(1Q42.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      109
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            52
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             39
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      8
[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"
D3V9, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q42.3) MUTATED     3 146
  AMP PEAK  3(1Q42.3) WILD-TYPE   3 284
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED      3  146
  AMP PEAK  3(1Q42.3) WILD-TYPE    3  284
     clus
vv    AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  NO                            3                             3
  YES                         146                           284
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  3(1Q42.3) MUTATED   115   8   7   9
  AMP PEAK  3(1Q42.3) WILD-TYPE 232  10  12  16
D3V10, multiclass
    clus
vv   AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  R0                         115                           232
  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                         4
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  3(1Q42.3) MUTATED                                           0    89
  AMP PEAK  3(1Q42.3) WILD-TYPE                                         1   185
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                                                              89
                                           clus
vv                                          AMP PEAK  3(1Q42.3) WILD-TYPE
  ASIAN                                                                55
  BLACK OR AFRICAN AMERICAN                                             4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  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"
D3V13, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q42.3) MUTATED     0 108
  AMP PEAK  3(1Q42.3) WILD-TYPE   4 205
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED      0  108
  AMP PEAK  3(1Q42.3) WILD-TYPE    4  205
                        clus
vv                       AMP PEAK  3(1Q42.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                         108
                        clus
vv                       AMP PEAK  3(1Q42.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           205
[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    94  58
  AMP PEAK  4(3Q26.2) WILD-TYPE 160  92
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                          152                           252 
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                           58                            92 
$`AMP PEAK  4(3Q26.2) MUTATED`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        19.56        11.01         9.44         6.61 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-6706 
       18.35         6.18        34.68        17.29         9.17        18.05 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-7196 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       21.11        30.90        12.82        15.32        28.73         3.45 
TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8284 TCGA-BR-8289 TCGA-BR-8295 
       12.76        14.43        11.44         8.05         2.66         2.20 
TCGA-BR-8296 TCGA-BR-8361 TCGA-BR-8367 TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8588 
       15.58        19.50        26.33        14.79        25.18        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8676 TCGA-BR-8687 TCGA-BR-A4CQ TCGA-BR-A4IU 
       15.81         9.34         7.53         8.22        22.26        13.41 
TCGA-BR-A4J4 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-5799 
        0.53        19.36        20.65        20.42        13.64         3.25 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.18         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         0.16         0.13         9.34        12.43        11.61 
TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4444 
       12.20         3.02        15.95         7.99         8.05        47.05 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5724 
       12.03         0.00        12.00        30.97         1.02        12.03 
TCGA-CG-5725 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-8570 TCGA-D7-8579 
       15.02        18.54        10.26        15.98        24.72        20.91 
TCGA-D7-A4YU TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-EQ-5647 
       16.44        14.76        11.24         9.76         2.96         0.62 
TCGA-EQ-A4SO TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8211 
       16.24        21.27         3.48        14.07        22.29        13.58 
TCGA-FP-8631 TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-A4G6 TCGA-HU-A4G9 
        0.56         0.23        26.47         5.92        12.30        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4H0 
        3.25        22.75        25.81        11.77         8.98         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RL 
       12.95        19.36        23.84         9.67        27.42         5.19 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
       13.08         1.41         6.44         5.56         1.81         7.82 
TCGA-KB-A6F7 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8N1 
       60.56        45.67        18.21         6.08        16.67       115.69 
TCGA-RD-A8N9 TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 
       35.61         0.92        48.79         5.46        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PD TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       35.24        21.73         7.73        16.31        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PP TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ 
       17.85        23.41        13.35        27.35        64.57        65.16 
TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       11.93        20.81        22.68         9.73        52.24         9.04 
TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R 
        2.01         4.54         5.72        64.18        21.04        42.54 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6J 
       18.41        40.08        32.94        29.98        54.12        21.11 
TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       12.43         0.79 

$`AMP PEAK  4(3Q26.2) WILD-TYPE`
TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4279 
        9.47         6.97         4.64         7.43        30.90         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
        6.61        15.95        13.87        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       26.10        32.78        25.61        19.89        12.16         8.98 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        32.94         9.21        24.76        35.24        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7959 
       15.42        28.01        18.15        12.43         9.07        18.71 
TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 
       17.49         0.69        12.26         9.60        20.55         0.56 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 
       12.95        16.31         7.40         6.18        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        19.17         0.26        15.85         3.72         5.39 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8677 
        9.21        20.22         1.12        13.45         6.28         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 
       11.54        15.81        16.44         9.86        15.68        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IV 
       12.56        13.87         7.53         6.08         1.48        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17        12.82         0.66 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       13.51         0.46         1.15        11.57         5.13         2.83 
TCGA-CD-5800 TCGA-CD-8524 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
       13.15         0.07         0.13         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.10         3.42        11.31         6.58         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       20.02        27.02         1.02        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       29.98        19.07        21.99         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       22.98         6.97        36.00         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        28.96        79.07        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        12.36        12.66        11.93        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-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 
       15.22        12.79        10.55        11.31        12.33        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YT 
       19.50        17.19        18.21        14.66        21.14        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY 
        5.92        15.16        13.78        13.71        11.31        11.44 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 
       15.65         8.38         4.34         7.40         7.13         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8209 
       14.47        72.23        11.38        19.53        17.06        59.54 
TCGA-FP-8210 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
        5.03         5.52        18.08         1.51        14.27        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT 
        5.59        11.84        21.37        29.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB 
        6.25        10.19         0.26        12.30         8.88         8.81 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       21.21         3.45        18.81         3.39        18.38         5.36 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        6.74        12.59         6.51        13.51         2.53         5.56 
TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZF 
       20.15        37.64         3.72        19.73         9.86         8.52 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
       61.25         4.60         9.24        11.05         8.61         5.13 
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-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DV TCGA-VQ-A8E7 
        8.94        16.87        19.04         5.79        13.25        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PE 
       27.88        32.48        28.96        34.29        46.26        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PY 
        2.50         1.87         9.27        15.65        26.24        14.33 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91V 
       36.69        11.70        61.22        18.74         1.71        36.16 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A94P TCGA-VQ-A94T 
        7.36         9.50        55.43         6.58         2.66        11.24 
TCGA-VQ-A94U TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-ZA-A8F6 
       22.09        28.41        17.13        26.04        16.14        10.62 

  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                         0.00                          0.07 
  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 
                        13.05                         12.64 
[1] "0.0 - 115.7 (13.1)" "0.1 - 122.3 (12.6)"
[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       14       12        10
  AMP PEAK  4(3Q26.2) WILD-TYPE       3        8       27       19        28
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  4(3Q26.2) MUTATED          22         2         31         21
  AMP PEAK  4(3Q26.2) WILD-TYPE        33         2         54         41
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK  4(3Q26.2) MUTATED           23       17
  AMP PEAK  4(3Q26.2) WILD-TYPE         18       29
D4V3, multiclass
            clus
vv           AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  STAGE I                              0                             3
  STAGE IA                             6                             8
  STAGE IB                            14                            27
  STAGE II                            12                            19
  STAGE IIA                           10                            28
  STAGE IIB                           22                            33
  STAGE III                            2                             2
  STAGE IIIA                          31                            54
  STAGE IIIB                          21                            41
  STAGE IIIC                          23                            18
  STAGE IV                            17                            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  4(3Q26.2) MUTATED     9  30  66  54
  AMP PEAK  4(3Q26.2) WILD-TYPE  13  60 129  65
D4V4, multiclass
    clus
vv   AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  T1                           9                            13
  T2                          30                            60
  T3                          66                           129
  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   42 46 31 37
  AMP PEAK  4(3Q26.2) WILD-TYPE 87 72 53 52
D4V5, multiclass
    clus
vv   AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  N0                          42                            87
  N1                          46                            72
  N2                          31                            53
  N3                          37                            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 245  20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(3Q26.2) MUTATED    142   10
  AMP PEAK  4(3Q26.2) WILD-TYPE  245   20
   clus
vv  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  0                         142                           245
  1                          10                            20
[1] 2 2
[1] FALSE
D4V7, binary
                               cls
clus                              0   1
  AMP PEAK  4(3Q26.2) MUTATED    58 105
  AMP PEAK  4(3Q26.2) WILD-TYPE 100 173
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(3Q26.2) MUTATED     58  105
  AMP PEAK  4(3Q26.2) WILD-TYPE  100  173
        clus
vv       AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  FEMALE                          58                           100
  MALE                           105                           173
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  4(3Q26.2) MUTATED                                      20
  AMP PEAK  4(3Q26.2) WILD-TYPE                                    51
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  4(3Q26.2) MUTATED                                                       63
  AMP PEAK  4(3Q26.2) WILD-TYPE                                                     99
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  4(3Q26.2) MUTATED                                                                  33
  AMP PEAK  4(3Q26.2) WILD-TYPE                                                                48
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  4(3Q26.2) MUTATED                                                 33
  AMP PEAK  4(3Q26.2) WILD-TYPE                                               45
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK  4(3Q26.2) MUTATED                                                          5
  AMP PEAK  4(3Q26.2) WILD-TYPE                                                       16
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK  4(3Q26.2) MUTATED                                                           3
  AMP PEAK  4(3Q26.2) WILD-TYPE                                                         5
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK  4(3Q26.2) MUTATED                                          5
  AMP PEAK  4(3Q26.2) WILD-TYPE                                        8
D4V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  4(3Q26.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      20
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     63
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          33
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           33
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    5
                                                                   clus
vv                                                                  AMP PEAK  4(3Q26.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        51
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       99
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            48
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             45
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      8
[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"
D4V9, binary
                               cls
clus                              0   1
  AMP PEAK  4(3Q26.2) MUTATED     2 161
  AMP PEAK  4(3Q26.2) WILD-TYPE   4 269
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(3Q26.2) MUTATED      2  161
  AMP PEAK  4(3Q26.2) WILD-TYPE    4  269
     clus
vv    AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  NO                            2                             4
  YES                         161                           269
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  4(3Q26.2) MUTATED   126   7   8   9
  AMP PEAK  4(3Q26.2) WILD-TYPE 221  11  11  16
D4V10, multiclass
    clus
vv   AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  R0                         126                           221
  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                         4
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  4(3Q26.2) MUTATED                                           0    98
  AMP PEAK  4(3Q26.2) WILD-TYPE                                         1   176
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                                                              98
                                           clus
vv                                          AMP PEAK  4(3Q26.2) WILD-TYPE
  ASIAN                                                                52
  BLACK OR AFRICAN AMERICAN                                             4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  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"
D4V13, binary
                               cls
clus                              0   1
  AMP PEAK  4(3Q26.2) MUTATED     3 108
  AMP PEAK  4(3Q26.2) WILD-TYPE   1 205
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(3Q26.2) MUTATED      3  108
  AMP PEAK  4(3Q26.2) WILD-TYPE    1  205
                        clus
vv                       AMP PEAK  4(3Q26.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         108
                        clus
vv                       AMP PEAK  4(3Q26.2) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           205
[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    73  47
  AMP PEAK  5(5P15.33) WILD-TYPE 181 103
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                           120                            284 
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                            47                            103 
$`AMP PEAK  5(5P15.33) MUTATED`
TCGA-BR-4187 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        4.64         9.21        35.24        15.42        28.01        18.15 
TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        3.45        11.44         0.69         8.05        12.95         2.66 
TCGA-BR-8296 TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8373 TCGA-BR-8485 
       15.58         0.26        17.52        26.33        14.79         9.21 
TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8687 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-5800 
       20.22        11.54         8.22        20.65        13.64        13.15 
TCGA-CD-5801 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8533 TCGA-CD-8535 
       13.18         0.07         0.10         0.13         0.13         0.13 
TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4438 
        3.42        12.43        11.61        12.20         7.99        54.08 
TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       14.01        47.05        12.03        18.97         7.07        12.00 
TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 
       22.98        36.00         0.99        12.03        15.02         4.01 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6526 TCGA-D7-6527 
       12.36        12.66        11.93        19.13        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8576 TCGA-D7-A6EX 
       15.22        10.55        11.31        24.72        14.66        11.31 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
        2.96        15.65         7.40         0.62         7.99        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-A8CX TCGA-HU-8238 TCGA-HU-8245 
        3.48        19.53        17.06         0.23         1.51        12.59 
TCGA-HU-8249 TCGA-HU-A4G2 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       14.17        24.30         3.25        22.75        25.81        11.77 
TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RL 
        6.25         2.10        12.30        27.42         3.45         5.19 
TCGA-IN-A6RR TCGA-IN-A7NT TCGA-KB-A6F5 TCGA-KB-A93G TCGA-R5-A7O7 TCGA-R5-A7ZE 
        6.74         5.56         5.56        20.15        45.67        18.21 
TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DU 
        8.61       122.30        57.44         8.94        35.61         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PH 
       13.25        13.02        18.48        35.24        21.73        12.79 
TCGA-VQ-A8PK TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X 
       17.85        36.69        18.74         1.71        36.16         9.50 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A94T TCGA-VQ-AA64 
       52.24         9.04         4.54         6.58        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       40.08        32.94        54.12        16.14        21.11         0.79 

$`AMP PEAK  5(5P15.33) WILD-TYPE`
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-4267 
        6.61         6.97         7.43        18.35        30.90         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        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        32.94        12.82        24.76        23.93 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73        12.43         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 
       17.49        14.43        12.26         9.60        20.55         0.56 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       16.31         2.20         7.40         6.18        19.50        13.08 
TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       22.19         0.95         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       19.17         0.26        15.85         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        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        15.81        16.44         9.86        15.68 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        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        12.82         0.66        19.36        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.42         1.15        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 
        3.25         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 
        0.16         0.10         0.10         0.10         9.34        11.31 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 
       15.95         1.02         8.05         4.01        29.98        19.07 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 
       21.99         0.00         9.01        30.97         6.97         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99         6.02       105.07        28.96        79.07        65.10 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       69.04        21.07         7.99        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6822 
       18.61        17.85        13.35        15.98        12.79        12.33 
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        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 
       13.71        11.24        11.44         9.76         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7916 
        7.13        16.24        14.47        21.27        11.38        14.07 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       22.29        59.54         5.03        13.58         0.56         5.52 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 
       18.08        26.47         5.92        14.27        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       10.62         0.76         5.59        12.30        11.84        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        10.19 
TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        0.26        12.95        19.36        23.84         9.67         8.88 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
        8.81        21.21        18.81         3.39        18.38         5.36 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU 
       13.08         1.41         6.44        12.59         6.51         1.81 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG 
        7.82        13.51         2.53        60.56        37.64         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       19.73         9.86         8.52        61.25         6.08         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-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
      115.69       116.38        71.38        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
        0.92        48.79        34.45        27.88        32.48         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       28.96        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-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D 
       26.24        27.35        64.57        14.33        65.16        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91Y 
       11.93        61.22        20.81        22.68         7.36         9.73 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P 
        2.01        55.43         5.72        64.18        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G 
       42.54        22.09        28.41        29.98        17.13        26.04 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        10.62 

  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                          0.07                           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 
                        12.510                         13.015 
[1] "0.1 - 122.3 (12.5)" "0.0 - 116.4 (13.0)"
[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        11
  AMP PEAK  5(5P15.33) WILD-TYPE       3       11       29       21        27
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  5(5P15.33) MUTATED          13         1         32         16
  AMP PEAK  5(5P15.33) WILD-TYPE        42         3         53         46
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK  5(5P15.33) MUTATED           10       15
  AMP PEAK  5(5P15.33) WILD-TYPE         31       31
D5V3, multiclass
            clus
vv           AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  STAGE I                               0                              3
  STAGE IA                              3                             11
  STAGE IB                             12                             29
  STAGE II                             10                             21
  STAGE IIA                            11                             27
  STAGE IIB                            13                             42
  STAGE III                             1                              3
  STAGE IIIA                           32                             53
  STAGE IIIB                           16                             46
  STAGE IIIC                           10                             31
  STAGE IV                             15                             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  5(5P15.33) MUTATED     2  29  69  25
  AMP PEAK  5(5P15.33) WILD-TYPE  20  61 126  94
D5V4, multiclass
    clus
vv   AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  T1                            2                             20
  T2                           29                             61
  T3                           69                            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 29 27
  AMP PEAK  5(5P15.33) WILD-TYPE 95 84 55 62
D5V5, multiclass
    clus
vv   AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  N0                           34                             95
  N1                           34                             84
  N2                           29                             55
  N3                           27                             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"
D5V6, binary
                                cls
clus                               0   1
  AMP PEAK  5(5P15.33) MUTATED   113   9
  AMP PEAK  5(5P15.33) WILD-TYPE 274  21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(5P15.33) MUTATED    113    9
  AMP PEAK  5(5P15.33) WILD-TYPE  274   21
   clus
vv  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  0                          113                            274
  1                            9                             21
[1] 2 2
[1] FALSE
D5V7, binary
                                cls
clus                               0   1
  AMP PEAK  5(5P15.33) MUTATED    42  86
  AMP PEAK  5(5P15.33) WILD-TYPE 116 192
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(5P15.33) MUTATED     42   86
  AMP PEAK  5(5P15.33) WILD-TYPE  116  192
        clus
vv       AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  FEMALE                           42                            116
  MALE                             86                            192
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  5(5P15.33) MUTATED                                      12
  AMP PEAK  5(5P15.33) WILD-TYPE                                    59
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  5(5P15.33) MUTATED                                                       40
  AMP PEAK  5(5P15.33) WILD-TYPE                                                    122
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  5(5P15.33) MUTATED                                                                  31
  AMP PEAK  5(5P15.33) WILD-TYPE                                                                50
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  5(5P15.33) MUTATED                                                 28
  AMP PEAK  5(5P15.33) WILD-TYPE                                               50
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK  5(5P15.33) MUTATED                                                          8
  AMP PEAK  5(5P15.33) WILD-TYPE                                                       13
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK  5(5P15.33) MUTATED                                                           4
  AMP PEAK  5(5P15.33) WILD-TYPE                                                         4
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK  5(5P15.33) MUTATED                                          3
  AMP PEAK  5(5P15.33) WILD-TYPE                                       10
D5V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  5(5P15.33) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      40
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           31
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            28
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     3
                                                                   clus
vv                                                                  AMP PEAK  5(5P15.33) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       122
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             50
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              50
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      10
[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"
D5V9, binary
                                cls
clus                               0   1
  AMP PEAK  5(5P15.33) MUTATED     2 126
  AMP PEAK  5(5P15.33) WILD-TYPE   4 304
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(5P15.33) MUTATED      2  126
  AMP PEAK  5(5P15.33) WILD-TYPE    4  304
     clus
vv    AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  NO                             2                              4
  YES                          126                            304
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  5(5P15.33) MUTATED   102   6   7   5
  AMP PEAK  5(5P15.33) WILD-TYPE 245  12  12  20
D5V10, multiclass
    clus
vv   AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  R0                          102                            245
  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                         6
                                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      75
  AMP PEAK  5(5P15.33) WILD-TYPE   199
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                                                               75
                                           clus
vv                                          AMP PEAK  5(5P15.33) WILD-TYPE
  ASIAN                                                                 61
  BLACK OR AFRICAN AMERICAN                                              6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                199
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V13, binary
                                cls
clus                               0   1
  AMP PEAK  5(5P15.33) MUTATED     1  86
  AMP PEAK  5(5P15.33) WILD-TYPE   3 227
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(5P15.33) MUTATED      1   86
  AMP PEAK  5(5P15.33) WILD-TYPE    3  227
                        clus
vv                       AMP PEAK  5(5P15.33) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           86
                        clus
vv                       AMP PEAK  5(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            227
[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    71  44
  AMP PEAK  6(5P13.1) WILD-TYPE 183 106
  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE 
                          115                           289 
  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE 
                           44                           106 
$`AMP PEAK  6(5P13.1) MUTATED`
TCGA-BR-4187 TCGA-BR-6458 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
        4.64        19.33         9.21        35.24        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8284 
       18.15         3.45        18.71        11.44         0.69         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8367 
       12.95         2.66        15.58         0.26        17.52        26.33 
TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8687 
       14.04        14.79         9.21        20.22        11.54         8.22 
TCGA-BR-A4CQ TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8525 
       22.26        20.65        13.64        13.18         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        0.10         0.13         3.42        12.43        11.61        12.20 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4466 
        7.99        54.08        47.05        12.03        21.99        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5722 TCGA-CG-5724 
        7.07        12.00        22.98        36.00         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5730 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6527 
       15.02         4.01        12.66        11.93        19.13        10.26 
TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8576 TCGA-D7-A6EX 
       15.22        10.55        11.31        24.72        14.66        11.31 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 
        2.96        15.65         0.62         7.99        72.23         3.48 
TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-A8CX TCGA-HU-8238 TCGA-HU-8245 TCGA-HU-8249 
       19.53        17.06         0.23         1.51        12.59        14.17 
TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.10        24.30         3.25        22.75        25.81        11.77 
TCGA-HU-A4H0 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RL TCGA-IN-A7NR 
        2.10        12.30        27.42         3.45         5.19         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-KB-A6F5 TCGA-KB-A93G TCGA-R5-A7O7 
        5.56         1.81         7.82         5.56        20.15        45.67 
TCGA-R5-A7ZE TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DV 
       18.21        57.44         8.94        35.61         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A91A 
       13.02        18.48        21.73        12.79        17.85        36.69 
TCGA-VQ-A91N TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A927 
       18.74         9.50         9.73        52.24         9.04         6.58 
TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6J TCGA-VQ-AA6K 
       11.24        40.08        32.94        54.12        21.11        12.43 
TCGA-ZQ-A9CR 
        0.79 

$`AMP PEAK  6(5P13.1) WILD-TYPE`
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-4267 
        6.61         6.97         7.43        18.35        30.90         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-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.68        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        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7722 
       31.20        32.94        12.82        24.76        23.93        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 
       28.73        12.43         9.07        12.76        17.49        14.43 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 
       12.26         9.60        20.55         0.56        16.31         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8366 
        7.40         6.18        19.50        13.08        22.19         0.95 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
        4.31         3.32        11.80        19.17         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        3.72         5.39        25.18         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        9.34        13.45         6.28         7.53         0.49        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       16.44         9.86        15.68        10.68        12.56        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        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL 
       19.36        13.51         0.46        20.42         1.15        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13         2.83         3.25        13.15         0.30         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.07         0.13         0.16         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI 
        0.13         0.10         9.34        11.31         6.58         0.10 
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-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 
        8.05         4.01        14.01        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-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 
      105.07        28.96        79.07        65.10        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
        7.99        12.36        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6822 
       17.85        13.35        17.19        15.98        12.79        12.33 
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        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 
       13.71        11.24        11.44         9.76         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        7.40         7.13        16.24        14.47        21.27        11.38 
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-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 
        5.52        18.08        26.47         5.92        14.27        11.41 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       10.62         0.76         5.59        12.30        11.84        24.20 
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         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
       10.19         0.26        12.95        19.36        23.84         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
        8.88         8.81        21.21        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
        5.36        13.08         1.41         6.44         6.74        12.59 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
       13.51         2.53        60.56        37.64         3.72        19.73 
TCGA-MX-A663 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
        9.86         8.52        61.25         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-A8NB TCGA-SW-A7EA 
       40.64       115.69       116.38        71.38        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.79         0.92        48.79        35.24        34.45        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       32.48         7.73        28.96        34.29        46.26        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       22.19         2.50         2.70         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       15.65        13.35        26.24        27.35        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S 
       65.16        11.70        11.93        61.22        20.81        22.68 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        1.71        36.16         7.36         2.01        55.43         4.54 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94U 
        5.72        64.18        21.04         2.66        42.54        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I 
       18.41        28.41        29.98        17.13        26.04        16.14 
TCGA-ZA-A8F6 
       10.62 

  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE 
                         0.07                          0.00 
  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE 
                        72.23                        122.30 
  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE 
                        12.43                         13.08 
[1] "0.1 - 72.2 (12.4)"  "0.0 - 122.3 (13.1)"
[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        12
  AMP PEAK  6(5P13.1) WILD-TYPE       3       10       29       22        26
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  6(5P13.1) MUTATED          13         1         26         13
  AMP PEAK  6(5P13.1) WILD-TYPE        42         3         59         49
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK  6(5P13.1) MUTATED           14       15
  AMP PEAK  6(5P13.1) WILD-TYPE         27       31
D6V3, multiclass
            clus
vv           AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  STAGE I                              0                             3
  STAGE IA                             4                            10
  STAGE IB                            12                            29
  STAGE II                             9                            22
  STAGE IIA                           12                            26
  STAGE IIB                           13                            42
  STAGE III                            1                             3
  STAGE IIIA                          26                            59
  STAGE IIIB                          13                            49
  STAGE IIIC                          14                            27
  STAGE IV                            15                            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  6(5P13.1) MUTATED     3  27  61  30
  AMP PEAK  6(5P13.1) WILD-TYPE  19  63 134  89
D6V4, multiclass
    clus
vv   AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  T1                           3                            19
  T2                          27                            63
  T3                          61                           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 21 30
  AMP PEAK  6(5P13.1) WILD-TYPE 95 83 63 59
D6V5, multiclass
    clus
vv   AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  N0                          34                            95
  N1                          35                            83
  N2                          21                            63
  N3                          30                            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"
D6V6, binary
                               cls
clus                              0   1
  AMP PEAK  6(5P13.1) MUTATED   108  10
  AMP PEAK  6(5P13.1) WILD-TYPE 279  20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(5P13.1) MUTATED    108   10
  AMP PEAK  6(5P13.1) WILD-TYPE  279   20
   clus
vv  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  0                         108                           279
  1                          10                            20
[1] 2 2
[1] FALSE
D6V7, binary
                               cls
clus                              0   1
  AMP PEAK  6(5P13.1) MUTATED    44  80
  AMP PEAK  6(5P13.1) WILD-TYPE 114 198
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(5P13.1) MUTATED     44   80
  AMP PEAK  6(5P13.1) WILD-TYPE  114  198
        clus
vv       AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  FEMALE                          44                           114
  MALE                            80                           198
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  6(5P13.1) MUTATED                                      12
  AMP PEAK  6(5P13.1) WILD-TYPE                                    59
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  6(5P13.1) MUTATED                                                       44
  AMP PEAK  6(5P13.1) WILD-TYPE                                                    118
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  6(5P13.1) MUTATED                                                                  27
  AMP PEAK  6(5P13.1) WILD-TYPE                                                                54
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  6(5P13.1) MUTATED                                                 24
  AMP PEAK  6(5P13.1) WILD-TYPE                                               54
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK  6(5P13.1) MUTATED                                                          8
  AMP PEAK  6(5P13.1) WILD-TYPE                                                       13
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK  6(5P13.1) MUTATED                                                           3
  AMP PEAK  6(5P13.1) WILD-TYPE                                                         5
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK  6(5P13.1) MUTATED                                          4
  AMP PEAK  6(5P13.1) WILD-TYPE                                        9
D6V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  6(5P13.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     44
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          27
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           24
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    4
                                                                   clus
vv                                                                  AMP PEAK  6(5P13.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      118
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            54
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             54
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      9
[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"
D6V9, binary
                               cls
clus                              0   1
  AMP PEAK  6(5P13.1) MUTATED     2 122
  AMP PEAK  6(5P13.1) WILD-TYPE   4 308
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(5P13.1) MUTATED      2  122
  AMP PEAK  6(5P13.1) WILD-TYPE    4  308
     clus
vv    AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  NO                            2                             4
  YES                         122                           308
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  6(5P13.1) MUTATED    97   7   7   5
  AMP PEAK  6(5P13.1) WILD-TYPE 250  11  12  20
D6V10, multiclass
    clus
vv   AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  R0                          97                           250
  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                         6
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  6(5P13.1) MUTATED                                           0    76
  AMP PEAK  6(5P13.1) WILD-TYPE                                         1   198
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                                                              76
                                           clus
vv                                          AMP PEAK  6(5P13.1) WILD-TYPE
  ASIAN                                                                65
  BLACK OR AFRICAN AMERICAN                                             6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  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"
D6V13, binary
                               cls
clus                              0   1
  AMP PEAK  6(5P13.1) MUTATED     1  85
  AMP PEAK  6(5P13.1) WILD-TYPE   3 228
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(5P13.1) MUTATED      1   85
  AMP PEAK  6(5P13.1) WILD-TYPE    3  228
                        clus
vv                       AMP PEAK  6(5P13.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          85
                        clus
vv                       AMP PEAK  6(5P13.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           228
[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    63  46
  AMP PEAK  7(6P21.1) WILD-TYPE 191 104
  AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE 
                          109                           295 
  AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE 
                           46                           104 
$`AMP PEAK  7(6P21.1) MUTATED`
TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6456 
       11.01         6.61         6.97        18.35         6.18        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 
       13.68        19.33         9.17         9.21        35.24        15.42 
TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8289 
       18.15        28.73         3.45        11.44        12.95         2.66 
TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 
       14.04        14.79        25.18         9.21        20.22        11.54 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-A4CQ TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI 
        9.86        15.68        22.26        20.65        20.42        13.64 
TCGA-CD-5799 TCGA-CD-5803 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48C 
        3.25         0.07         0.13         3.42         9.34        11.61 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4477 
        7.99        54.08        19.07        12.03        18.97        30.97 
TCGA-CG-5718 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-6518 TCGA-D7-6527 
       36.00        79.07         4.01        69.04        19.13        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8576 
       15.22        15.98        10.55        11.31        12.33        14.66 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-8122 TCGA-FP-7735 
       14.27        16.44         2.96        15.65         7.99         3.48 
TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8249 
       19.53        17.06         0.56         5.52         5.92        14.17 
TCGA-HU-A4GF TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-8663 TCGA-IN-A6RI 
       25.81        23.84        12.30         9.67         3.39        18.38 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT 
        5.19        13.08         1.41         6.74        12.59         5.56 
TCGA-IP-7968 TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-RD-A7BT TCGA-RD-A8MV 
        2.53        37.64        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        35.24 
TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PU TCGA-VQ-A91S 
        7.73        22.19         2.70        17.85        27.35        22.68 
TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O 
        1.71         9.50         9.04         4.54        64.18        21.04 
TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G 
       42.54        18.41        40.08        29.98        17.13        26.04 
TCGA-ZQ-A9CR 
        0.79 

$`AMP PEAK  7(6P21.1) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4187 
       26.70        11.70        19.56         9.47         9.44         4.64 
TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        7.43        30.90         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.87        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        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 
       32.94        12.82        24.76        23.93        28.01        15.32 
TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       12.43         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        12.26         9.60        20.55         8.05         0.56 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
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-8381 TCGA-BR-8382 
        4.31         3.32        11.80        19.17         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        3.72         5.39         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        15.81        16.44 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        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        12.82         0.66        19.36        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 
        0.46         1.15        11.57         5.13         2.83        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.18         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        0.10        11.31        12.43         6.58        12.20         0.10 
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-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4460 
        8.05         4.01        14.01        29.98        47.05        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 
        0.00         9.01         7.07        12.00        22.98         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-5733 TCGA-CG-5734 TCGA-D7-5577 
       15.02        28.96        65.10        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.66        11.93        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8572 
       17.85        13.35        17.19        12.79        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YV 
       19.50        17.19        18.21        21.14        20.91         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       15.16        13.78        14.76        13.71        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.44         9.76         8.38         4.34         7.40         7.13 
TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62        16.24        14.47        72.23        21.27        11.38 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A8CX 
       14.07        22.29        59.54         5.03        13.58         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       18.08        26.47         1.51        14.27        12.59        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ 
       11.84        24.20         3.25        22.75        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         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB 
        0.26         2.10        12.95        19.36         8.88         8.81 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RP 
       27.42        21.21         3.45        18.81         5.36         6.44 
TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 
        6.51         1.81         7.82        13.51         5.56        60.56 
TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZF TCGA-R5-A7ZI 
       20.15         3.72        19.73         9.86         8.52        61.25 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
        6.08         4.60         9.24        11.05         5.13        16.67 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
       40.64       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-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        34.45        27.88        32.48        28.96        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO 
       46.26        16.31         2.50        12.79         1.87         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        26.24        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       65.16        36.69        11.70        11.93        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 
       20.81        36.16         7.36         9.73        52.24         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-A94U 
       55.43         6.58         5.72         2.66        11.24        22.09 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       28.41        32.94        54.12        16.14        21.11        12.43 
TCGA-ZA-A8F6 
       10.62 

  AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE 
                         0.07                          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 
                        14.04                         12.66 
[1] "0.1 - 122.3 (14.0)" "0.0 - 116.4 (12.7)"
[1] "hr=" "1.1"
D7V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  7(6P21.1) MUTATED         2        3       15       10         9
  AMP PEAK  7(6P21.1) WILD-TYPE       1       11       26       21        29
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  7(6P21.1) MUTATED          16         0         26         16
  AMP PEAK  7(6P21.1) WILD-TYPE        39         4         59         46
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK  7(6P21.1) MUTATED            7       12
  AMP PEAK  7(6P21.1) WILD-TYPE         34       34
D7V3, multiclass
            clus
vv           AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE
  STAGE I                              2                             1
  STAGE IA                             3                            11
  STAGE IB                            15                            26
  STAGE II                            10                            21
  STAGE IIA                            9                            29
  STAGE IIB                           16                            39
  STAGE III                            0                             4
  STAGE IIIA                          26                            59
  STAGE IIIB                          16                            46
  STAGE IIIC                           7                            34
  STAGE IV                            12                            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  7(6P21.1) MUTATED     6  31  54  25
  AMP PEAK  7(6P21.1) WILD-TYPE  16  59 141  94
D7V4, multiclass
    clus
vv   AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE
  T1                           6                            16
  T2                          31                            59
  T3                          54                           141
  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   36 37 25 20
  AMP PEAK  7(6P21.1) WILD-TYPE 93 81 59 69
D7V5, multiclass
    clus
vv   AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE
  N0                          36                            93
  N1                          37                            81
  N2                          25                            59
  N3                          20                            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   108   5
  AMP PEAK  7(6P21.1) WILD-TYPE 279  25
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(6P21.1) MUTATED    108    5
  AMP PEAK  7(6P21.1) WILD-TYPE  279   25
   clus
vv  AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE
  0                         108                           279
  1                           5                            25
[1] 2 2
[1] FALSE
D7V7, binary
                               cls
clus                              0   1
  AMP PEAK  7(6P21.1) MUTATED    40  81
  AMP PEAK  7(6P21.1) WILD-TYPE 118 197
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(6P21.1) MUTATED     40   81
  AMP PEAK  7(6P21.1) WILD-TYPE  118  197
        clus
vv       AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE
  FEMALE                          40                           118
  MALE                            81                           197
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  7(6P21.1) MUTATED                                       4
  AMP PEAK  7(6P21.1) WILD-TYPE                                    67
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  7(6P21.1) MUTATED                                                       50
  AMP PEAK  7(6P21.1) WILD-TYPE                                                    112
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  7(6P21.1) MUTATED                                                                  30
  AMP PEAK  7(6P21.1) WILD-TYPE                                                                51
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  7(6P21.1) MUTATED                                                 30
  AMP PEAK  7(6P21.1) WILD-TYPE                                               48
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK  7(6P21.1) MUTATED                                                          3
  AMP PEAK  7(6P21.1) WILD-TYPE                                                       18
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK  7(6P21.1) MUTATED                                                           2
  AMP PEAK  7(6P21.1) WILD-TYPE                                                         6
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK  7(6P21.1) MUTATED                                          2
  AMP PEAK  7(6P21.1) WILD-TYPE                                       11
D7V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  7(6P21.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     50
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          30
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           30
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    2
                                                                   clus
vv                                                                  AMP PEAK  7(6P21.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        67
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      112
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            51
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             48
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     11
[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"
D7V9, binary
                               cls
clus                              0   1
  AMP PEAK  7(6P21.1) MUTATED     3 118
  AMP PEAK  7(6P21.1) WILD-TYPE   3 312
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(6P21.1) MUTATED      3  118
  AMP PEAK  7(6P21.1) WILD-TYPE    3  312
     clus
vv    AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE
  NO                            3                             3
  YES                         118                           312
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  7(6P21.1) MUTATED    94   4   5  10
  AMP PEAK  7(6P21.1) WILD-TYPE 253  14  14  15
D7V10, multiclass
    clus
vv   AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE
  R0                          94                           253
  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                         6
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  7(6P21.1) MUTATED                                           1    81
  AMP PEAK  7(6P21.1) WILD-TYPE                                         0   193
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                                                              81
                                           clus
vv                                          AMP PEAK  7(6P21.1) WILD-TYPE
  ASIAN                                                                70
  BLACK OR AFRICAN AMERICAN                                             6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               193
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V13, binary
                               cls
clus                              0   1
  AMP PEAK  7(6P21.1) MUTATED     1  84
  AMP PEAK  7(6P21.1) WILD-TYPE   3 229
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(6P21.1) MUTATED      1   84
  AMP PEAK  7(6P21.1) WILD-TYPE    3  229
                        clus
vv                       AMP PEAK  7(6P21.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          84
                        clus
vv                       AMP PEAK  7(6P21.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           229
[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    44  32
  AMP PEAK  8(6Q12) WILD-TYPE 210 118
  AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE 
                         76                         328 
  AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE 
                         32                         118 
$`AMP PEAK  8(6Q12) MUTATED`
TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6458 
       11.01         6.61         6.97         6.18        17.29        19.33 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7723 TCGA-BR-8060 TCGA-BR-8286 
        9.21        35.24        15.42        28.73        11.44        12.95 
TCGA-BR-8289 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8678 
        2.66        14.04        14.79        25.18         9.21        11.54 
TCGA-BR-8686 TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI 
       15.68         0.72        13.51        20.65        20.42        13.64 
TCGA-CD-5799 TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CG-4436 
        3.25         0.13         3.42         9.34        12.43         7.99 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5730 
       54.08         4.01        18.97        30.97         1.02         4.01 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8576 
       17.19        10.26        10.55        11.31        12.33        14.66 
TCGA-D7-A4YT TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-A4BF 
       14.27         2.96         7.99         3.48        19.53         5.52 
TCGA-HU-A4GF TCGA-HU-A4GT TCGA-HU-A4H6 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL 
       25.81         6.51         9.67         3.39        18.38         5.19 
TCGA-IN-A6RO TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A663 TCGA-RD-A7BT TCGA-RD-A8MW 
        1.41        60.56        37.64         9.86         8.61        37.91 
TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8P5 TCGA-VQ-A8PE 
      115.69         8.94        13.25        13.02         7.73        22.19 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A922 
        2.70        17.85        22.68         1.71         9.50         9.04 
TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6F 
       42.54        40.08        29.98        54.12 

$`AMP PEAK  8(6Q12) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4187 
       26.70        11.70        19.56         9.47         9.44         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        7.43        18.35        30.90         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       15.95        13.87        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-7703 
       21.11        30.90        31.20        32.94        12.82        24.76 
TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 
       23.93        28.01        18.15        15.32        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 
       12.26         9.60        20.55         8.05         0.56        16.31 
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        19.50        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        19.17         0.26        15.85         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        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
        9.86         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        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        12.82         0.66        19.36 
TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 
        0.46         1.15        11.57         5.13         2.83        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.18         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        0.13         0.10        11.31        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
        1.02         8.05        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 
       12.03        21.99         0.00         9.01         7.07        12.00 
TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       22.98         6.97        36.00         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
      105.07        12.03        15.02        28.96        79.07        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        12.36        12.66        11.93 
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-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8572 
       13.35        15.22        15.98        12.79        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU 
       19.50        17.19        18.21        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        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        11.44         9.76        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
        7.40         7.13         0.62        16.24        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-A8CX TCGA-HF-A5NB TCGA-HJ-7597 
        5.03        13.58         0.56         0.23        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        1.51         5.92        14.27        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ 
       11.84        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         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 
        2.10        12.95        19.36        23.84        12.30         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ 
        8.81        27.42        21.21         3.45        18.81         5.36 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       13.08         6.44         6.74        12.59         6.51         5.56 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93G 
        1.81         7.82        13.51         2.53         5.56        20.15 
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        61.25 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
        6.08         4.60         9.24        11.05         5.13        16.67 
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-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-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       18.48        35.24        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH 
       28.96        34.29        46.26        16.31         2.50        12.79 
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        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       27.35        64.57        14.33        65.16        36.69        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W 
       11.93        61.22        18.74        20.81        36.16         7.36 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
        9.73        52.24         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-A94U 
        5.72        64.18        21.04         2.66        11.24        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I 
       18.41        28.41        32.94        17.13        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11        12.43        10.62         0.79 

  AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE 
                       0.13                        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 
                     11.935                      12.920 
[1] "0.1 - 115.7 (11.9)" "0.0 - 122.3 (12.9)"
[1] "hr=" "1.2"
D8V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  8(6Q12) MUTATED         2        1       11        6         8
  AMP PEAK  8(6Q12) WILD-TYPE       1       13       30       25        30
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  8(6Q12) MUTATED          12         0         17         11
  AMP PEAK  8(6Q12) WILD-TYPE        43         4         68         51
                             vv
clus                          STAGE IIIC STAGE IV
  AMP PEAK  8(6Q12) MUTATED            4       11
  AMP PEAK  8(6Q12) WILD-TYPE         37       35
D8V3, multiclass
            clus
vv           AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE
  STAGE I                            2                           1
  STAGE IA                           1                          13
  STAGE IB                          11                          30
  STAGE II                           6                          25
  STAGE IIA                          8                          30
  STAGE IIB                         12                          43
  STAGE III                          0                           4
  STAGE IIIA                        17                          68
  STAGE IIIB                        11                          51
  STAGE IIIC                         4                          37
  STAGE IV                          11                          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  8(6Q12) MUTATED     4  20  41  19
  AMP PEAK  8(6Q12) WILD-TYPE  18  70 154 100
D8V4, multiclass
    clus
vv   AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE
  T1                         4                          18
  T2                        20                          70
  T3                        41                         154
  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    27  26  14  16
  AMP PEAK  8(6Q12) WILD-TYPE 102  92  70  73
D8V5, multiclass
    clus
vv   AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE
  N0                        27                         102
  N1                        26                          92
  N2                        14                          70
  N3                        16                          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"
D8V6, binary
                             cls
clus                            0   1
  AMP PEAK  8(6Q12) MUTATED    76   6
  AMP PEAK  8(6Q12) WILD-TYPE 311  24
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(6Q12) MUTATED     76    6
  AMP PEAK  8(6Q12) WILD-TYPE  311   24
   clus
vv  AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE
  0                        76                         311
  1                         6                          24
[1] 2 2
[1] FALSE
D8V7, binary
                             cls
clus                            0   1
  AMP PEAK  8(6Q12) MUTATED    32  54
  AMP PEAK  8(6Q12) WILD-TYPE 126 224
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(6Q12) MUTATED     32   54
  AMP PEAK  8(6Q12) WILD-TYPE  126  224
        clus
vv       AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE
  FEMALE                        32                         126
  MALE                          54                         224
[1] 2 2
[1] FALSE
                             vv
clus                          STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  8(6Q12) MUTATED                                       4
  AMP PEAK  8(6Q12) WILD-TYPE                                    67
                             vv
clus                          STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  8(6Q12) MUTATED                                                       36
  AMP PEAK  8(6Q12) WILD-TYPE                                                    126
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  8(6Q12) MUTATED                                                                  27
  AMP PEAK  8(6Q12) WILD-TYPE                                                                54
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  8(6Q12) MUTATED                                                 15
  AMP PEAK  8(6Q12) WILD-TYPE                                               63
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK  8(6Q12) MUTATED                                                          1
  AMP PEAK  8(6Q12) WILD-TYPE                                                       20
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK  8(6Q12) MUTATED                                                           1
  AMP PEAK  8(6Q12) WILD-TYPE                                                         7
                             vv
clus                          STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK  8(6Q12) MUTATED                                          2
  AMP PEAK  8(6Q12) WILD-TYPE                                       11
D8V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  8(6Q12) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                   36
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        27
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                         15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                  1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                 1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                  2
                                                                   clus
vv                                                                  AMP PEAK  8(6Q12) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      67
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          54
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           63
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   11
[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"
D8V9, binary
                             cls
clus                            0   1
  AMP PEAK  8(6Q12) MUTATED     2  84
  AMP PEAK  8(6Q12) WILD-TYPE   4 346
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(6Q12) MUTATED      2   84
  AMP PEAK  8(6Q12) WILD-TYPE    4  346
     clus
vv    AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE
  NO                          2                           4
  YES                        84                         346
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  8(6Q12) MUTATED    65   3   5   8
  AMP PEAK  8(6Q12) WILD-TYPE 282  15  14  17
D8V10, multiclass
    clus
vv   AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE
  R0                        65                         282
  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                         8
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  8(6Q12) MUTATED                                           1    55
  AMP PEAK  8(6Q12) WILD-TYPE                                         0   219
D8V12, multiclass
                                           clus
vv                                          AMP PEAK  8(6Q12) MUTATED
  ASIAN                                                            14
  BLACK OR AFRICAN AMERICAN                                         3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         1
  WHITE                                                            55
                                           clus
vv                                          AMP PEAK  8(6Q12) WILD-TYPE
  ASIAN                                                              74
  BLACK OR AFRICAN AMERICAN                                           8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V13, binary
                             cls
clus                            0   1
  AMP PEAK  8(6Q12) MUTATED     0  60
  AMP PEAK  8(6Q12) WILD-TYPE   4 253
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(6Q12) MUTATED      0   60
  AMP PEAK  8(6Q12) WILD-TYPE    4  253
                        clus
vv                       AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE
  HISPANIC OR LATINO                             0                           4
  NOT HISPANIC OR LATINO                        60                         253
[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    42  33
  AMP PEAK  9(6Q21) WILD-TYPE 212 117
  AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE 
                         75                         329 
  AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE 
                         33                         117 
$`AMP PEAK  9(6Q21) MUTATED`
TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-6456 TCGA-BR-7197 TCGA-BR-7704 
       11.01         6.61         6.97        17.29         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-8060 TCGA-BR-8289 TCGA-BR-8369 TCGA-BR-8373 
       15.42        18.15        11.44         2.66        14.04        14.79 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-A452 TCGA-BR-A4CQ 
       25.18         9.21        11.54        15.68         7.53        22.26 
TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J7 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8528 
        1.48         0.72        19.36         3.25        13.15         0.10 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
        9.34        12.43         3.02         7.99        54.08         4.01 
TCGA-CG-4444 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5724 TCGA-D7-6521 TCGA-D7-6527 
       47.05        18.97        30.97        12.03        18.54        10.26 
TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-A4YT TCGA-EQ-8122 
       15.22        10.55        11.31        12.33        14.27         7.99 
TCGA-EQ-A4SO TCGA-FP-A4BF TCGA-HU-A4GH TCGA-HU-A4GT TCGA-HU-A4H2 TCGA-HU-A4H6 
       16.24         5.52        11.77         6.51        12.95         9.67 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-MX-A663 
        3.45        18.81         3.39         1.81         5.56         9.86 
TCGA-R5-A7O7 TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-VQ-A8DU 
       45.67         8.61        16.67        37.91         8.94         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PJ 
       13.25        13.02        18.48        35.24        22.19         2.70 
TCGA-VQ-A8PK TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A92D 
       17.85        22.68         1.71         9.50         9.04        64.18 
TCGA-VQ-A94R TCGA-VQ-AA6D TCGA-VQ-AA6J 
       42.54        17.13        21.11 

$`AMP PEAK  9(6Q21) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4187 
       26.70        11.70        19.56         9.47         9.44         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        7.43        18.35        30.90         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        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       12.82        24.76        23.93        28.01        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.56        12.95        16.31         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        19.50        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        19.17 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-8487 
        0.26        15.85         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        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 
        0.49        15.81        16.44         9.86         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       12.56        13.87         6.08        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 
        8.98        14.17         0.53        12.82         0.66        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        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        5.13         2.83        13.18         0.30         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.07         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 
        0.10         0.13         0.13         0.10         3.42        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         0.10        12.62        20.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 
       27.02        15.95         1.02         8.05        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
       19.07        12.03        21.99         0.00         9.01         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        22.98         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-5727 
        6.02         0.99       105.07        15.02        28.96        79.07 
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        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
       12.66        11.93        19.13        20.55        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8570 
       17.85        13.35        17.19        15.98        12.79        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-A4YY TCGA-D7-A4Z0 
       20.91        16.44         5.92        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       13.71        11.24        11.31        11.44         9.76         2.96 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34         7.40         7.13         0.62 
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-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-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        0.56         0.23        18.08        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       14.27        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        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-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 
        0.10         6.25        10.19         0.26         2.10        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         8.88         8.81        27.42        21.21 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
       18.38         5.36         5.19        13.08         1.41         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X 
        6.74        12.59         6.51         5.56         7.82        13.51 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53        60.56        20.15        37.64         3.72        19.73 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        61.25         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       11.05         5.13       122.30        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-A8DL TCGA-VQ-A8DT TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        0.92        48.79        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
        7.73        28.96        34.29        46.26        16.31         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       12.79         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       26.24        27.35        64.57        14.33        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V 
       11.70        11.93        61.22        18.74        20.81        36.16 
TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        7.36         9.73        52.24         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-A94U 
        6.58         5.72        21.04         2.66        11.24        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        40.08        28.41        32.94        29.98        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        12.43        10.62         0.79 

  AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE 
                        0.1                         0.0 
  AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE 
                      64.18                      122.30 
  AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE 
                      12.03                       12.95 
[1] "0.1 - 64.2 (12.0)"  "0.0 - 122.3 (12.9)"
[1] "hr=" "1.4"
D9V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  9(6Q21) MUTATED         0        1        9        5         4
  AMP PEAK  9(6Q21) WILD-TYPE       3       13       32       26        34
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  9(6Q21) MUTATED           9         1         22         11
  AMP PEAK  9(6Q21) WILD-TYPE        46         3         63         51
                             vv
clus                          STAGE IIIC STAGE IV
  AMP PEAK  9(6Q21) MUTATED            4       13
  AMP PEAK  9(6Q21) WILD-TYPE         37       33
D9V3, multiclass
            clus
vv           AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE
  STAGE I                            0                           3
  STAGE IA                           1                          13
  STAGE IB                           9                          32
  STAGE II                           5                          26
  STAGE IIA                          4                          34
  STAGE IIB                          9                          46
  STAGE III                          1                           3
  STAGE IIIA                        22                          63
  STAGE IIIB                        11                          51
  STAGE IIIC                         4                          37
  STAGE IV                          13                          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  9(6Q21) MUTATED     1  20  33  25
  AMP PEAK  9(6Q21) WILD-TYPE  21  70 162  94
D9V4, multiclass
    clus
vv   AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE
  T1                         1                          21
  T2                        20                          70
  T3                        33                         162
  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 111  92  66  73
D9V5, multiclass
    clus
vv   AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE
  N0                        18                         111
  N1                        26                          92
  N2                        18                          66
  N3                        16                          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"
D9V6, binary
                             cls
clus                            0   1
  AMP PEAK  9(6Q21) MUTATED    70   8
  AMP PEAK  9(6Q21) WILD-TYPE 317  22
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q21) MUTATED     70    8
  AMP PEAK  9(6Q21) WILD-TYPE  317   22
   clus
vv  AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE
  0                        70                         317
  1                         8                          22
[1] 2 2
[1] FALSE
D9V7, binary
                             cls
clus                            0   1
  AMP PEAK  9(6Q21) MUTATED    25  56
  AMP PEAK  9(6Q21) WILD-TYPE 133 222
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q21) MUTATED     25   56
  AMP PEAK  9(6Q21) WILD-TYPE  133  222
        clus
vv       AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE
  FEMALE                        25                         133
  MALE                          56                         222
[1] 2 2
[1] FALSE
                             vv
clus                          STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  9(6Q21) MUTATED                                       7
  AMP PEAK  9(6Q21) WILD-TYPE                                    64
                             vv
clus                          STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  9(6Q21) MUTATED                                                       28
  AMP PEAK  9(6Q21) WILD-TYPE                                                    134
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  9(6Q21) MUTATED                                                                  22
  AMP PEAK  9(6Q21) WILD-TYPE                                                                59
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  9(6Q21) MUTATED                                                 19
  AMP PEAK  9(6Q21) WILD-TYPE                                               59
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK  9(6Q21) MUTATED                                                          1
  AMP PEAK  9(6Q21) WILD-TYPE                                                       20
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK  9(6Q21) MUTATED                                                           2
  AMP PEAK  9(6Q21) WILD-TYPE                                                         6
                             vv
clus                          STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK  9(6Q21) MUTATED                                          2
  AMP PEAK  9(6Q21) WILD-TYPE                                       11
D9V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  9(6Q21) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                   28
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        22
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                         19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                  1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                 2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                  2
                                                                   clus
vv                                                                  AMP PEAK  9(6Q21) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      64
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          59
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           59
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   11
[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"
D9V9, binary
                             cls
clus                            0   1
  AMP PEAK  9(6Q21) MUTATED     2  79
  AMP PEAK  9(6Q21) WILD-TYPE   4 351
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q21) MUTATED      2   79
  AMP PEAK  9(6Q21) WILD-TYPE    4  351
     clus
vv    AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE
  NO                          2                           4
  YES                        79                         351
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  9(6Q21) MUTATED    61   2   6   6
  AMP PEAK  9(6Q21) WILD-TYPE 286  16  13  19
D9V10, multiclass
    clus
vv   AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE
  R0                        61                         286
  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                         7
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  9(6Q21) MUTATED                                           1    48
  AMP PEAK  9(6Q21) WILD-TYPE                                         0   226
D9V12, multiclass
                                           clus
vv                                          AMP PEAK  9(6Q21) MUTATED
  ASIAN                                                            15
  BLACK OR AFRICAN AMERICAN                                         4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         1
  WHITE                                                            48
                                           clus
vv                                          AMP PEAK  9(6Q21) WILD-TYPE
  ASIAN                                                              73
  BLACK OR AFRICAN AMERICAN                                           7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  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"
D9V13, binary
                             cls
clus                            0   1
  AMP PEAK  9(6Q21) MUTATED     1  54
  AMP PEAK  9(6Q21) WILD-TYPE   3 259
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q21) MUTATED      1   54
  AMP PEAK  9(6Q21) WILD-TYPE    3  259
                        clus
vv                       AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE
  HISPANIC OR LATINO                             1                           3
  NOT HISPANIC OR LATINO                        54                         259
[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  81
  AMP PEAK 10(7P22.1) WILD-TYPE 125  69
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                          210                           194 
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                           81                            69 
$`AMP PEAK 10(7P22.1) MUTATED`
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 
       11.70        11.01         6.61         6.97         4.64        18.35 
TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       17.29        19.33         9.17        32.78        25.61        18.05 
TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.11         9.21        24.76        35.24        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
       18.15         3.45        12.76        18.71        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8296 
        0.69         8.05         0.56        12.95         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8366 
        7.40         6.18        19.50        13.08        22.19         0.95 
TCGA-BR-8370 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 
        3.32        14.79         0.26         5.39         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U 
        1.12        16.44         9.86         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        22.26         1.48        12.89         0.72         0.53 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 
       19.36        13.51        20.42         1.15        13.64         3.25 
TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8535 
       13.18         0.07         0.10         0.16         0.13         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        0.10         3.42        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       12.20        20.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       54.08         4.01        21.99        18.97         7.07        12.00 
TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 
       22.98        36.00        12.03        28.96        79.07         4.01 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 
       21.07         7.99        12.66        11.93        19.13        18.84 
TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 
       18.54        17.19        15.22        15.98        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       12.33        24.72        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EX TCGA-D7-A6F0 
       20.91        14.27        16.44        15.16        11.31         2.96 
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-7998 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 
       22.29        17.06         0.56         5.52         0.23        26.47 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.59        14.17        12.30         3.25        22.75        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         6.25        10.19         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7808 
       12.95        23.84        12.30         9.67        27.42         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP 
       18.81         3.39        18.38         5.19         1.41         6.44 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G 
       12.59         6.51         1.81         5.56        60.56        20.15 
TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       37.64         9.86        45.67        18.21         8.52        61.25 
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        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PF TCGA-VQ-A8PH 
       21.73        34.45        34.29        46.26         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
        2.70        17.85        27.35        14.33        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W 
       11.70        11.93        18.74        20.81         1.71         7.36 
TCGA-VQ-A91X TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R 
        9.50         2.01         4.54        64.18        21.04        42.54 
TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        22.09        18.41        40.08        32.94        29.98 
TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       54.12        16.14        21.11        12.43        10.62         0.79 

$`AMP PEAK 10(7P22.1) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4188 TCGA-BR-4201 
       26.70        19.56         9.47         9.44         7.43        30.90 
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        32.94        12.82        23.93        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8078 TCGA-BR-8080 
       28.73        12.43         9.07        17.49        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8367 
       20.55         2.66        16.31         0.26        17.52        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8384 
        4.31        14.04        11.80        19.17        15.85         3.72 
TCGA-BR-8484 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       25.18        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-A44T 
        7.53         0.49        11.54        15.81        15.68        12.56 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 
        6.08        13.41        13.51         8.98        14.17        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.66         0.46        20.65        11.57         5.13         2.83 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.15         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-A487 TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.13         0.10         0.10         9.34         0.10        12.62 
TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
        3.02         1.02        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 
       12.03         0.00         9.01        30.97         6.97         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5728 
        0.99         6.02         0.99       105.07        15.02        65.10 
TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       69.04        12.36        20.55        18.61        17.85        13.35 
TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-A4YV TCGA-D7-A4YY 
       10.26        12.79        16.80        19.50         5.92        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 
       14.76        13.71        11.24        11.44         9.76         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
        4.34         7.40         7.13         0.62         7.99        16.24 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-A5NB 
       21.27        11.38        59.54         5.03        13.58        18.08 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        14.27        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ 
        0.76        24.30         5.59        11.84        24.20        21.37 
TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.98         6.51         0.26        19.36         8.88         8.81 
TCGA-IN-7806 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-AB1V 
       21.21         5.36        13.08         6.74         5.56         7.82 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A804 TCGA-R5-A805 
       13.51         2.53         3.72        19.73         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 
       11.05         5.13        16.67        37.91        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8E0 
       71.38        35.61        16.87        19.04         0.92        18.48 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PD TCGA-VQ-A8PE 
       27.88        32.48         7.73        28.96        16.31        22.19 
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        26.24 
TCGA-VQ-A8PX TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91Y TCGA-VQ-A91Z 
       64.57        61.22        22.68        36.16         9.73        52.24 
TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-AA69 
        9.04        55.43         6.58         5.72         2.66        28.41 
TCGA-VQ-AA6D TCGA-VQ-AA6G 
       17.13        26.04 

  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                         0.07                          0.00 
  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 
                        12.95                         12.79 
[1] "0.1 - 122.3 (12.9)" "0.0 - 116.4 (12.8)"
[1] "hr=" "1"  
D10V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 10(7P22.1) MUTATED         3        8       21       15        19
  AMP PEAK 10(7P22.1) WILD-TYPE       0        6       20       16        19
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 10(7P22.1) MUTATED          27         3         46         31
  AMP PEAK 10(7P22.1) WILD-TYPE        28         1         39         31
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 10(7P22.1) MUTATED           25       21
  AMP PEAK 10(7P22.1) WILD-TYPE         16       25
D10V3, multiclass
            clus
vv           AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  STAGE I                              3                             0
  STAGE IA                             8                             6
  STAGE IB                            21                            20
  STAGE II                            15                            16
  STAGE IIA                           19                            19
  STAGE IIB                           27                            28
  STAGE III                            3                             1
  STAGE IIIA                          46                            39
  STAGE IIIB                          31                            31
  STAGE IIIC                          25                            16
  STAGE IV                            21                            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 10(7P22.1) MUTATED    12  44 107  58
  AMP PEAK 10(7P22.1) WILD-TYPE  10  46  88  61
D10V4, multiclass
    clus
vv   AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  T1                          12                            10
  T2                          44                            46
  T3                         107                            88
  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 55 51 46
  AMP PEAK 10(7P22.1) WILD-TYPE 62 63 33 43
D10V5, multiclass
    clus
vv   AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  N0                          67                            62
  N1                          55                            63
  N2                          51                            33
  N3                          46                            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"
D10V6, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P22.1) MUTATED   202  13
  AMP PEAK 10(7P22.1) WILD-TYPE 185  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P22.1) MUTATED    202   13
  AMP PEAK 10(7P22.1) WILD-TYPE  185   17
   clus
vv  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  0                         202                           185
  1                          13                            17
[1] 2 2
[1] FALSE
D10V7, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P22.1) MUTATED    72 156
  AMP PEAK 10(7P22.1) WILD-TYPE  86 122
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P22.1) MUTATED     72  156
  AMP PEAK 10(7P22.1) WILD-TYPE   86  122
        clus
vv       AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  FEMALE                          72                            86
  MALE                           156                           122
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 10(7P22.1) MUTATED                                      25
  AMP PEAK 10(7P22.1) WILD-TYPE                                    46
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 10(7P22.1) MUTATED                                                       82
  AMP PEAK 10(7P22.1) WILD-TYPE                                                     80
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 10(7P22.1) MUTATED                                                                  52
  AMP PEAK 10(7P22.1) WILD-TYPE                                                                29
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 10(7P22.1) MUTATED                                                 45
  AMP PEAK 10(7P22.1) WILD-TYPE                                               33
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 10(7P22.1) MUTATED                                                          8
  AMP PEAK 10(7P22.1) WILD-TYPE                                                       13
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 10(7P22.1) MUTATED                                                           5
  AMP PEAK 10(7P22.1) WILD-TYPE                                                         3
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 10(7P22.1) MUTATED                                          9
  AMP PEAK 10(7P22.1) WILD-TYPE                                        4
D10V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 10(7P22.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      25
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     82
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          52
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           45
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    9
                                                                   clus
vv                                                                  AMP PEAK 10(7P22.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       80
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            29
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             33
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      4
[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"
D10V9, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P22.1) MUTATED     3 225
  AMP PEAK 10(7P22.1) WILD-TYPE   3 205
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P22.1) MUTATED      3  225
  AMP PEAK 10(7P22.1) WILD-TYPE    3  205
     clus
vv    AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  NO                            3                             3
  YES                         225                           205
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 10(7P22.1) MUTATED   184   9   9  12
  AMP PEAK 10(7P22.1) WILD-TYPE 163   9  10  13
D10V10, multiclass
    clus
vv   AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  R0                         184                           163
  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                         3
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 10(7P22.1) MUTATED                                           1   142
  AMP PEAK 10(7P22.1) WILD-TYPE                                         0   132
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                                                             142
                                           clus
vv                                          AMP PEAK 10(7P22.1) WILD-TYPE
  ASIAN                                                                43
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               132
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V13, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P22.1) MUTATED     3 158
  AMP PEAK 10(7P22.1) WILD-TYPE   1 155
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P22.1) MUTATED      3  158
  AMP PEAK 10(7P22.1) WILD-TYPE    1  155
                        clus
vv                       AMP PEAK 10(7P22.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         158
                        clus
vv                       AMP PEAK 10(7P22.1) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           155
[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   113  83
  AMP PEAK 11(7P11.2) WILD-TYPE 141  67
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                          196                           208 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                           83                            67 
$`AMP PEAK 11(7P11.2) MUTATED`
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 
       11.70        11.01         6.61         6.97         4.64        18.35 
TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       17.29        19.33         9.17        32.78        25.61        18.05 
TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 
       21.11         9.21        24.76        35.24        15.42        18.15 
TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8284 
        3.45        12.76        18.71        14.43         0.69         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-8486 
        0.95         3.32        14.79         0.26         5.39        20.22 
TCGA-BR-8487 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U 
        1.12        16.44         9.86         8.22        10.68        13.87 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       22.26         1.48        12.89         0.72        14.17         0.53 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5801 
       19.36        13.51        20.42        13.64         3.25        13.18 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.07         0.10         0.16         0.13         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4304 
        3.42        11.61         6.58        12.20        20.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4469 
       15.95         7.99         4.01        21.99        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
       12.00        22.98        36.00        12.03        28.96        79.07 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 
       21.07         7.99        12.66        11.93        19.13        18.84 
TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-6822 
       18.54        17.19        15.22        15.98        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       24.72        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-F1-6874 
       16.44        15.16        11.31         2.96        15.65        14.47 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 
       72.23         3.48        19.53        14.07        17.06         0.56 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-A4G2 
        5.52         0.23        26.47         5.92        14.17        24.30 
TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ 
       12.30         3.25        25.81        11.77         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.25        10.19         2.10        12.95        19.36        23.84 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL 
       27.42         3.45        18.81         3.39        18.38         5.19 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU 
        1.41         6.44         6.74        12.59         6.51         1.81 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7ZE 
        5.56        60.56        20.15        37.64         9.86        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV 
        8.52        61.25         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        35.24        21.73        34.45        34.29 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PU 
        2.50        12.79         2.70        17.85         1.87        27.35 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91N 
       14.33        65.16        36.69        11.70        11.93        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z 
       20.81         1.71        36.16         7.36         9.50        52.24 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T 
        9.04         2.01         4.54        21.04        42.54        11.24 
TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I 
       22.09        40.08        32.94        29.98        54.12        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11        12.43        10.62         0.79 

$`AMP PEAK 11(7P11.2) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4188 TCGA-BR-4201 
       26.70        19.56         9.47         9.44         7.43        30.90 
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        32.94        12.82        23.93        28.01 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8060 
       15.32        28.73        12.43         9.07        17.49        11.44 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       12.26         9.60        20.55        12.95         2.66        16.31 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8367 TCGA-BR-8368 
        6.18        19.50         0.26        22.19        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        19.17        15.85         3.72        25.18 
TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        9.21        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-A44T 
        7.53         0.49        11.54        15.81        15.68        12.56 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J5 
        7.53         6.08        13.41        13.51         8.98        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM 
        0.66         0.46        20.65         1.15        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 
        2.83        13.15         0.30         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-A487 TCGA-CD-A489 
        0.07         0.13         0.10         0.10         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4437 
       12.43         0.10        12.62         3.02         1.02         8.05 
TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
       54.08        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 
        0.00         9.01        30.97         6.97         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        6.02         0.99       105.07        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       69.04        12.36        20.55        18.61        17.85        13.35 
TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-A4YT 
       10.26        12.79        10.55        16.80        19.50        14.27 
TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
        5.92        13.78        14.76        13.71        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
        9.76         8.38         4.34         7.40         7.13         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7998 TCGA-FP-8209 
        7.99        16.24        21.27        11.38        22.29        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
        5.03        13.58        18.08         1.51        14.27        12.59 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 
       11.41        12.10        10.62         0.76         5.59        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GY 
       24.20        22.75        21.37        29.98         6.51         0.26 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-A6RJ 
       12.30         9.67         8.88         8.81        21.21         5.36 
TCGA-IN-A6RN TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-MX-A5UG 
       13.08         5.56         7.82        13.51         2.53         3.72 
TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW 
       19.73        45.67         4.60         9.24        11.05         5.13 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 TCGA-RD-A8NB 
       37.91        40.64       116.38        71.38        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       19.04         5.79         0.92        27.88        32.48         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PO TCGA-VQ-A8PP 
       28.96        46.26        16.31        22.19         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A91K TCGA-VQ-A91S 
       15.65        13.35        26.24        64.57        61.22        22.68 
TCGA-VQ-A91Y TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P 
        9.73        55.43         6.58         5.72        64.18         2.66 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G 
       18.41        28.41        17.13        26.04 

  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                         0.07                          0.00 
  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 
                       13.215                        12.575 
[1] "0.1 - 122.3 (13.2)" "0.0 - 116.4 (12.6)"
[1] "hr=" "1.3"
D11V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 11(7P11.2) MUTATED         3        8       20       12        16
  AMP PEAK 11(7P11.2) WILD-TYPE       0        6       21       19        22
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 11(7P11.2) MUTATED          26         3         45         29
  AMP PEAK 11(7P11.2) WILD-TYPE        29         1         40         33
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 11(7P11.2) MUTATED           23       20
  AMP PEAK 11(7P11.2) WILD-TYPE         18       26
D11V3, multiclass
            clus
vv           AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  STAGE I                              3                             0
  STAGE IA                             8                             6
  STAGE IB                            20                            21
  STAGE II                            12                            19
  STAGE IIA                           16                            22
  STAGE IIB                           26                            29
  STAGE III                            3                             1
  STAGE IIIA                          45                            40
  STAGE IIIB                          29                            33
  STAGE IIIC                          23                            18
  STAGE IV                            20                            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 11(7P11.2) MUTATED    12  38 100  56
  AMP PEAK 11(7P11.2) WILD-TYPE  10  52  95  63
D11V4, multiclass
    clus
vv   AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  T1                          12                            10
  T2                          38                            52
  T3                         100                            95
  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 53 45 45
  AMP PEAK 11(7P11.2) WILD-TYPE 67 65 39 44
D11V5, multiclass
    clus
vv   AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  N0                          62                            67
  N1                          53                            65
  N2                          45                            39
  N3                          45                            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"
D11V6, binary
                               cls
clus                              0   1
  AMP PEAK 11(7P11.2) MUTATED   191  11
  AMP PEAK 11(7P11.2) WILD-TYPE 196  19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED    191   11
  AMP PEAK 11(7P11.2) WILD-TYPE  196   19
   clus
vv  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  0                         191                           196
  1                          11                            19
[1] 2 2
[1] FALSE
D11V7, binary
                               cls
clus                              0   1
  AMP PEAK 11(7P11.2) MUTATED    68 145
  AMP PEAK 11(7P11.2) WILD-TYPE  90 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED     68  145
  AMP PEAK 11(7P11.2) WILD-TYPE   90  133
        clus
vv       AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  FEMALE                          68                            90
  MALE                           145                           133
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 11(7P11.2) MUTATED                                      25
  AMP PEAK 11(7P11.2) WILD-TYPE                                    46
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 11(7P11.2) MUTATED                                                       76
  AMP PEAK 11(7P11.2) WILD-TYPE                                                     86
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 11(7P11.2) MUTATED                                                                  48
  AMP PEAK 11(7P11.2) WILD-TYPE                                                                33
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 11(7P11.2) MUTATED                                                 43
  AMP PEAK 11(7P11.2) WILD-TYPE                                               35
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 11(7P11.2) MUTATED                                                          7
  AMP PEAK 11(7P11.2) WILD-TYPE                                                       14
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 11(7P11.2) MUTATED                                                           3
  AMP PEAK 11(7P11.2) WILD-TYPE                                                         5
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 11(7P11.2) MUTATED                                          9
  AMP PEAK 11(7P11.2) WILD-TYPE                                        4
D11V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 11(7P11.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      25
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     76
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          48
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           43
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    9
                                                                   clus
vv                                                                  AMP PEAK 11(7P11.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       86
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            33
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      4
[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"
D11V9, binary
                               cls
clus                              0   1
  AMP PEAK 11(7P11.2) MUTATED     2 211
  AMP PEAK 11(7P11.2) WILD-TYPE   4 219
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED      2  211
  AMP PEAK 11(7P11.2) WILD-TYPE    4  219
     clus
vv    AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  NO                            2                             4
  YES                         211                           219
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 11(7P11.2) MUTATED   174   9   8  11
  AMP PEAK 11(7P11.2) WILD-TYPE 173   9  11  14
D11V10, multiclass
    clus
vv   AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  R0                         174                           173
  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                         2
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 11(7P11.2) MUTATED                                           1   130
  AMP PEAK 11(7P11.2) WILD-TYPE                                         0   144
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                                                             130
                                           clus
vv                                          AMP PEAK 11(7P11.2) WILD-TYPE
  ASIAN                                                                46
  BLACK OR AFRICAN AMERICAN                                             2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               144
[1] 4 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     1 146
  AMP PEAK 11(7P11.2) WILD-TYPE   3 167
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED      1  146
  AMP PEAK 11(7P11.2) WILD-TYPE    3  167
                        clus
vv                       AMP PEAK 11(7P11.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         146
                        clus
vv                       AMP PEAK 11(7P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           167
[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   112  74
  AMP PEAK 12(7Q21.2) WILD-TYPE 142  76
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                          186                           218 
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                           74                            76 
$`AMP PEAK 12(7Q21.2) MUTATED`
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 
       11.70        19.56        11.01         9.44         6.97         4.64 
TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       18.35        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        21.11         9.21        24.76        35.24 
TCGA-BR-7715 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8284 
       15.42        12.76        18.71        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         0.26         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        16.44         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-8527 TCGA-CD-8528 
       20.42         1.15         3.25        13.18         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.13         0.16         0.13         0.13         0.10         3.42 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 
       12.43        11.61         6.58        12.20        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       27.02        15.95         7.99        54.08         4.01        14.01 
TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5718 
       12.03        18.97         7.07        12.00        22.98        36.00 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5733 TCGA-D7-5578 
       12.03        15.02        28.96        79.07        21.07        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 
       11.93        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        15.16 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-F1-6874 TCGA-F1-6875 
       11.24        11.31         2.96        15.65        14.47        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A8CX 
        3.48        19.53        22.29        17.06         0.56         0.23 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GF 
       26.47         5.92        14.17        24.30        12.30        25.81 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         0.10         6.25        10.19         2.10        12.95 
TCGA-HU-A4H3 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP 
       19.36         3.45         3.39         5.19         1.41         6.44 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G 
        6.51         5.56         1.81         5.56        60.56        20.15 
TCGA-MX-A663 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A8MV 
        9.86         8.52        61.25         6.08         8.61       122.30 
TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-VQ-A8DT TCGA-VQ-A8DV 
       37.91       115.69        57.44         8.94        48.79        13.25 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PB 
       18.48        35.24        21.73        34.45         7.73        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-A91Q TCGA-VQ-A91S 
       65.16        36.69        11.70        11.93        20.81        22.68 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A923 TCGA-VQ-A925 
        1.71        36.16         7.36         9.50         2.01         4.54 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA6A 
       64.18        21.04        42.54        11.24        18.41        32.94 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       29.98        54.12        16.14        21.11        10.62         0.79 

$`AMP PEAK 12(7Q21.2) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 
       26.70         9.47         6.61         7.43        30.90         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-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 
       39.12        19.89        12.16         8.98        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       32.94        12.82        23.93        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8077 
       28.73        12.43         3.45         9.07        17.49         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       12.26         9.60        20.55        12.95         2.66        16.31 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8367 TCGA-BR-8368 
        6.18        19.50         0.26        22.19        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8485 
       14.04        11.80        19.17        15.85         3.72         9.21 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T 
        0.49        11.54        15.81        15.68         8.22        12.56 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IZ TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QI 
        8.98        12.82         0.66        19.36         0.46        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
       11.57         5.13         2.83        13.15         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-A487 
        0.07         0.07         0.07         0.10         0.10         9.34 
TCGA-CD-A489 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4443 
       11.31         0.10        12.62         1.02         8.05        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4477 
       47.05        19.07        21.99         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        12.36        20.55 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 
       18.61        17.85        10.55        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        13.71 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.44         9.76         8.38         4.34         7.40         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7916 
        0.62         7.99        16.24        21.27        11.38        14.07 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HU-8238 
       59.54         5.03        13.58         5.52        18.08         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       14.27        12.59        11.41        12.10        10.62         0.76 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH 
        5.59        11.84        24.20         3.25        22.75        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H4 TCGA-HU-A4H5 
       21.37        29.98         6.51         0.26        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
        9.67         8.88         8.81        27.42        21.21        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-AB1V 
       18.38         5.36        13.08         6.74        12.59         7.82 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 
       13.51         2.53        37.64         3.72        19.73        45.67 
TCGA-R5-A7ZE TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
       18.21         4.60         9.24        11.05         5.13        16.67 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
       40.64       116.38        71.38        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        27.88        32.48 
TCGA-VQ-A8P8 TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PO TCGA-VQ-A8PP 
       28.96        46.26        16.31        22.19         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91K 
       15.65        13.35        26.24        27.35        64.57        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 
       18.74         9.73        52.24         9.04        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D 
        5.72         2.66        22.09        40.08        28.41        17.13 
TCGA-VQ-AA6G TCGA-VQ-AA6K 
       26.04        12.43 

  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                         0.07                          0.00 
  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 
                       13.215                        12.590 
[1] "0.1 - 122.3 (13.2)" "0.0 - 116.4 (12.6)"
[1] "hr=" "1.1"
D12V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 12(7Q21.2) MUTATED         2        6       20       15        18
  AMP PEAK 12(7Q21.2) WILD-TYPE       1        8       21       16        20
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 12(7Q21.2) MUTATED          23         3         38         31
  AMP PEAK 12(7Q21.2) WILD-TYPE        32         1         47         31
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 12(7Q21.2) MUTATED           20       18
  AMP PEAK 12(7Q21.2) WILD-TYPE         21       28
D12V3, multiclass
            clus
vv           AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  STAGE I                              2                             1
  STAGE IA                             6                             8
  STAGE IB                            20                            21
  STAGE II                            15                            16
  STAGE IIA                           18                            20
  STAGE IIB                           23                            32
  STAGE III                            3                             1
  STAGE IIIA                          38                            47
  STAGE IIIB                          31                            31
  STAGE IIIC                          20                            21
  STAGE IV                            18                            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 12(7Q21.2) MUTATED     9  43  94  50
  AMP PEAK 12(7Q21.2) WILD-TYPE  13  47 101  69
D12V4, multiclass
    clus
vv   AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  T1                           9                            13
  T2                          43                            47
  T3                          94                           101
  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 44 46 42
  AMP PEAK 12(7Q21.2) WILD-TYPE 67 74 38 47
D12V5, multiclass
    clus
vv   AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  N0                          62                            67
  N1                          44                            74
  N2                          46                            38
  N3                          42                            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"
D12V6, binary
                               cls
clus                              0   1
  AMP PEAK 12(7Q21.2) MUTATED   180  11
  AMP PEAK 12(7Q21.2) WILD-TYPE 207  19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7Q21.2) MUTATED    180   11
  AMP PEAK 12(7Q21.2) WILD-TYPE  207   19
   clus
vv  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  0                         180                           207
  1                          11                            19
[1] 2 2
[1] FALSE
D12V7, binary
                               cls
clus                              0   1
  AMP PEAK 12(7Q21.2) MUTATED    62 141
  AMP PEAK 12(7Q21.2) WILD-TYPE  96 137
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7Q21.2) MUTATED     62  141
  AMP PEAK 12(7Q21.2) WILD-TYPE   96  137
        clus
vv       AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  FEMALE                          62                            96
  MALE                           141                           137
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 12(7Q21.2) MUTATED                                      26
  AMP PEAK 12(7Q21.2) WILD-TYPE                                    45
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 12(7Q21.2) MUTATED                                                       75
  AMP PEAK 12(7Q21.2) WILD-TYPE                                                     87
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 12(7Q21.2) MUTATED                                                                  50
  AMP PEAK 12(7Q21.2) WILD-TYPE                                                                31
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 12(7Q21.2) MUTATED                                                 33
  AMP PEAK 12(7Q21.2) WILD-TYPE                                               45
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 12(7Q21.2) MUTATED                                                          8
  AMP PEAK 12(7Q21.2) WILD-TYPE                                                       13
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 12(7Q21.2) MUTATED                                                           4
  AMP PEAK 12(7Q21.2) WILD-TYPE                                                         4
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 12(7Q21.2) MUTATED                                          5
  AMP PEAK 12(7Q21.2) WILD-TYPE                                        8
D12V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 12(7Q21.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      26
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     75
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          50
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           33
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    5
                                                                   clus
vv                                                                  AMP PEAK 12(7Q21.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        45
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       87
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            31
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             45
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      8
[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"
D12V9, binary
                               cls
clus                              0   1
  AMP PEAK 12(7Q21.2) MUTATED     2 201
  AMP PEAK 12(7Q21.2) WILD-TYPE   4 229
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7Q21.2) MUTATED      2  201
  AMP PEAK 12(7Q21.2) WILD-TYPE    4  229
     clus
vv    AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  NO                            2                             4
  YES                         201                           229
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 12(7Q21.2) MUTATED   168   5   7  11
  AMP PEAK 12(7Q21.2) WILD-TYPE 179  13  12  14
D12V10, multiclass
    clus
vv   AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  R0                         168                           179
  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                         2
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 12(7Q21.2) MUTATED                                           1   125
  AMP PEAK 12(7Q21.2) WILD-TYPE                                         0   149
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                                                             125
                                           clus
vv                                          AMP PEAK 12(7Q21.2) WILD-TYPE
  ASIAN                                                                51
  BLACK OR AFRICAN AMERICAN                                             2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               149
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V13, binary
                               cls
clus                              0   1
  AMP PEAK 12(7Q21.2) MUTATED     2 139
  AMP PEAK 12(7Q21.2) WILD-TYPE   2 174
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7Q21.2) MUTATED      2  139
  AMP PEAK 12(7Q21.2) WILD-TYPE    2  174
                        clus
vv                       AMP PEAK 12(7Q21.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         139
                        clus
vv                       AMP PEAK 12(7Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           174
[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  72
  AMP PEAK 13(7Q22.1) WILD-TYPE 143  78
  AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE 
                          183                           221 
  AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE 
                           72                            78 
$`AMP PEAK 13(7Q22.1) MUTATED`
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 
       11.70        19.56        11.01         9.44         6.97         4.64 
TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       18.35        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        21.11         9.21        24.76        35.24        15.42 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8284 TCGA-BR-8285 
       12.76        18.71        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 
       12.95         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         0.26         5.39        20.22 
TCGA-BR-8487 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4IY 
        1.12        16.44         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        19.36        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5801 TCGA-CD-8527 TCGA-CD-8528 
       20.42         1.15        13.64        13.18         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A48A 
        0.13         0.16         0.13         0.10         3.42        12.43 
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-4441 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4466 
        7.99         4.01        14.01        29.98        12.03        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        7.07        12.00        36.00        12.03        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5733 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 
       79.07        21.07        12.66        11.93        19.13        18.84 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.54        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       12.79        24.72        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EV TCGA-D7-A6F0 
       21.14        20.91        16.44        15.16        11.24         2.96 
TCGA-D7-A6F2 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7998 TCGA-FP-8099 
       15.65        14.47        72.23         3.48        22.29        17.06 
TCGA-FP-8631 TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-A4G2 
        0.56         0.23        26.47         5.92        14.17        24.30 
TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX 
       12.30         3.25        25.81         8.98         0.10        10.19 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RL 
        2.10        12.95        19.36         3.45         3.39         5.19 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 
        1.41         6.44         6.51         5.56         1.81         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI 
       60.56        20.15         9.86        45.67         8.52        61.25 
TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 
        6.08         8.61       122.30        37.91       115.69        57.44 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       48.79        13.25        18.48        35.24        21.73        34.45 
TCGA-VQ-A8P5 TCGA-VQ-A8PB TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PK 
        7.73        34.29        22.19         2.50         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
        1.87        14.33        65.16        36.69        11.70        11.93 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       20.81        22.68         1.71        36.16         7.36         9.50 
TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T 
        2.01         4.54        64.18        21.04        42.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6I 
       18.41        32.94        29.98        17.13        54.12        16.14 
TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11        10.62         0.79 

$`AMP PEAK 13(7Q22.1) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 
       26.70         9.47         6.61         7.43        30.90         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-6458 TCGA-BR-6563 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 
       19.33        39.12        19.89        12.16         8.98        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 
       31.20        32.94        12.82        23.93        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8058 
       15.32        28.73        12.43         3.45         9.07        17.49 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8289 TCGA-BR-8291 
        0.69        12.26         9.60        20.55         2.66        16.31 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8367 TCGA-BR-8368 
        6.18        19.50         0.26        22.19        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        19.17        15.85         3.72        25.18 
TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        9.21        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 
        7.53         0.49        11.54        15.81        15.68         8.22 
TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       12.56         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-BR-A4QL 
       13.51         8.98        12.82         0.66         0.46        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13         2.83         3.25        13.15         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.07         0.07         0.07         0.10         0.10         0.13 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4306 
        9.34        11.31         0.10        12.62         3.02         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 
        8.05        54.08        47.05        19.07        21.99         0.00 
TCGA-CG-4465 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 
        9.01        22.98        30.97         6.97         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
        6.02         0.99       105.07        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6818 
        7.99        12.36        20.55        18.61        17.85        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YY 
       11.31        12.33        16.80        14.27         5.92        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 
       14.76        13.71        11.31        11.44         9.76         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
        4.34         7.40         7.13         0.62         7.99        16.24 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8209 TCGA-FP-8210 
       21.27        11.38        19.53        14.07        59.54         5.03 
TCGA-FP-8211 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
       13.58         5.52        18.08         1.51        14.27        12.59 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 
       11.41        12.10        10.62         0.76         5.59        11.84 
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 
        6.25         0.26        23.84        12.30         9.67         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ 
        8.81        27.42        21.21        18.81        18.38         5.36 
TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
       13.08         6.74        12.59         7.82        13.51         2.53 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZE TCGA-R5-A804 TCGA-R5-A805 
       37.64         3.72        19.73        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-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-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PC 
        5.46        13.02        27.88        32.48        28.96        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PH TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       16.31        12.79         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Y 
       26.24        27.35        64.57        61.22        18.74         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P 
       52.24         9.04        55.43         6.58         5.72         2.66 
TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6G TCGA-VQ-AA6K 
       22.09        40.08        28.41        26.04        12.43 

  AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE 
                         0.07                          0.00 
  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 
                        13.64                         12.43 
[1] "0.1 - 122.3 (13.6)" "0.0 - 116.4 (12.4)"
[1] "hr=" "1"  
D13V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 13(7Q22.1) MUTATED         2        7       20       15        19
  AMP PEAK 13(7Q22.1) WILD-TYPE       1        7       21       16        19
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 13(7Q22.1) MUTATED          20         3         37         32
  AMP PEAK 13(7Q22.1) WILD-TYPE        35         1         48         30
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 13(7Q22.1) MUTATED           20       17
  AMP PEAK 13(7Q22.1) WILD-TYPE         21       29
D13V3, multiclass
            clus
vv           AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE
  STAGE I                              2                             1
  STAGE IA                             7                             7
  STAGE IB                            20                            21
  STAGE II                            15                            16
  STAGE IIA                           19                            19
  STAGE IIB                           20                            35
  STAGE III                            3                             1
  STAGE IIIA                          37                            48
  STAGE IIIB                          32                            30
  STAGE IIIC                          20                            21
  STAGE IV                            17                            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 13(7Q22.1) MUTATED    10  41  93  50
  AMP PEAK 13(7Q22.1) WILD-TYPE  12  49 102  69
D13V4, multiclass
    clus
vv   AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE
  T1                          10                            12
  T2                          41                            49
  T3                          93                           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 13(7Q22.1) MUTATED   65 39 45 42
  AMP PEAK 13(7Q22.1) WILD-TYPE 64 79 39 47
D13V5, multiclass
    clus
vv   AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE
  N0                          65                            64
  N1                          39                            79
  N2                          45                            39
  N3                          42                            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"
D13V6, binary
                               cls
clus                              0   1
  AMP PEAK 13(7Q22.1) MUTATED   178  11
  AMP PEAK 13(7Q22.1) WILD-TYPE 209  19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7Q22.1) MUTATED    178   11
  AMP PEAK 13(7Q22.1) WILD-TYPE  209   19
   clus
vv  AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE
  0                         178                           209
  1                          11                            19
[1] 2 2
[1] FALSE
D13V7, binary
                               cls
clus                              0   1
  AMP PEAK 13(7Q22.1) MUTATED    61 140
  AMP PEAK 13(7Q22.1) WILD-TYPE  97 138
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7Q22.1) MUTATED     61  140
  AMP PEAK 13(7Q22.1) WILD-TYPE   97  138
        clus
vv       AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE
  FEMALE                          61                            97
  MALE                           140                           138
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 13(7Q22.1) MUTATED                                      26
  AMP PEAK 13(7Q22.1) WILD-TYPE                                    45
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 13(7Q22.1) MUTATED                                                       73
  AMP PEAK 13(7Q22.1) WILD-TYPE                                                     89
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 13(7Q22.1) MUTATED                                                                  48
  AMP PEAK 13(7Q22.1) WILD-TYPE                                                                33
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 13(7Q22.1) MUTATED                                                 36
  AMP PEAK 13(7Q22.1) WILD-TYPE                                               42
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 13(7Q22.1) MUTATED                                                          8
  AMP PEAK 13(7Q22.1) WILD-TYPE                                                       13
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 13(7Q22.1) MUTATED                                                           4
  AMP PEAK 13(7Q22.1) WILD-TYPE                                                         4
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 13(7Q22.1) MUTATED                                          5
  AMP PEAK 13(7Q22.1) WILD-TYPE                                        8
D13V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 13(7Q22.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      26
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     73
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          48
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    5
                                                                   clus
vv                                                                  AMP PEAK 13(7Q22.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        45
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       89
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            33
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             42
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      8
[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"
D13V9, binary
                               cls
clus                              0   1
  AMP PEAK 13(7Q22.1) MUTATED     2 199
  AMP PEAK 13(7Q22.1) WILD-TYPE   4 231
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7Q22.1) MUTATED      2  199
  AMP PEAK 13(7Q22.1) WILD-TYPE    4  231
     clus
vv    AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE
  NO                            2                             4
  YES                         199                           231
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 13(7Q22.1) MUTATED   167   4   6  12
  AMP PEAK 13(7Q22.1) WILD-TYPE 180  14  13  13
D13V10, multiclass
    clus
vv   AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE
  R0                         167                           180
  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                         2
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 13(7Q22.1) MUTATED                                           1   125
  AMP PEAK 13(7Q22.1) WILD-TYPE                                         0   149
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                                                             125
                                           clus
vv                                          AMP PEAK 13(7Q22.1) WILD-TYPE
  ASIAN                                                                52
  BLACK OR AFRICAN AMERICAN                                             2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               149
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V13, binary
                               cls
clus                              0   1
  AMP PEAK 13(7Q22.1) MUTATED     3 137
  AMP PEAK 13(7Q22.1) WILD-TYPE   1 176
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7Q22.1) MUTATED      3  137
  AMP PEAK 13(7Q22.1) WILD-TYPE    1  176
                        clus
vv                       AMP PEAK 13(7Q22.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         137
                        clus
vv                       AMP PEAK 13(7Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           176
[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   103  55
  AMP PEAK 14(8P23.1) WILD-TYPE 151  95
  AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE 
                          158                           246 
  AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE 
                           55                            95 
$`AMP PEAK 14(8P23.1) MUTATED`
TCGA-B7-5816 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       26.70        11.01         9.47         6.61         6.97         4.64 
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
       30.90        34.68        15.95        13.87        13.68        19.33 
TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7704 
       25.61        19.89        30.90        31.20        32.94        35.24 
TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7957 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8284 
       23.93        18.15         9.07        11.44        12.26         8.05 
TCGA-BR-8289 TCGA-BR-8297 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8372 
        2.66         7.40         4.31        14.04         3.32        19.17 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8590 
        0.26        15.85         5.39        25.18        20.22         9.34 
TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4J2 
       13.45         7.53        22.26         1.48        13.41        14.17 
TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-CD-5799 
       12.82        19.36         0.46        20.42        11.57         3.25 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8530 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48C 
        0.07         0.07         0.16         0.10         9.34        11.61 
TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4460 
        6.58        12.62        15.95        14.01        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5722 TCGA-CG-5726 
        0.00        18.97         7.07        12.00         0.99        28.96 
TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6524 TCGA-D7-6527 
       65.10        21.07        12.66        11.93        17.85        10.26 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-8576 
       12.79        10.55        11.31        12.33        18.21        14.66 
TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6EX 
       20.91         5.92        15.16        14.76        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-F1-A448 TCGA-FP-7829 
       11.44         2.96         8.38         4.34        21.27        19.53 
TCGA-FP-8099 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8602 
       17.06         5.52        18.08        26.47        14.27        11.41 
TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
       24.30        12.30        11.84        24.20         3.25        25.81 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
       29.98         8.98         0.10         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-A6RL 
       19.36        23.84        12.30         8.88         8.81         5.19 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UJ 
       12.59         5.56        60.56        20.15        37.64        19.73 
TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8N1 
        9.86        45.67        61.25         6.08        16.67       115.69 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8P2 
       35.61        16.87        19.04        48.79         5.46        27.88 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PO 
       28.96        34.29        16.31        22.19         2.70         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91E 
       23.41        26.24        27.35        64.57        14.33        11.93 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A925 
       61.22        18.74        20.81        36.16         7.36         4.54 
TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA6I TCGA-VQ-AA6J 
        5.72        21.04        42.54        22.09        16.14        21.11 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

$`AMP PEAK 14(8P23.1) WILD-TYPE`
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4267 
       11.70        19.56         9.44         7.43        18.35         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6456 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
        9.57         6.61        17.29        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-7196 
       32.78        18.05        12.16         8.98        21.11        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
        9.21        24.76        15.42        28.01        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       12.43         3.45        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 
        0.69         9.60        20.55         0.56        12.95        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
        2.20        15.58         6.18        19.50        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        15.81         6.28 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J6 
       13.51        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        13.64         5.13         2.83 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.15        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
        0.10         0.13         0.10         0.10         0.13         0.13 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 
        3.42        11.31        12.43        12.20         0.10        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4465 TCGA-CG-4475 
        4.01        29.98        47.05        19.07         9.01        22.98 
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-5727 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        79.07         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
        7.99        12.36        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-8570 
       18.61        13.35        17.19        15.22        15.98        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU 
       16.80        19.50        17.19        21.14        14.27        16.44 
TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A74A TCGA-D7-A74B 
       13.78        13.71         9.76        15.65         7.40         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
        0.62         7.99        16.24        14.47        72.23        11.38 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        3.48        14.07        22.29        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A8CX TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        0.56         0.23         1.51         5.92        12.59        14.17 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4GD TCGA-HU-A4GH 
       12.10        10.62         0.76         5.59        22.75        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H6 TCGA-HU-A4HD 
       21.37         6.51         6.25        10.19         9.67        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       21.21         3.45        18.81         3.39        18.38         5.36 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NU 
       13.08         1.41         6.44         6.74         6.51         1.81 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-MX-A5UG TCGA-R5-A7ZE 
        7.82        13.51         2.53         5.56         3.72        18.21 
TCGA-R5-A7ZF TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        8.52         4.60         9.24        11.05         8.61         5.13 
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-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        8.94         5.79         0.92        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PC 
       35.24        21.73        34.45        32.48         7.73        46.26 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A8PS 
        2.50        12.79        17.85         1.87        15.65        13.35 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X 
       65.16        36.69        11.70        22.68         1.71         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
        9.73        52.24         9.04         2.01        55.43         6.58 
TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       64.18         2.66        11.24        18.41        40.08        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6K 
       32.94        29.98        17.13        54.12        26.04        12.43 

  AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE 
                         0.00                          0.07 
  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 
                       13.775                        12.575 
[1] "0.0 - 115.7 (13.8)" "0.1 - 122.3 (12.6)"
[1] "hr=" "1.2"
D14V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 14(8P23.1) MUTATED         1        7       19       13        13
  AMP PEAK 14(8P23.1) WILD-TYPE       2        7       22       18        25
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 14(8P23.1) MUTATED          28         1         32         18
  AMP PEAK 14(8P23.1) WILD-TYPE        27         3         53         44
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 14(8P23.1) MUTATED           15       19
  AMP PEAK 14(8P23.1) WILD-TYPE         26       27
D14V3, multiclass
            clus
vv           AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE
  STAGE I                              1                             2
  STAGE IA                             7                             7
  STAGE IB                            19                            22
  STAGE II                            13                            18
  STAGE IIA                           13                            25
  STAGE IIB                           28                            27
  STAGE III                            1                             3
  STAGE IIIA                          32                            53
  STAGE IIIB                          18                            44
  STAGE IIIC                          15                            26
  STAGE IV                            19                            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 14(8P23.1) MUTATED    11  41  68  49
  AMP PEAK 14(8P23.1) WILD-TYPE  11  49 127  70
D14V4, multiclass
    clus
vv   AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE
  T1                          11                            11
  T2                          41                            49
  T3                          68                           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 30 35
  AMP PEAK 14(8P23.1) WILD-TYPE 78 69 54 54
D14V5, multiclass
    clus
vv   AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE
  N0                          51                            78
  N1                          49                            69
  N2                          30                            54
  N3                          35                            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"
D14V6, binary
                               cls
clus                              0   1
  AMP PEAK 14(8P23.1) MUTATED   159  10
  AMP PEAK 14(8P23.1) WILD-TYPE 228  20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(8P23.1) MUTATED    159   10
  AMP PEAK 14(8P23.1) WILD-TYPE  228   20
   clus
vv  AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE
  0                         159                           228
  1                          10                            20
[1] 2 2
[1] FALSE
D14V7, binary
                               cls
clus                              0   1
  AMP PEAK 14(8P23.1) MUTATED    76  99
  AMP PEAK 14(8P23.1) WILD-TYPE  82 179
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(8P23.1) MUTATED     76   99
  AMP PEAK 14(8P23.1) WILD-TYPE   82  179
        clus
vv       AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE
  FEMALE                          76                            82
  MALE                            99                           179
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 14(8P23.1) MUTATED                                      30
  AMP PEAK 14(8P23.1) WILD-TYPE                                    41
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 14(8P23.1) MUTATED                                                       59
  AMP PEAK 14(8P23.1) WILD-TYPE                                                    103
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 14(8P23.1) MUTATED                                                                  33
  AMP PEAK 14(8P23.1) WILD-TYPE                                                                48
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 14(8P23.1) MUTATED                                                 32
  AMP PEAK 14(8P23.1) WILD-TYPE                                               46
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 14(8P23.1) MUTATED                                                         10
  AMP PEAK 14(8P23.1) WILD-TYPE                                                       11
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 14(8P23.1) MUTATED                                                           5
  AMP PEAK 14(8P23.1) WILD-TYPE                                                         3
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 14(8P23.1) MUTATED                                          5
  AMP PEAK 14(8P23.1) WILD-TYPE                                        8
D14V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 14(8P23.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      30
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     59
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          33
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    5
                                                                   clus
vv                                                                  AMP PEAK 14(8P23.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        41
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      103
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            48
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             46
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      8
[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"
D14V9, binary
                               cls
clus                              0   1
  AMP PEAK 14(8P23.1) MUTATED     4 171
  AMP PEAK 14(8P23.1) WILD-TYPE   2 259
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(8P23.1) MUTATED      4  171
  AMP PEAK 14(8P23.1) WILD-TYPE    2  259
     clus
vv    AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE
  NO                            4                             2
  YES                         171                           259
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 14(8P23.1) MUTATED   137   8   6  14
  AMP PEAK 14(8P23.1) WILD-TYPE 210  10  13  11
D14V10, multiclass
    clus
vv   AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE
  R0                         137                           210
  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                         7
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 14(8P23.1) MUTATED                                           0   110
  AMP PEAK 14(8P23.1) WILD-TYPE                                         1   164
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                                                             110
                                           clus
vv                                          AMP PEAK 14(8P23.1) WILD-TYPE
  ASIAN                                                                54
  BLACK OR AFRICAN AMERICAN                                             7
  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"
D14V13, binary
                               cls
clus                              0   1
  AMP PEAK 14(8P23.1) MUTATED     3 123
  AMP PEAK 14(8P23.1) WILD-TYPE   1 190
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(8P23.1) MUTATED      3  123
  AMP PEAK 14(8P23.1) WILD-TYPE    1  190
                        clus
vv                       AMP PEAK 14(8P23.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         123
                        clus
vv                       AMP PEAK 14(8P23.1) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           190
[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   177 105
  AMP PEAK 15(8Q24.21) WILD-TYPE  77  45
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                           282                            122 
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                           105                             45 
$`AMP PEAK 15(8Q24.21) MUTATED`
TCGA-B7-5816 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 
       26.70        11.01         9.47         9.44         6.97         4.64 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         6.18         9.57        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6707 
       13.87        17.29        13.68         9.17        25.61        19.89 
TCGA-BR-6709 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7197 
       12.16        21.11        30.90        31.20        32.94         9.21 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 
       35.24        23.93        15.42        28.01        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        12.76        18.71        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 
       12.26         9.60         8.05        12.95         2.66         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8367 TCGA-BR-8368 
       15.58         7.40         6.18        13.08        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       14.04         3.32        19.17         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
        5.39         9.21        20.22        12.79         9.34        13.45 
TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U 
        7.53        11.54        16.44         8.22        10.68        13.87 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4J1 TCGA-BR-A4J2 
        7.53        22.26         1.48        13.41         0.72        14.17 
TCGA-BR-A4J5 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5800 
       12.82         0.46        20.42        13.64        11.57        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.30         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.16         0.13         0.13         0.10         3.42         9.34 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       12.43        11.61         6.58        12.62        20.02         3.02 
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-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       29.98        47.05        19.07        12.03        21.99         0.00 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        12.00        22.98         6.97        36.00 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        0.99        12.03        28.96        79.07        65.10         4.01 
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        11.93        19.13 
TCGA-D7-6520 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 
       18.84        17.85        13.35        17.19        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8576 
       12.79        10.55        11.31        12.33        24.72        14.66 
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        15.16        14.76 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        11.44         2.96        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 
        4.34         7.40         0.62         7.99        16.24        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF 
       21.27         3.48        19.53        17.06         0.56         5.52 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
        0.23        18.08        26.47         5.92        14.27        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 
       14.17        11.41         0.76        24.30        12.30        11.84 
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         6.25         0.26         2.10 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       19.36        23.84        12.30         8.88         8.81        27.42 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45         3.39        18.38         5.36         5.19        13.08 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
        1.41         6.44         6.74        12.59         6.51         5.56 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G 
        1.81         7.82         2.53         5.56        60.56        20.15 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       37.64         3.72        19.73         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        61.25         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N4 TCGA-RD-A8N6 TCGA-RD-A8N9 
        8.61        16.67       115.69        71.38         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-A8E7 TCGA-VQ-A8P2 
       13.25        13.02        18.48        35.24        34.45        27.88 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PH 
        7.73        28.96        34.29        16.31        22.19        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PT 
        2.70        17.85         1.87         9.27        23.41        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91S 
       27.35        64.57        36.69        11.93        18.74        22.68 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 
        1.71        36.16         7.36         9.50        52.24         9.04 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R 
        4.54         6.58         5.72        64.18        21.04        42.54 
TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6D 
       11.24        22.09        18.41        40.08        29.98        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       54.12        16.14        21.11        12.43        10.62         0.79 

$`AMP PEAK 15(8Q24.21) WILD-TYPE`
TCGA-B7-5818 TCGA-B7-A5TI TCGA-BR-4183 TCGA-BR-4188 TCGA-BR-4280 TCGA-BR-6458 
       11.70        19.56         6.61         7.43         6.61        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6710 TCGA-BR-7196 
       39.12        26.10        32.78        18.05         8.98        12.82 
TCGA-BR-7703 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8081 
       24.76        15.32        12.43        17.49        11.44        20.55 
TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        0.56        16.31        19.50         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        15.81 
TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-A44T 
        6.28         0.49        15.81         9.86        15.68        12.56 
TCGA-BR-A453 TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J4 TCGA-BR-A4J6 
        6.08        13.51        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 
       19.36        13.51        20.65         1.15         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
        3.25        13.18         0.07         0.13         0.10         0.10 
TCGA-CD-A489 TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4465 
       11.31        12.20         0.10        27.02         1.02         9.01 
TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5725 
       30.97         1.02         0.99         6.02       105.07        15.02 
TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6527 TCGA-D7-8572 
       12.36        20.55        18.54        18.61        10.26        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YY TCGA-D7-A6ET 
       19.50        17.19        18.21        21.14        13.78        13.71 
TCGA-D7-A6EZ TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 
        9.76         7.13        14.47        11.38        14.07        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HU-8238 TCGA-HU-8604 TCGA-HU-8608 
       59.54         5.03        13.58         1.51        12.10        10.62 
TCGA-HU-A4G3 TCGA-HU-A4GJ TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-IN-7806 
        5.59        21.37        10.19        12.95         9.67        21.21 
TCGA-IN-8462 TCGA-IN-AB1X TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       18.81        13.51         5.13       122.30        37.91        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N5 TCGA-VQ-A8E3 TCGA-VQ-A8P3 TCGA-VQ-A8PC TCGA-VQ-A8PF 
      116.38        57.44        21.73        32.48        46.26         2.50 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91K 
       15.65        13.35        14.33        65.16        11.70        61.22 
TCGA-VQ-A91Q TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A94P TCGA-VQ-AA69 
       20.81         9.73         2.01        55.43         2.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6G 
       32.94        26.04 

  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                          0.00                           0.07 
  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 
                        12.605                         13.510 
[1] "0.0 - 115.7 (12.6)" "0.1 - 122.3 (13.5)"
[1] "hr=" "1.1"
D15V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 15(8Q24.21) MUTATED         3       13       28       22        23
  AMP PEAK 15(8Q24.21) WILD-TYPE       0        1       13        9        15
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 15(8Q24.21) MUTATED          40         3         61         38
  AMP PEAK 15(8Q24.21) WILD-TYPE        15         1         24         24
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 15(8Q24.21) MUTATED           28       32
  AMP PEAK 15(8Q24.21) WILD-TYPE         13       14
D15V3, multiclass
            clus
vv           AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  STAGE I                               3                              0
  STAGE IA                             13                              1
  STAGE IB                             28                             13
  STAGE II                             22                              9
  STAGE IIA                            23                             15
  STAGE IIB                            40                             15
  STAGE III                             3                              1
  STAGE IIIA                           61                             24
  STAGE IIIB                           38                             24
  STAGE IIIC                           28                             13
  STAGE IV                             32                             14
[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    21  63 134  78
  AMP PEAK 15(8Q24.21) WILD-TYPE   1  27  61  41
D15V4, multiclass
    clus
vv   AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  T1                           21                              1
  T2                           63                             27
  T3                          134                             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   88 85 54 65
  AMP PEAK 15(8Q24.21) WILD-TYPE 41 33 30 24
D15V5, multiclass
    clus
vv   AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  N0                           88                             41
  N1                           85                             33
  N2                           54                             30
  N3                           65                             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   270  20
  AMP PEAK 15(8Q24.21) WILD-TYPE 117  10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8Q24.21) MUTATED    270   20
  AMP PEAK 15(8Q24.21) WILD-TYPE  117   10
   clus
vv  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  0                          270                            117
  1                           20                             10
[1] 2 2
[1] FALSE
D15V7, binary
                                cls
clus                               0   1
  AMP PEAK 15(8Q24.21) MUTATED   110 195
  AMP PEAK 15(8Q24.21) WILD-TYPE  48  83
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8Q24.21) MUTATED    110  195
  AMP PEAK 15(8Q24.21) WILD-TYPE   48   83
        clus
vv       AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  FEMALE                          110                             48
  MALE                            195                             83
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 15(8Q24.21) MUTATED                                      41
  AMP PEAK 15(8Q24.21) WILD-TYPE                                    30
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 15(8Q24.21) MUTATED                                                      113
  AMP PEAK 15(8Q24.21) WILD-TYPE                                                     49
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 15(8Q24.21) MUTATED                                                                  61
  AMP PEAK 15(8Q24.21) WILD-TYPE                                                                20
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 15(8Q24.21) MUTATED                                                 57
  AMP PEAK 15(8Q24.21) WILD-TYPE                                               21
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 15(8Q24.21) MUTATED                                                         16
  AMP PEAK 15(8Q24.21) WILD-TYPE                                                        5
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 15(8Q24.21) MUTATED                                                           6
  AMP PEAK 15(8Q24.21) WILD-TYPE                                                         2
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 15(8Q24.21) MUTATED                                          9
  AMP PEAK 15(8Q24.21) WILD-TYPE                                        4
D15V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 15(8Q24.21) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       41
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     113
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           61
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            57
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     9
                                                                   clus
vv                                                                  AMP PEAK 15(8Q24.21) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         30
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        49
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             20
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       4
[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"
D15V9, binary
                                cls
clus                               0   1
  AMP PEAK 15(8Q24.21) MUTATED     5 300
  AMP PEAK 15(8Q24.21) WILD-TYPE   1 130
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8Q24.21) MUTATED      5  300
  AMP PEAK 15(8Q24.21) WILD-TYPE    1  130
     clus
vv    AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  NO                             5                              1
  YES                          300                            130
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 15(8Q24.21) MUTATED   239  15  12  20
  AMP PEAK 15(8Q24.21) WILD-TYPE 108   3   7   5
D15V10, multiclass
    clus
vv   AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  R0                          239                            108
  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                        11
  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     190
  AMP PEAK 15(8Q24.21) WILD-TYPE    84
D15V12, multiclass
                                           clus
vv                                          AMP PEAK 15(8Q24.21) MUTATED
  ASIAN                                                               57
  BLACK OR AFRICAN AMERICAN                                           11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              190
                                           clus
vv                                          AMP PEAK 15(8Q24.21) WILD-TYPE
  ASIAN                                                                 31
  BLACK OR AFRICAN AMERICAN                                              0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                 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"
D15V13, binary
                                cls
clus                               0   1
  AMP PEAK 15(8Q24.21) MUTATED     3 214
  AMP PEAK 15(8Q24.21) WILD-TYPE   1  99
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8Q24.21) MUTATED      3  214
  AMP PEAK 15(8Q24.21) WILD-TYPE    1   99
                        clus
vv                       AMP PEAK 15(8Q24.21) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          214
                        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  19
  AMP PEAK 16(9P24.1) WILD-TYPE 216 131
  AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE 
                           57                           347 
  AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE 
                           19                           131 
$`AMP PEAK 16(9P24.1) MUTATED`
TCGA-B7-A5TK TCGA-BR-4267 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-7707 
        9.47         6.18        18.05        19.89        12.16        23.93 
TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8588 
       14.43         9.60         0.56         2.66         2.20        12.79 
TCGA-BR-8678 TCGA-BR-A4IY TCGA-BR-A4J4 TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5801 
       11.54        12.89         0.53        13.64         2.83        13.18 
TCGA-CD-8535 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4460 
        0.13        12.43        12.20         7.99         8.05        21.99 
TCGA-CG-4477 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-A4YT TCGA-D7-A6EY 
       30.97        15.22        10.55        12.33        14.27        11.44 
TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-A8CX TCGA-HF-A5NB 
        0.62        16.24        72.23        21.27         0.23        18.08 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4GD 
       14.17        12.10        10.62         0.76        12.30        22.75 
TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-IN-8663 TCGA-KB-A6F7 
        8.98         2.10        12.95        12.30         3.39        60.56 
TCGA-KB-A93G TCGA-R5-A7ZI TCGA-VQ-A8DU TCGA-VQ-A8PC TCGA-VQ-A8PP TCGA-VQ-A91S 
       20.15        61.25         5.46        46.26        23.41        22.68 
TCGA-VQ-A91V TCGA-VQ-A94T TCGA-VQ-AA6D 
       36.16        11.24        17.13 

$`AMP PEAK 16(9P24.1) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        19.56        11.01         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4279 
        6.97         4.64         7.43        18.35        30.90         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-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        35.24        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 
       18.71        17.49        11.44         0.69        12.26        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        8.05        12.95        16.31        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       19.50        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        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22         1.12        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
        6.08        22.26         1.48        13.41        13.51         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17        12.82         0.66        19.36        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        11.57         5.13 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 
        3.25        13.15         0.30         0.07         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58         0.10        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-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        12.00        22.98         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-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        79.07        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        12.36        12.66        11.93        19.13 
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-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8570 
       17.19        10.26        15.98        12.79        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-A4YY TCGA-D7-A4Z0 
       20.91        16.44         5.92        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       13.71        11.24        11.31         9.76         2.96        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 
        8.38         4.34         7.40         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-A4BF TCGA-HJ-7597 
       59.54         5.03        13.58         0.56         5.52        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-A4G2 
        1.51         5.92        14.27        12.59        11.41        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH 
        5.59        11.84        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         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
        0.26        19.36        23.84         9.67         8.88         8.81 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ 
       27.42        21.21         3.45        18.81        18.38         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
        5.19        13.08         1.41         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         5.56         1.81         7.82        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 
        5.56        37.64         3.72        19.73         9.86        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       18.21         8.52         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-A8DV 
       16.87        19.04         5.79         0.92        48.79        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.02        18.48        35.24        21.73        34.45        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE 
       32.48         7.73        28.96        34.29        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-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       15.65        13.35        26.24        27.35        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       65.16        36.69        11.70        11.93        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       20.81         1.71         7.36         9.50         9.73        52.24 
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-A94U TCGA-VQ-AA64 
       64.18        21.04         2.66        42.54        22.09        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       40.08        28.41        32.94        29.98        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        21.11        12.43        10.62         0.79 

  AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE 
                         0.13                          0.00 
  AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE 
                        72.23                        122.30 
  AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE 
                        12.33                         13.02 
[1] "0.1 - 72.2 (12.3)"  "0.0 - 122.3 (13.0)"
[1] "hr=" "1.1"
D16V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 16(9P24.1) MUTATED         1        3       10        3         6
  AMP PEAK 16(9P24.1) WILD-TYPE       2       11       31       28        32
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 16(9P24.1) MUTATED           5         1         12          9
  AMP PEAK 16(9P24.1) WILD-TYPE        50         3         73         53
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 16(9P24.1) MUTATED            6        5
  AMP PEAK 16(9P24.1) WILD-TYPE         35       41
D16V3, multiclass
            clus
vv           AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE
  STAGE I                              1                             2
  STAGE IA                             3                            11
  STAGE IB                            10                            31
  STAGE II                             3                            28
  STAGE IIA                            6                            32
  STAGE IIB                            5                            50
  STAGE III                            1                             3
  STAGE IIIA                          12                            73
  STAGE IIIB                           9                            53
  STAGE IIIC                           6                            35
  STAGE IV                             5                            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
  AMP PEAK 16(9P24.1) MUTATED     5  16  21  21
  AMP PEAK 16(9P24.1) WILD-TYPE  17  74 174  98
D16V4, multiclass
    clus
vv   AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE
  T1                           5                            17
  T2                          16                            74
  T3                          21                           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  19   7  14
  AMP PEAK 16(9P24.1) WILD-TYPE 107  99  77  75
D16V5, multiclass
    clus
vv   AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE
  N0                          22                           107
  N1                          19                            99
  N2                           7                            77
  N3                          14                            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"
D16V6, binary
                               cls
clus                              0   1
  AMP PEAK 16(9P24.1) MUTATED    57   4
  AMP PEAK 16(9P24.1) WILD-TYPE 330  26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(9P24.1) MUTATED     57    4
  AMP PEAK 16(9P24.1) WILD-TYPE  330   26
   clus
vv  AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE
  0                          57                           330
  1                           4                            26
[1] 2 2
[1] FALSE
D16V7, binary
                               cls
clus                              0   1
  AMP PEAK 16(9P24.1) MUTATED    23  41
  AMP PEAK 16(9P24.1) WILD-TYPE 135 237
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(9P24.1) MUTATED     23   41
  AMP PEAK 16(9P24.1) WILD-TYPE  135  237
        clus
vv       AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE
  FEMALE                          23                           135
  MALE                            41                           237
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 16(9P24.1) MUTATED                                       7
  AMP PEAK 16(9P24.1) WILD-TYPE                                    64
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 16(9P24.1) MUTATED                                                       24
  AMP PEAK 16(9P24.1) WILD-TYPE                                                    138
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 16(9P24.1) MUTATED                                                                   9
  AMP PEAK 16(9P24.1) WILD-TYPE                                                                72
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 16(9P24.1) MUTATED                                                 14
  AMP PEAK 16(9P24.1) WILD-TYPE                                               64
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 16(9P24.1) MUTATED                                                          5
  AMP PEAK 16(9P24.1) WILD-TYPE                                                       16
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 16(9P24.1) MUTATED                                                           2
  AMP PEAK 16(9P24.1) WILD-TYPE                                                         6
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 16(9P24.1) MUTATED                                          3
  AMP PEAK 16(9P24.1) WILD-TYPE                                       10
D16V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 16(9P24.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     24
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           9
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    3
                                                                   clus
vv                                                                  AMP PEAK 16(9P24.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        64
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      138
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            72
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             64
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     10
[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"
D16V9, binary
                               cls
clus                              0   1
  AMP PEAK 16(9P24.1) MUTATED     3  61
  AMP PEAK 16(9P24.1) WILD-TYPE   3 369
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(9P24.1) MUTATED      3   61
  AMP PEAK 16(9P24.1) WILD-TYPE    3  369
     clus
vv    AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE
  NO                            3                             3
  YES                          61                           369
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 16(9P24.1) MUTATED    50   4   2   4
  AMP PEAK 16(9P24.1) WILD-TYPE 297  14  17  21
D16V10, multiclass
    clus
vv   AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE
  R0                          50                           297
  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                         9
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 16(9P24.1) MUTATED                                           0    32
  AMP PEAK 16(9P24.1) WILD-TYPE                                         1   242
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                                                              32
                                           clus
vv                                          AMP PEAK 16(9P24.1) WILD-TYPE
  ASIAN                                                                71
  BLACK OR AFRICAN AMERICAN                                             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               242
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V13, binary
                               cls
clus                              0   1
  AMP PEAK 16(9P24.1) MUTATED     2  45
  AMP PEAK 16(9P24.1) WILD-TYPE   2 268
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(9P24.1) MUTATED      2   45
  AMP PEAK 16(9P24.1) WILD-TYPE    2  268
                        clus
vv                       AMP PEAK 16(9P24.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          45
                        clus
vv                       AMP PEAK 16(9P24.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           268
[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  30
  AMP PEAK 17(9P13.2) WILD-TYPE 200 120
  AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE 
                           84                           320 
  AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE 
                           30                           120 
$`AMP PEAK 17(9P13.2) MUTATED`
TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-7707 TCGA-BR-7717 
        9.47         6.61        19.89        12.16        23.93        18.15 
TCGA-BR-7959 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       18.71         9.60        12.95         2.66        16.31         2.20 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8678 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ 
       20.22        12.79        11.54        13.87         7.53        22.26 
TCGA-BR-A4J4 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-8526 
        0.53        20.42        13.64         2.83        13.18         0.07 
TCGA-CD-8535 TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4444 TCGA-CG-4460 
        0.13        12.20         7.99         8.05        47.05        21.99 
TCGA-CG-4466 TCGA-CG-4477 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.97        30.97        11.93        17.19        10.26        15.22 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A4YT TCGA-D7-A4Z0 TCGA-D7-A6EX 
       10.55        12.33        18.21        14.27        14.76        11.31 
TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A747 TCGA-EQ-5647 TCGA-F1-A448 TCGA-FP-A8CX 
       11.44         2.96         8.38         0.62        21.27         0.23 
TCGA-HF-A5NB TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GP 
       18.08        14.17         0.76        12.30        22.75         8.98 
TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-8663 TCGA-IN-AB1V TCGA-KB-A6F7 
       12.95        12.30         9.67         3.39         7.82        60.56 
TCGA-KB-A93G TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-RD-A8MV TCGA-RD-A8N1 
       20.15        18.21         8.52        61.25       122.30       115.69 
TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8PC TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       35.61        48.79         5.46        46.26         2.70        17.85 
TCGA-VQ-A8PP TCGA-VQ-A8PS TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       23.41        13.35        18.74        20.81        22.68         1.71 
TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA6D TCGA-VQ-AA6F 
        9.50        52.24        64.18        11.24        17.13        54.12 

$`AMP PEAK 17(9P13.2) WILD-TYPE`
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-4267 TCGA-BR-4279 
        4.64         7.43        18.35        30.90         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-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       18.05         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       12.82         9.21        24.76        35.24        15.42        28.01 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 
       17.49        14.43        11.44         0.69        12.26        20.55 
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        19.50 
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        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       10.68        12.56         6.08         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QL 
       19.36        13.51         0.46        20.65         1.15        11.57 
TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        5.13         3.25        13.15         0.30         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61         6.58         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4438 TCGA-CG-4440 
        3.02        27.02        15.95         1.02        54.08         4.01 
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-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        22.98         6.97        36.00         1.02 
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-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
        7.99        12.36        12.66        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6817 
       18.54        18.61        17.85        13.35        15.98        12.79 
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-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        16.44         5.92        15.16        13.78 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A 
       13.71        11.24         9.76        15.65         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
        7.13         7.99        16.24        14.47        72.23        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-A4BF TCGA-HJ-7597 TCGA-HU-8238 
        5.03        13.58         0.56         5.52        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        14.27        12.59        11.41        12.10        10.62 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
       24.30         5.59        11.84        24.20         3.25        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         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H8 
       10.19         0.26         2.10        19.36        23.84         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI 
        8.81        27.42        21.21         3.45        18.81        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR 
        5.36         5.19        13.08         1.41         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 
       12.59         6.51         5.56         1.81        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 
        5.56        37.64         3.72        19.73         9.86        45.67 
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-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       16.67        37.91        40.64       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DV 
        8.94        16.87        19.04         5.79         0.92        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.02        18.48        35.24        21.73        34.45        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE 
       32.48         7.73        28.96        34.29        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PT 
        2.50        12.79         1.87         9.27        15.65        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       27.35        64.57        14.33        65.16        36.69        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A922 
       11.93        61.22        36.16         7.36         9.73         9.04 
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-A94R TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
        2.66        42.54        22.09        18.41        40.08        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        29.98        26.04        16.14        21.11        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

  AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE 
                         0.07                          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 
                       13.265                        12.775 
[1] "0.1 - 122.3 (13.3)" "0.0 - 116.4 (12.8)"
[1] "hr=" "1.2"
D17V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 17(9P13.2) MUTATED         1        4       14        6         4
  AMP PEAK 17(9P13.2) WILD-TYPE       2       10       27       25        34
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 17(9P13.2) MUTATED           8         0         24         13
  AMP PEAK 17(9P13.2) WILD-TYPE        47         4         61         49
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 17(9P13.2) MUTATED            3       10
  AMP PEAK 17(9P13.2) WILD-TYPE         38       36
D17V3, multiclass
            clus
vv           AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE
  STAGE I                              1                             2
  STAGE IA                             4                            10
  STAGE IB                            14                            27
  STAGE II                             6                            25
  STAGE IIA                            4                            34
  STAGE IIB                            8                            47
  STAGE III                            0                             4
  STAGE IIIA                          24                            61
  STAGE IIIB                          13                            49
  STAGE IIIC                           3                            38
  STAGE IV                            10                            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
  AMP PEAK 17(9P13.2) MUTATED     7  23  37  21
  AMP PEAK 17(9P13.2) WILD-TYPE  15  67 158  98
D17V4, multiclass
    clus
vv   AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE
  T1                           7                            15
  T2                          23                            67
  T3                          37                           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    25  30  17  16
  AMP PEAK 17(9P13.2) WILD-TYPE 104  88  67  73
D17V5, multiclass
    clus
vv   AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE
  N0                          25                           104
  N1                          30                            88
  N2                          17                            67
  N3                          16                            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"
D17V6, binary
                               cls
clus                              0   1
  AMP PEAK 17(9P13.2) MUTATED    81   6
  AMP PEAK 17(9P13.2) WILD-TYPE 306  24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9P13.2) MUTATED     81    6
  AMP PEAK 17(9P13.2) WILD-TYPE  306   24
   clus
vv  AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE
  0                          81                           306
  1                           6                            24
[1] 2 2
[1] FALSE
D17V7, binary
                               cls
clus                              0   1
  AMP PEAK 17(9P13.2) MUTATED    36  53
  AMP PEAK 17(9P13.2) WILD-TYPE 122 225
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9P13.2) MUTATED     36   53
  AMP PEAK 17(9P13.2) WILD-TYPE  122  225
        clus
vv       AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE
  FEMALE                          36                           122
  MALE                            53                           225
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 17(9P13.2) MUTATED                                       9
  AMP PEAK 17(9P13.2) WILD-TYPE                                    62
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 17(9P13.2) MUTATED                                                       26
  AMP PEAK 17(9P13.2) WILD-TYPE                                                    136
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 17(9P13.2) MUTATED                                                                  17
  AMP PEAK 17(9P13.2) WILD-TYPE                                                                64
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 17(9P13.2) MUTATED                                                 23
  AMP PEAK 17(9P13.2) WILD-TYPE                                               55
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 17(9P13.2) MUTATED                                                          8
  AMP PEAK 17(9P13.2) WILD-TYPE                                                       13
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 17(9P13.2) MUTATED                                                           3
  AMP PEAK 17(9P13.2) WILD-TYPE                                                         5
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 17(9P13.2) MUTATED                                          3
  AMP PEAK 17(9P13.2) WILD-TYPE                                       10
D17V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 17(9P13.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     26
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           23
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    3
                                                                   clus
vv                                                                  AMP PEAK 17(9P13.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      136
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            64
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             55
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     10
[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"
D17V9, binary
                               cls
clus                              0   1
  AMP PEAK 17(9P13.2) MUTATED     3  86
  AMP PEAK 17(9P13.2) WILD-TYPE   3 344
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9P13.2) MUTATED      3   86
  AMP PEAK 17(9P13.2) WILD-TYPE    3  344
     clus
vv    AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE
  NO                            3                             3
  YES                          86                           344
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 17(9P13.2) MUTATED    73   5   3   3
  AMP PEAK 17(9P13.2) WILD-TYPE 274  13  16  22
D17V10, multiclass
    clus
vv   AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE
  R0                          73                           274
  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                         9
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 17(9P13.2) MUTATED                                           0    52
  AMP PEAK 17(9P13.2) WILD-TYPE                                         1   222
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                                                              52
                                           clus
vv                                          AMP PEAK 17(9P13.2) WILD-TYPE
  ASIAN                                                                71
  BLACK OR AFRICAN AMERICAN                                             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V13, binary
                               cls
clus                              0   1
  AMP PEAK 17(9P13.2) MUTATED     2  58
  AMP PEAK 17(9P13.2) WILD-TYPE   2 255
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9P13.2) MUTATED      2   58
  AMP PEAK 17(9P13.2) WILD-TYPE    2  255
                        clus
vv                       AMP PEAK 17(9P13.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          58
                        clus
vv                       AMP PEAK 17(9P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           255
[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    72  39
  AMP PEAK 18(9Q34.3) WILD-TYPE 182 111
  AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE 
                          111                           293 
  AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE 
                           39                           111 
$`AMP PEAK 18(9Q34.3) MUTATED`
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6564 
        9.47         9.44         6.61        18.35        17.29        26.10 
TCGA-BR-6707 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 
       19.89         9.21        35.24        23.93        15.42        18.15 
TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8360 
       18.71        11.44         9.60         2.66         2.20         6.18 
TCGA-BR-8361 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8682 TCGA-BR-A44U TCGA-BR-A4CQ 
       19.50        20.22        12.79        16.44        13.87        22.26 
TCGA-BR-A4J4 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-CD-5800 TCGA-CD-5801 
        0.53         0.46        20.65        20.42        13.15        13.18 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CG-4301 TCGA-CG-4304 
        0.13         3.42         9.34        12.43         3.02        27.02 
TCGA-CG-4436 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5718 TCGA-D7-5578 TCGA-D7-5579 
        7.99        18.97        30.97        36.00        12.66        11.93 
TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-A4YT TCGA-D7-A4YX 
       17.19        15.22        10.55        11.31        14.27        15.16 
TCGA-D7-A4Z0 TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       14.76        11.31        11.44         9.76         2.96        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 
        8.38         4.34         0.62        16.24        72.23        21.27 
TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8610 
        5.52        18.08        26.47         1.51        14.17         0.76 
TCGA-HU-A4G6 TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H5 TCGA-HU-A4HD 
       12.30        25.81         8.98         6.25        12.30        27.42 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RO TCGA-IN-A6RS TCGA-KB-A6F5 
        3.45        18.81         3.39         1.41        12.59         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-R5-A7O7 TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS 
       60.56        20.15        45.67        61.25         4.60        11.05 
TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E0 
      122.30       115.69        35.61        48.79         5.46        18.48 
TCGA-VQ-A8E7 TCGA-VQ-A8PC TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A91N TCGA-VQ-A91Q 
       34.45        46.26        27.35        14.33        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 
       22.68         1.71        36.16         9.50        52.24         9.04 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6D TCGA-VQ-AA6F 
        5.72        64.18        11.24        40.08        17.13        54.12 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       21.11        12.43         0.79 

$`AMP PEAK 18(9Q34.3) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-BR-4184 TCGA-BR-4187 
       26.70        11.70        19.56        11.01         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        7.43        30.90         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        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7716 
       30.90        31.20        32.94        12.82        24.76        28.01 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43         0.69        12.26        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8362 
        0.56        12.95        16.31        15.58         7.40        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        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 
       15.85         3.72         5.39        25.18         9.21         1.12 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        15.81         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       12.56         7.53         6.08         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       19.36        13.51         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 
        2.83         3.25         0.30         0.07         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG 
        0.10         0.13         0.10        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         0.10        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-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
       19.07        12.03        21.99         0.00         9.01         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       12.00        22.98         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-5727 
        0.99       105.07        12.03        15.02        28.96        79.07 
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        12.36 
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-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8570 
       13.35        10.26        15.98        12.79        12.33        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-A4YY TCGA-D7-A6ET TCGA-D7-A6EV 
       20.91        16.44         5.92        13.78        13.71        11.24 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A72C TCGA-FP-7735 
        7.40         7.13         7.99        14.47        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-8211 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       13.58         0.56         0.23         5.92        14.27        12.59 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 
       11.41        12.10        10.62        24.30         5.59        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        22.75        11.77        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       19.36        23.84         9.67         8.88         8.81        21.21 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38         5.36         5.19        13.08         6.44         6.74 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51         5.56         1.81         7.82        13.51         2.53 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       37.64         3.72        19.73         9.86        18.21         8.52 
TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW 
        6.08         9.24         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-A8E2 
       19.04         5.79         0.92        13.25        13.02        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        27.88        32.48         7.73        28.96        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-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        26.24 
TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       64.57        65.16        36.69        11.70        11.93        61.22 
TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
        7.36         9.73         2.01        55.43         4.54         6.58 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 
       21.04         2.66        42.54        22.09        18.41        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-ZA-A8F6 
       32.94        29.98        26.04        16.14        10.62 

  AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE 
                         0.13                          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 
                        14.27                         12.62 
[1] "0.1 - 122.3 (14.3)" "0.0 - 116.4 (12.6)"
[1] "hr=" "1.3"
D18V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 18(9Q34.3) MUTATED         1        6       14        6         8
  AMP PEAK 18(9Q34.3) WILD-TYPE       2        8       27       25        30
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 18(9Q34.3) MUTATED          16         1         29         13
  AMP PEAK 18(9Q34.3) WILD-TYPE        39         3         56         49
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 18(9Q34.3) MUTATED            7       14
  AMP PEAK 18(9Q34.3) WILD-TYPE         34       32
D18V3, multiclass
            clus
vv           AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE
  STAGE I                              1                             2
  STAGE IA                             6                             8
  STAGE IB                            14                            27
  STAGE II                             6                            25
  STAGE IIA                            8                            30
  STAGE IIB                           16                            39
  STAGE III                            1                             3
  STAGE IIIA                          29                            56
  STAGE IIIB                          13                            49
  STAGE IIIC                           7                            34
  STAGE IV                            14                            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 18(9Q34.3) MUTATED     8  26  54  29
  AMP PEAK 18(9Q34.3) WILD-TYPE  14  64 141  90
D18V4, multiclass
    clus
vv   AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE
  T1                           8                            14
  T2                          26                            64
  T3                          54                           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 37 26 20
  AMP PEAK 18(9Q34.3) WILD-TYPE 95 81 58 69
D18V5, multiclass
    clus
vv   AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE
  N0                          34                            95
  N1                          37                            81
  N2                          26                            58
  N3                          20                            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"
D18V6, binary
                               cls
clus                              0   1
  AMP PEAK 18(9Q34.3) MUTATED   108   9
  AMP PEAK 18(9Q34.3) WILD-TYPE 279  21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(9Q34.3) MUTATED    108    9
  AMP PEAK 18(9Q34.3) WILD-TYPE  279   21
   clus
vv  AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE
  0                         108                           279
  1                           9                            21
[1] 2 2
[1] FALSE
D18V7, binary
                               cls
clus                              0   1
  AMP PEAK 18(9Q34.3) MUTATED    42  79
  AMP PEAK 18(9Q34.3) WILD-TYPE 116 199
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(9Q34.3) MUTATED     42   79
  AMP PEAK 18(9Q34.3) WILD-TYPE  116  199
        clus
vv       AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE
  FEMALE                          42                           116
  MALE                            79                           199
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 18(9Q34.3) MUTATED                                      15
  AMP PEAK 18(9Q34.3) WILD-TYPE                                    56
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 18(9Q34.3) MUTATED                                                       42
  AMP PEAK 18(9Q34.3) WILD-TYPE                                                    120
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 18(9Q34.3) MUTATED                                                                  19
  AMP PEAK 18(9Q34.3) WILD-TYPE                                                                62
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 18(9Q34.3) MUTATED                                                 27
  AMP PEAK 18(9Q34.3) WILD-TYPE                                               51
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 18(9Q34.3) MUTATED                                                          9
  AMP PEAK 18(9Q34.3) WILD-TYPE                                                       12
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 18(9Q34.3) MUTATED                                                           4
  AMP PEAK 18(9Q34.3) WILD-TYPE                                                         4
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 18(9Q34.3) MUTATED                                          5
  AMP PEAK 18(9Q34.3) WILD-TYPE                                        8
D18V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 18(9Q34.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     42
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          19
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           27
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    5
                                                                   clus
vv                                                                  AMP PEAK 18(9Q34.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      120
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            62
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             51
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      8
[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"
D18V9, binary
                               cls
clus                              0   1
  AMP PEAK 18(9Q34.3) MUTATED     3 118
  AMP PEAK 18(9Q34.3) WILD-TYPE   3 312
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(9Q34.3) MUTATED      3  118
  AMP PEAK 18(9Q34.3) WILD-TYPE    3  312
     clus
vv    AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE
  NO                            3                             3
  YES                         118                           312
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 18(9Q34.3) MUTATED    99   6   2   7
  AMP PEAK 18(9Q34.3) WILD-TYPE 248  12  17  18
D18V10, multiclass
    clus
vv   AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE
  R0                          99                           248
  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                         4
  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   198
D18V12, multiclass
                                           clus
vv                                          AMP PEAK 18(9Q34.3) MUTATED
  ASIAN                                                              21
  BLACK OR AFRICAN AMERICAN                                           4
  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                                                               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"
D18V13, binary
                               cls
clus                              0   1
  AMP PEAK 18(9Q34.3) MUTATED     3  81
  AMP PEAK 18(9Q34.3) WILD-TYPE   1 232
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(9Q34.3) MUTATED      3   81
  AMP PEAK 18(9Q34.3) WILD-TYPE    1  232
                        clus
vv                       AMP PEAK 18(9Q34.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          81
                        clus
vv                       AMP PEAK 18(9Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           232
[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    68  43
  AMP PEAK 19(10P11.22) WILD-TYPE 186 107
  AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE 
                            111                             293 
  AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE 
                             43                             107 
$`AMP PEAK 19(10P11.22) MUTATED`
TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6565 TCGA-BR-6801 TCGA-BR-7197 
        6.61        17.29        13.68         9.17        21.11         9.21 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-8077 
       35.24        15.42        28.01        18.15        28.73         0.69 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8483 TCGA-BR-8485 
        2.66         2.20        15.58         7.40         5.39         9.21 
TCGA-BR-8486 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J7 
       20.22        16.44         9.86        12.89         0.72        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5801 TCGA-CD-8524 
       13.51        20.65         1.15        13.64        13.18         0.07 
TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        0.07         0.16         9.34        12.43        11.61        12.20 
TCGA-CG-4300 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-4477 
       20.02         4.01        47.05        21.99        12.00        30.97 
TCGA-CG-5730 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6818 
        4.01        19.13        20.55        17.19        15.22        10.55 
TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A 
       21.14        16.44        11.24        11.31        15.65         7.40 
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-FP-A8CX TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8610 
        0.23         1.51         5.92        14.17        11.41         0.76 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
       12.30        24.20        22.75        25.81        11.77         8.98 
TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7808 
        6.25        12.95        23.84         9.67        27.42         3.45 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RR TCGA-IN-A7NR TCGA-KB-A93H TCGA-MX-A663 
        3.39        18.38         6.74         6.51        37.64         9.86 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7C1 
       45.67        18.21         6.08        11.05         8.61        16.67 
TCGA-RD-A8MV TCGA-VQ-A8DU TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE 
      122.30         5.46        21.73         7.73        46.26        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91E 
       12.79        17.85        64.57        14.33        36.69        11.93 
TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A94O 
       18.74        22.68         1.71         9.50         9.04        21.04 
TCGA-VQ-A94U TCGA-VQ-AA6I TCGA-VQ-AA6J 
       22.09        16.14        21.11 

$`AMP PEAK 19(10P11.22) WILD-TYPE`
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-4191 TCGA-BR-4201 TCGA-BR-4267 
        6.97         4.64         7.43        18.35        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6458 
        9.57         6.61        34.68        15.95        13.87        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10        32.78        25.61        18.05        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        32.94        12.82 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       24.76        23.93        15.32        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 
       12.76        18.71        17.49        14.43        11.44        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 
        9.60        20.55         8.05         0.56        12.95        16.31 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        19.50        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-8484 
       19.17        14.79         0.26        15.85         3.72        25.18 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 
        7.53         0.49        11.54        15.81        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
        1.48        13.41        13.51         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM 
       12.82         0.66         0.46        20.42        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 
        2.83         3.25        13.15         0.30         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.07         0.10         0.13         0.10         0.10         0.13 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI 
        0.13         0.10         3.42        11.31         6.58         0.10 
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-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
        8.05        54.08        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        22.98         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-5727 TCGA-CG-5728 TCGA-CG-5732 
       12.03        15.02        28.96        79.07        65.10        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 
       21.07         7.99        12.36        12.66        11.93        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-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.79        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       17.19        18.21        14.66        20.91        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ 
       15.16        13.78        14.76        13.71        11.44         9.76 
TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 
        2.96         8.38         4.34         7.13        16.24        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-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 
       13.58         0.56         5.52        18.08        26.47        14.27 
TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 
       12.59        12.10        10.62        24.30         5.59        11.84 
TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
        3.25        21.37        29.98         0.10         6.51        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB 
        0.26         2.10        19.36        12.30         8.88         8.81 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO 
       21.21        18.81         5.36         5.19        13.08         1.41 
TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
        6.44        12.59         5.56         1.81         7.82        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        60.56        20.15         3.72        19.73 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BW TCGA-RD-A8MW 
        8.52        61.25         4.60         9.24         5.13        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-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.25        13.02        18.48        35.24        34.45        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PJ 
       32.48        28.96        34.29        16.31         2.50         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        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91V 
       27.35        65.16        11.70        61.22        20.81        36.16 
TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        7.36         9.73        52.24         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
        6.58         5.72        64.18         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        40.08        28.41        32.94        29.98        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       54.12        26.04        12.43        10.62         0.79 

  AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE 
                           0.07                            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 
                          12.95                           12.79 
[1] "0.1 - 122.3 (12.9)" "0.0 - 116.4 (12.8)"
[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        7        4        12
  AMP PEAK 19(10P11.22) WILD-TYPE       2        7       34       27        26
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 19(10P11.22) MUTATED          20         2         23         20
  AMP PEAK 19(10P11.22) WILD-TYPE        35         2         62         42
                                 vv
clus                              STAGE IIIC STAGE IV
  AMP PEAK 19(10P11.22) MUTATED            7       13
  AMP PEAK 19(10P11.22) WILD-TYPE         34       33
D19V3, multiclass
            clus
vv           AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE
  STAGE I                                1                               2
  STAGE IA                               7                               7
  STAGE IB                               7                              34
  STAGE II                               4                              27
  STAGE IIA                             12                              26
  STAGE IIB                             20                              35
  STAGE III                              2                               2
  STAGE IIIA                            23                              62
  STAGE IIIB                            20                              42
  STAGE IIIC                             7                              34
  STAGE IV                              13                              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 19(10P11.22) MUTATED     7  17  63  30
  AMP PEAK 19(10P11.22) WILD-TYPE  15  73 132  89
D19V4, multiclass
    clus
vv   AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE
  T1                             7                              15
  T2                            17                              73
  T3                            63                             132
  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   38 30 23 24
  AMP PEAK 19(10P11.22) WILD-TYPE 91 88 61 65
D19V5, multiclass
    clus
vv   AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE
  N0                            38                              91
  N1                            30                              88
  N2                            23                              61
  N3                            24                              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"
D19V6, binary
                                 cls
clus                                0   1
  AMP PEAK 19(10P11.22) MUTATED   104   8
  AMP PEAK 19(10P11.22) WILD-TYPE 283  22
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(10P11.22) MUTATED    104    8
  AMP PEAK 19(10P11.22) WILD-TYPE  283   22
   clus
vv  AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE
  0                           104                             283
  1                             8                              22
[1] 2 2
[1] FALSE
D19V7, binary
                                 cls
clus                                0   1
  AMP PEAK 19(10P11.22) MUTATED    44  74
  AMP PEAK 19(10P11.22) WILD-TYPE 114 204
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(10P11.22) MUTATED     44   74
  AMP PEAK 19(10P11.22) WILD-TYPE  114  204
        clus
vv       AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE
  FEMALE                            44                             114
  MALE                              74                             204
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 19(10P11.22) MUTATED                                      14
  AMP PEAK 19(10P11.22) WILD-TYPE                                    57
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 19(10P11.22) MUTATED                                                       42
  AMP PEAK 19(10P11.22) WILD-TYPE                                                    120
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 19(10P11.22) MUTATED                                                                  23
  AMP PEAK 19(10P11.22) WILD-TYPE                                                                58
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 19(10P11.22) MUTATED                                                 30
  AMP PEAK 19(10P11.22) WILD-TYPE                                               48
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 19(10P11.22) MUTATED                                                          4
  AMP PEAK 19(10P11.22) WILD-TYPE                                                       17
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 19(10P11.22) MUTATED                                                           1
  AMP PEAK 19(10P11.22) WILD-TYPE                                                         7
                                 vv
clus                              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 19(10P11.22) MUTATED                                          3
  AMP PEAK 19(10P11.22) WILD-TYPE                                       10
D19V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 19(10P11.22) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        14
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       42
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            23
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             30
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      3
                                                                   clus
vv                                                                  AMP PEAK 19(10P11.22) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          57
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        120
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              58
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               48
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       10
[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"
D19V9, binary
                                 cls
clus                                0   1
  AMP PEAK 19(10P11.22) MUTATED     3 115
  AMP PEAK 19(10P11.22) WILD-TYPE   3 315
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(10P11.22) MUTATED      3  115
  AMP PEAK 19(10P11.22) WILD-TYPE    3  315
     clus
vv    AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE
  NO                              3                               3
  YES                           115                             315
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 19(10P11.22) MUTATED    97   3   5   5
  AMP PEAK 19(10P11.22) WILD-TYPE 250  15  14  20
D19V10, multiclass
    clus
vv   AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE
  R0                            97                             250
  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                         5
                                 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      67
  AMP PEAK 19(10P11.22) WILD-TYPE   207
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                                                                67
                                           clus
vv                                          AMP PEAK 19(10P11.22) WILD-TYPE
  ASIAN                                                                  57
  BLACK OR AFRICAN AMERICAN                                               5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               0
  WHITE                                                                 207
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V13, binary
                                 cls
clus                                0   1
  AMP PEAK 19(10P11.22) MUTATED     1  86
  AMP PEAK 19(10P11.22) WILD-TYPE   3 227
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(10P11.22) MUTATED      1   86
  AMP PEAK 19(10P11.22) WILD-TYPE    3  227
                        clus
vv                       AMP PEAK 19(10P11.22) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            86
                        clus
vv                       AMP PEAK 19(10P11.22) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             227
[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    50  35
  AMP PEAK 20(10Q22.2) WILD-TYPE 204 115
  AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE 
                            85                            319 
  AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE 
                            35                            115 
$`AMP PEAK 20(10Q22.2) MUTATED`
TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-7197 
        6.61        18.35        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        15.42        18.15        14.43         0.69        12.95 
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        16.44 
TCGA-BR-8683 TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PF 
        9.86        12.89         0.72        19.36        20.65         1.15 
TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8530 TCGA-CD-8533 TCGA-CG-4300 TCGA-CG-4444 
       13.18         0.07         0.16         0.13        20.02        47.05 
TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4477 TCGA-CG-5732 TCGA-D7-6519 TCGA-D7-6520 
       19.07        21.99        30.97        69.04        20.55        18.84 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6EX 
       10.55        12.33        18.21        16.44        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A74A TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-8631 TCGA-HU-8238 
        9.76         7.40        16.24        72.23         0.56         1.51 
TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GP TCGA-HU-A4GU 
       11.41         0.76        12.30        24.20         8.98         6.25 
TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RN 
       12.95         9.67        27.42         3.45         3.39        13.08 
TCGA-IN-A6RP TCGA-IN-A7NU TCGA-R5-A7ZE TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        6.44         1.81        18.21         9.24        11.05         8.61 
TCGA-RD-A8MV TCGA-RD-A8N9 TCGA-VQ-A8E3 TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PM 
      122.30        35.61        21.73        46.26        12.79         1.87 
TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91E 
       13.35        27.35        64.57        14.33        36.69        11.93 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94U 
       18.74        20.81         4.54         5.72        64.18        22.09 
TCGA-VQ-AA64 
       18.41 

$`AMP PEAK 20(10Q22.2) WILD-TYPE`
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-4267 TCGA-BR-4279 
        6.97         4.64         7.43        30.90         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-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        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       24.76        23.93        28.01        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 
        3.45         9.07        12.76        18.71        17.49        11.44 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 
       12.26         9.60        20.55         8.05         0.56        16.31 
TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        2.20         6.18        19.50        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 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
        6.08        22.26         1.48        13.41        13.51         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
       14.17         0.53        12.82         0.66        13.51         0.46 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.15         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.10         0.13         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20         0.10        12.62         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
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-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        22.98         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-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10         4.01        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       12.66        11.93        19.13        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
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-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       14.76        13.71        11.44         2.96        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 
        4.34         7.13         0.62         7.99        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-8211 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB 
       59.54         5.03        13.58         5.52         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
       26.47         5.92        14.27        12.59        14.17        12.10 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD 
       10.62        24.30         5.59        11.84         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-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
       10.19         0.26         2.10        19.36        23.84        12.30 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ 
        8.88         8.81        21.21        18.81        18.38         5.36 
TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
        5.19         1.41         6.74        12.59         6.51         5.56 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G 
        7.82        13.51         2.53         5.56        60.56        20.15 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZF 
       37.64         3.72        19.73         9.86        45.67         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW 
       61.25         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        35.24        34.45        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE 
       32.48         7.73        28.96        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 
       26.24        65.16        11.70        61.22        22.68         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       36.16         7.36         9.50         9.73        52.24         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        40.08        28.41        32.94        29.98        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        21.11        12.43        10.62 
TCGA-ZQ-A9CR 
        0.79 

  AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE 
                          0.07                           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 
                         13.18                          12.66 
[1] "0.1 - 122.3 (13.2)" "0.0 - 116.4 (12.7)"
[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       3        9       37       23        35
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 20(10Q22.2) MUTATED          11         2         22         16
  AMP PEAK 20(10Q22.2) WILD-TYPE        44         2         63         46
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 20(10Q22.2) MUTATED            6       10
  AMP PEAK 20(10Q22.2) WILD-TYPE         35       36
D20V3, multiclass
            clus
vv           AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE
  STAGE I                               0                              3
  STAGE IA                              5                              9
  STAGE IB                              4                             37
  STAGE II                              8                             23
  STAGE IIA                             3                             35
  STAGE IIB                            11                             44
  STAGE III                             2                              2
  STAGE IIIA                           22                             63
  STAGE IIIB                           16                             46
  STAGE IIIC                            6                             35
  STAGE IV                             10                             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
  AMP PEAK 20(10Q22.2) MUTATED     6  15  43  23
  AMP PEAK 20(10Q22.2) WILD-TYPE  16  75 152  96
D20V4, multiclass
    clus
vv   AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE
  T1                            6                             16
  T2                           15                             75
  T3                           43                            152
  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  19
  AMP PEAK 20(10Q22.2) WILD-TYPE 106  97  60  70
D20V5, multiclass
    clus
vv   AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE
  N0                           23                            106
  N1                           21                             97
  N2                           24                             60
  N3                           19                             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"
D20V6, binary
                                cls
clus                               0   1
  AMP PEAK 20(10Q22.2) MUTATED    82   3
  AMP PEAK 20(10Q22.2) WILD-TYPE 305  27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(10Q22.2) MUTATED     82    3
  AMP PEAK 20(10Q22.2) WILD-TYPE  305   27
   clus
vv  AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE
  0                           82                            305
  1                            3                             27
[1] 2 2
[1] FALSE
D20V7, binary
                                cls
clus                               0   1
  AMP PEAK 20(10Q22.2) MUTATED    32  56
  AMP PEAK 20(10Q22.2) WILD-TYPE 126 222
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(10Q22.2) MUTATED     32   56
  AMP PEAK 20(10Q22.2) WILD-TYPE  126  222
        clus
vv       AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE
  FEMALE                           32                            126
  MALE                             56                            222
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 20(10Q22.2) MUTATED                                      12
  AMP PEAK 20(10Q22.2) WILD-TYPE                                    59
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 20(10Q22.2) MUTATED                                                       28
  AMP PEAK 20(10Q22.2) WILD-TYPE                                                    134
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 20(10Q22.2) MUTATED                                                                  18
  AMP PEAK 20(10Q22.2) WILD-TYPE                                                                63
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 20(10Q22.2) MUTATED                                                 21
  AMP PEAK 20(10Q22.2) WILD-TYPE                                               57
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 20(10Q22.2) MUTATED                                                          4
  AMP PEAK 20(10Q22.2) WILD-TYPE                                                       17
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 20(10Q22.2) MUTATED                                                           2
  AMP PEAK 20(10Q22.2) WILD-TYPE                                                         6
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 20(10Q22.2) MUTATED                                          3
  AMP PEAK 20(10Q22.2) WILD-TYPE                                       10
D20V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 20(10Q22.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      28
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           18
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     3
                                                                   clus
vv                                                                  AMP PEAK 20(10Q22.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             63
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              57
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      10
[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"
D20V9, binary
                                cls
clus                               0   1
  AMP PEAK 20(10Q22.2) MUTATED     2  86
  AMP PEAK 20(10Q22.2) WILD-TYPE   4 344
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(10Q22.2) MUTATED      2   86
  AMP PEAK 20(10Q22.2) WILD-TYPE    4  344
     clus
vv    AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE
  NO                             2                              4
  YES                           86                            344
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 20(10Q22.2) MUTATED    77   1   3   4
  AMP PEAK 20(10Q22.2) WILD-TYPE 270  17  16  21
D20V10, multiclass
    clus
vv   AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE
  R0                           77                            270
  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      20                         1
  AMP PEAK 20(10Q22.2) WILD-TYPE    68                        10
                                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      56
  AMP PEAK 20(10Q22.2) WILD-TYPE   218
D20V12, multiclass
                                           clus
vv                                          AMP PEAK 20(10Q22.2) MUTATED
  ASIAN                                                               20
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               56
                                           clus
vv                                          AMP PEAK 20(10Q22.2) WILD-TYPE
  ASIAN                                                                 68
  BLACK OR AFRICAN AMERICAN                                             10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V13, binary
                                cls
clus                               0   1
  AMP PEAK 20(10Q22.2) MUTATED     0  64
  AMP PEAK 20(10Q22.2) WILD-TYPE   4 249
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(10Q22.2) MUTATED      0   64
  AMP PEAK 20(10Q22.2) WILD-TYPE    4  249
                        clus
vv                       AMP PEAK 20(10Q22.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           64
                        clus
vv                       AMP PEAK 20(10Q22.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            249
[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    50  34
  AMP PEAK 21(10Q26.13) WILD-TYPE 204 116
  AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE 
                             84                             320 
  AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE 
                             34                             116 
$`AMP PEAK 21(10Q26.13) MUTATED`
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6564 
        6.61         4.64        18.35        17.29        13.68        26.10 
TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-8077 
       31.20         9.21        35.24        15.42        28.01         0.69 
TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8682 
        9.60        12.95         2.66        15.58         7.40        16.44 
TCGA-BR-A4J1 TCGA-BR-A4J7 TCGA-BR-A4PF TCGA-CD-5801 TCGA-CD-8525 TCGA-CD-8527 
        0.72        19.36         1.15        13.18         0.07         0.07 
TCGA-CD-8530 TCGA-CD-8533 TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4443 TCGA-CG-4449 
        0.16         0.13        20.02        27.02        29.98        19.07 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5730 TCGA-CG-5732 
        7.07        12.00        30.97        36.00         4.01        69.04 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-8572 
       20.55        18.84        17.19        15.22        10.55        16.80 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-EQ-5647 
       14.27        16.44        11.24        11.31         9.76         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-8099 TCGA-HU-8238 TCGA-HU-8602 
        7.99        72.23         3.48        17.06         1.51        11.41 
TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GY TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.76        12.30        24.20         0.26        12.30         9.67 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RP TCGA-KB-A6F5 TCGA-R5-A7ZE TCGA-R5-A7ZR 
        3.39        18.38         6.44         5.56        18.21         6.08 
TCGA-RD-A7BS TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8PC TCGA-VQ-A8PH 
       11.05         5.46        18.48        21.73        46.26        12.79 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       64.57        14.33        11.93        18.74        20.81        22.68 
TCGA-VQ-A91Y TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94U TCGA-VQ-AA64 
        9.73         4.54         5.72        64.18        22.09        18.41 

$`AMP PEAK 21(10Q26.13) WILD-TYPE`
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-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        6.97         7.43        30.90         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 
       34.68        15.95        13.87        19.33        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-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 
       21.11        30.90        32.94        12.82        24.76        23.93 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       18.15        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 
       12.76        18.71        17.49        14.43        11.44        12.26 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8360 
       20.55         8.05         0.56        16.31         2.20         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       19.50        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        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         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        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
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        12.82         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        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13         2.83         3.25        13.15         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.07         0.10         0.13         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         3.42         9.34        11.31        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         0.10        12.62         3.02 
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-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       14.01        47.05        12.03        21.99         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       18.97        22.98         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-5727 
        0.99       105.07        12.03        15.02        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       65.10        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 
       19.13        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-D7-8573 
       15.98        12.79        11.31        12.33        24.72        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YV 
       17.19        18.21        14.66        21.14        20.91         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6F0 
       15.16        13.78        14.76        13.71        11.44         2.96 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-A4SO 
       15.65         8.38         4.34         7.40         7.13        16.24 
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-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX 
       59.54         5.03        13.58         0.56         5.52         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
       18.08        26.47         5.92        14.27        12.59        14.17 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GC 
       12.10        10.62        24.30         5.59        11.84         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         6.25        10.19         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       19.36        23.84         8.88         8.81        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO 
        3.45        18.81         5.36         5.19        13.08         1.41 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51         5.56         1.81         7.82 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG 
       13.51         2.53        60.56        20.15        37.64         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
       19.73         9.86        45.67         8.52        61.25         4.60 
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-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-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        35.24        34.45        27.88        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
        7.73        28.96        34.29        16.31        22.19         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-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       13.35        26.24        27.35        65.16        36.69        11.70 
TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z 
       61.22         1.71        36.16         7.36         9.50        52.24 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A94O TCGA-VQ-A94P 
        9.04         2.01        55.43         6.58        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       42.54        11.24        40.08        28.41        32.94        29.98 
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        21.11        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

  AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE 
                           0.07                            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 
                         13.065                          12.805 
[1] "0.1 - 72.2 (13.1)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
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       2        8       34       23        33
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 21(10Q26.13) MUTATED          10         1         22         10
  AMP PEAK 21(10Q26.13) WILD-TYPE        45         3         63         52
                                 vv
clus                              STAGE IIIC STAGE IV
  AMP PEAK 21(10Q26.13) MUTATED            5       10
  AMP PEAK 21(10Q26.13) WILD-TYPE         36       36
D21V3, multiclass
            clus
vv           AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE
  STAGE I                                1                               2
  STAGE IA                               6                               8
  STAGE IB                               7                              34
  STAGE II                               8                              23
  STAGE IIA                              5                              33
  STAGE IIB                             10                              45
  STAGE III                              1                               3
  STAGE IIIA                            22                              63
  STAGE IIIB                            10                              52
  STAGE IIIC                             5                              36
  STAGE IV                              10                              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
  AMP PEAK 21(10Q26.13) MUTATED     7  20  39  19
  AMP PEAK 21(10Q26.13) WILD-TYPE  15  70 156 100
D21V4, multiclass
    clus
vv   AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE
  T1                             7                              15
  T2                            20                              70
  T3                            39                             156
  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 101  98  63  74
D21V5, multiclass
    clus
vv   AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE
  N0                            28                             101
  N1                            20                              98
  N2                            21                              63
  N3                            15                              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"
D21V6, binary
                                 cls
clus                                0   1
  AMP PEAK 21(10Q26.13) MUTATED    81   3
  AMP PEAK 21(10Q26.13) WILD-TYPE 306  27
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(10Q26.13) MUTATED     81    3
  AMP PEAK 21(10Q26.13) WILD-TYPE  306   27
   clus
vv  AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE
  0                            81                             306
  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 125 223
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(10Q26.13) MUTATED     33   55
  AMP PEAK 21(10Q26.13) WILD-TYPE  125  223
        clus
vv       AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE
  FEMALE                            33                             125
  MALE                              55                             223
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 21(10Q26.13) MUTATED                                       9
  AMP PEAK 21(10Q26.13) WILD-TYPE                                    62
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 21(10Q26.13) MUTATED                                                       29
  AMP PEAK 21(10Q26.13) WILD-TYPE                                                    133
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 21(10Q26.13) MUTATED                                                                  18
  AMP PEAK 21(10Q26.13) WILD-TYPE                                                                63
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 21(10Q26.13) MUTATED                                                 21
  AMP PEAK 21(10Q26.13) WILD-TYPE                                               57
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 21(10Q26.13) MUTATED                                                          5
  AMP PEAK 21(10Q26.13) WILD-TYPE                                                       16
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 21(10Q26.13) MUTATED                                                           3
  AMP PEAK 21(10Q26.13) WILD-TYPE                                                         5
                                 vv
clus                              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 21(10Q26.13) MUTATED                                          2
  AMP PEAK 21(10Q26.13) WILD-TYPE                                       11
D21V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 21(10Q26.13) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       29
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            18
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      2
                                                                   clus
vv                                                                  AMP PEAK 21(10Q26.13) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              63
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               57
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       11
[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"
D21V9, binary
                                 cls
clus                                0   1
  AMP PEAK 21(10Q26.13) MUTATED     2  86
  AMP PEAK 21(10Q26.13) WILD-TYPE   4 344
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(10Q26.13) MUTATED      2   86
  AMP PEAK 21(10Q26.13) WILD-TYPE    4  344
     clus
vv    AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE
  NO                              2                               4
  YES                            86                             344
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 21(10Q26.13) MUTATED    73   2   4   6
  AMP PEAK 21(10Q26.13) WILD-TYPE 274  16  15  19
D21V10, multiclass
    clus
vv   AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE
  R0                            73                             274
  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                         6
                                 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   222
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                                               6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V13, binary
                                 cls
clus                                0   1
  AMP PEAK 21(10Q26.13) MUTATED     0  59
  AMP PEAK 21(10Q26.13) WILD-TYPE   4 254
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(10Q26.13) MUTATED      0   59
  AMP PEAK 21(10Q26.13) WILD-TYPE    4  254
                        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                                   4
  NOT HISPANIC OR LATINO                             254
[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    44  35
  AMP PEAK 22(11P13) WILD-TYPE 210 115
  AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE 
                          79                          325 
  AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE 
                          35                          115 
$`AMP PEAK 22(11P13) MUTATED`
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6458 
       11.70        11.01         9.44        13.87        17.29        19.33 
TCGA-BR-6564 TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       26.10        18.15         3.45        11.44         0.69         9.60 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8485 TCGA-BR-8590 TCGA-BR-8678 TCGA-BR-8686 
       15.58         7.40         9.21         9.34        11.54        15.68 
TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J2 TCGA-BR-A4J8 
       12.56         6.08        22.26        12.89        14.17        13.51 
TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-A487 TCGA-CD-A4MH 
        0.07         0.10         0.16         0.13         9.34        12.20 
TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5722 
       20.02        54.08        19.07        12.00         6.97         0.99 
TCGA-D7-6822 TCGA-D7-8576 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-FP-7916 TCGA-FP-8099 
       12.33        14.66         0.62         7.99        14.07        17.06 
TCGA-FP-8631 TCGA-FP-A8CX TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-A4G2 TCGA-HU-A4HD 
        0.56         0.23         5.92        14.17        24.30        27.42 
TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RO TCGA-IN-A7NT TCGA-IN-A7NU 
        3.45        18.38         5.36         1.41         5.56         1.81 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-RD-A7BT TCGA-RD-A7C1 
        5.56        37.64        18.21        61.25         8.61        16.67 
TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
      115.69        57.44         5.46        13.02        18.48        35.24 
TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91S TCGA-VQ-A91X 
       22.19         2.70        27.35        64.57        22.68         9.50 
TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A94U TCGA-VQ-AA6B TCGA-VQ-AA6F 
        9.73         9.04         4.54        22.09        29.98        54.12 
TCGA-VQ-AA6K 
       12.43 

$`AMP PEAK 22(11P13) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       26.70        19.56         9.47         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        7.43        18.35        30.90         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 
       34.68        15.95        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        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       35.24        23.93        15.42        28.01        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       12.43         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       12.26        20.55         8.05         0.56        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       16.31         2.20         6.18        19.50        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        19.17        14.79         0.26        15.85 
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-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
       15.81        13.45         6.28         7.53         0.49        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 
       16.44         9.86         8.22        10.68        13.87         7.53 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 
        1.48        13.41        13.51         8.98         0.72         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
       12.82         0.66        19.36         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        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 
       13.15        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.07         0.13         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI 
        3.42        11.31        12.43        11.61         6.58         0.10 
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-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 
        8.05         4.01        14.01        29.98        47.05        12.03 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       21.99         0.00         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 
       30.97        36.00         1.02         0.99         6.02       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
       12.03        15.02        28.96        79.07        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        12.36        12.66        11.93 
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-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       10.55        11.31        24.72        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-A6EX 
       15.16        13.78        14.76        13.71        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44         9.76         2.96        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.40         7.13        16.24        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-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 
       13.58         5.52        18.08        26.47         1.51        14.27 
TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 
       12.59        11.41        12.10        10.62         0.76         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        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 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       23.84        12.30         9.67         8.88         8.81        21.21 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.81         3.39         5.19        13.08         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 
       12.59         6.51         7.82        13.51         2.53        60.56 
TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZF 
       20.15         3.72        19.73         9.86        45.67         8.52 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV 
        6.08         4.60         9.24        11.05         5.13       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N6 TCGA-RD-A8N9 
       37.91        40.64       116.38        71.38         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-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        34.45        27.88        32.48         7.73        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK 
       34.29        46.26        16.31         2.50        12.79        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        26.24 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        65.16        36.69        11.70        11.93        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Z 
       18.74        20.81         1.71        36.16         7.36        52.24 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O 
        2.01        55.43         6.58         5.72        64.18        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        40.08        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       32.94        17.13        26.04        16.14        21.11        10.62 
TCGA-ZQ-A9CR 
        0.79 

  AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE 
                        0.07                         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 
                       12.33                        12.95 
[1] "0.1 - 115.7 (12.3)" "0.0 - 122.3 (12.9)"
[1] "hr=" "1.3"
D22V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 22(11P13) MUTATED         1        2        6        4         3
  AMP PEAK 22(11P13) WILD-TYPE       2       12       35       27        35
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 22(11P13) MUTATED          15         1         17         10
  AMP PEAK 22(11P13) WILD-TYPE        40         3         68         52
                              vv
clus                           STAGE IIIC STAGE IV
  AMP PEAK 22(11P13) MUTATED           11       13
  AMP PEAK 22(11P13) WILD-TYPE         30       33
D22V3, multiclass
            clus
vv           AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE
  STAGE I                             1                            2
  STAGE IA                            2                           12
  STAGE IB                            6                           35
  STAGE II                            4                           27
  STAGE IIA                           3                           35
  STAGE IIB                          15                           40
  STAGE III                           1                            3
  STAGE IIIA                         17                           68
  STAGE IIIB                         10                           52
  STAGE IIIC                         11                           30
  STAGE IV                           13                           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 22(11P13) MUTATED     4   9  40  31
  AMP PEAK 22(11P13) WILD-TYPE  18  81 155  88
D22V4, multiclass
    clus
vv   AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE
  T1                          4                           18
  T2                          9                           81
  T3                         40                          155
  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    18  25  21  18
  AMP PEAK 22(11P13) WILD-TYPE 111  93  63  71
D22V5, multiclass
    clus
vv   AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE
  N0                         18                          111
  N1                         25                           93
  N2                         21                           63
  N3                         18                           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"
D22V6, binary
                              cls
clus                             0   1
  AMP PEAK 22(11P13) MUTATED    74   7
  AMP PEAK 22(11P13) WILD-TYPE 313  23
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(11P13) MUTATED     74    7
  AMP PEAK 22(11P13) WILD-TYPE  313   23
   clus
vv  AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE
  0                         74                          313
  1                          7                           23
[1] 2 2
[1] FALSE
D22V7, binary
                              cls
clus                             0   1
  AMP PEAK 22(11P13) MUTATED    26  61
  AMP PEAK 22(11P13) WILD-TYPE 132 217
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(11P13) MUTATED     26   61
  AMP PEAK 22(11P13) WILD-TYPE  132  217
        clus
vv       AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE
  FEMALE                         26                          132
  MALE                           61                          217
[1] 2 2
[1] FALSE
                              vv
clus                           STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 22(11P13) MUTATED                                      13
  AMP PEAK 22(11P13) WILD-TYPE                                    58
                              vv
clus                           STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 22(11P13) MUTATED                                                       32
  AMP PEAK 22(11P13) WILD-TYPE                                                    130
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 22(11P13) MUTATED                                                                  14
  AMP PEAK 22(11P13) WILD-TYPE                                                                67
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 22(11P13) MUTATED                                                 17
  AMP PEAK 22(11P13) WILD-TYPE                                               61
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 22(11P13) MUTATED                                                          5
  AMP PEAK 22(11P13) WILD-TYPE                                                       16
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 22(11P13) MUTATED                                                           0
  AMP PEAK 22(11P13) WILD-TYPE                                                         8
                              vv
clus                           STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 22(11P13) MUTATED                                          5
  AMP PEAK 22(11P13) WILD-TYPE                                        8
D22V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 22(11P13) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     13
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    32
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                          17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                  0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   5
                                                                   clus
vv                                                                  AMP PEAK 22(11P13) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       58
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           67
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            61
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     8
[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"
D22V9, binary
                              cls
clus                             0   1
  AMP PEAK 22(11P13) MUTATED     2  85
  AMP PEAK 22(11P13) WILD-TYPE   4 345
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(11P13) MUTATED      2   85
  AMP PEAK 22(11P13) WILD-TYPE    4  345
     clus
vv    AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE
  NO                           2                            4
  YES                         85                          345
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 22(11P13) MUTATED    64   4   7   5
  AMP PEAK 22(11P13) WILD-TYPE 283  14  12  20
D22V10, multiclass
    clus
vv   AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE
  R0                         64                          283
  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                         8
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 22(11P13) MUTATED                                           1    53
  AMP PEAK 22(11P13) WILD-TYPE                                         0   221
D22V12, multiclass
                                           clus
vv                                          AMP PEAK 22(11P13) MUTATED
  ASIAN                                                             18
  BLACK OR AFRICAN AMERICAN                                          3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                             53
                                           clus
vv                                          AMP PEAK 22(11P13) WILD-TYPE
  ASIAN                                                               70
  BLACK OR AFRICAN AMERICAN                                            8
  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"
D22V13, binary
                              cls
clus                             0   1
  AMP PEAK 22(11P13) MUTATED     1  59
  AMP PEAK 22(11P13) WILD-TYPE   3 254
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(11P13) MUTATED      1   59
  AMP PEAK 22(11P13) WILD-TYPE    3  254
                        clus
vv                       AMP PEAK 22(11P13) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         59
                        clus
vv                       AMP PEAK 22(11P13) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          254
[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    49  34
  AMP PEAK 23(11P11.2) WILD-TYPE 205 116
  AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE 
                            83                            321 
  AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE 
                            34                            116 
$`AMP PEAK 23(11P11.2) MUTATED`
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6458 
       11.01         9.44         6.61        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 
       11.54        15.68         8.22        22.26         1.48        12.89 
TCGA-BR-A4J8 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-A487 TCGA-CD-A4MH 
       13.51         0.07         0.10         0.16         9.34        12.20 
TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4472 TCGA-CG-5717 
       20.02        54.08         4.01        47.05        12.00         6.97 
TCGA-CG-5722 TCGA-D7-6520 TCGA-D7-6822 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YT 
        0.99        18.84        12.33        14.66        21.14        14.27 
TCGA-D7-A6F2 TCGA-EQ-8122 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A8CX 
       15.65         7.99        14.07        17.06         0.56         0.23 
TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-A4G2 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 
        5.92        14.17        24.30        12.30        27.42         3.45 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A7NT TCGA-IN-A7NU 
       18.38         5.36        13.08         1.41         5.56         1.81 
TCGA-IN-AB1V TCGA-KB-A6F5 TCGA-KB-A93H TCGA-R5-A7ZI TCGA-RD-A7BT TCGA-RD-A7C1 
        7.82         5.56        37.64        61.25         8.61        16.67 
TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
      115.69         8.94         5.46        13.02        18.48        35.24 
TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91E 
       22.19         2.70        27.35        64.57        14.33        11.93 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A925 
       22.68         1.71         9.50         9.73         9.04         4.54 
TCGA-VQ-A92D TCGA-VQ-A94U TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       64.18        22.09        29.98        17.13        54.12 

$`AMP PEAK 23(11P11.2) WILD-TYPE`
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-4267 TCGA-BR-4279 TCGA-BR-4280 
        7.43        18.35        30.90         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       34.68        15.95        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 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 
       24.76        35.24        23.93        15.42        28.01        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73        12.43         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       14.43        12.26         9.60        20.55         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       12.95         2.66        16.31         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       19.50        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        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        15.81        16.44         9.86 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU 
       10.68        12.56        13.87         7.53         6.08        13.41 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       13.51         8.98         0.72        14.17         0.53        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36         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 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 
       13.18         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.10         0.10         0.13         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI 
        3.42        11.31        12.43        11.61         6.58         0.10 
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-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
        8.05        14.01        29.98        19.07        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         6.02       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        79.07        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        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       20.55        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        10.55        11.31 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8579 
       24.72        16.80        19.50        17.19        18.21        20.91 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 
       11.24        11.31        11.44         9.76         2.96         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 
        4.34         7.40         7.13         0.62        16.24        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-HF-A5NB TCGA-HJ-7597 
       59.54         5.03        13.58         5.52        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        1.51        14.27        12.59        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76         5.59        12.30        11.84        24.20         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-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        19.36        23.84         9.67         8.88         8.81 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR 
       21.21        18.81         3.39         5.19         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93G 
       12.59         6.51        13.51         2.53        60.56        20.15 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73         9.86        45.67        18.21         8.52 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV 
        6.08         4.60         9.24        11.05         5.13       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
       37.91        40.64       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-A8DV 
       16.87        19.04         5.79         0.92        48.79        13.25 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        34.45        27.88        32.48         7.73        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK 
       34.29        46.26        16.31         2.50        12.79        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        26.24 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       65.16        36.69        11.70        61.22        18.74        20.81 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
       36.16         7.36        52.24         2.01        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
        5.72        21.04         2.66        42.54        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       40.08        28.41        32.94        26.04        16.14        21.11 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        10.62         0.79 

  AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE 
                          0.07                           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 
                         12.33                          12.82 
[1] "0.1 - 115.7 (12.3)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.2"
D23V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 23(11P11.2) MUTATED         1        3        9        2         2
  AMP PEAK 23(11P11.2) WILD-TYPE       2       11       32       29        36
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 23(11P11.2) MUTATED          14         1         21         12
  AMP PEAK 23(11P11.2) WILD-TYPE        41         3         64         50
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 23(11P11.2) MUTATED           10       12
  AMP PEAK 23(11P11.2) WILD-TYPE         31       34
D23V3, multiclass
            clus
vv           AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE
  STAGE I                               1                              2
  STAGE IA                              3                             11
  STAGE IB                              9                             32
  STAGE II                              2                             29
  STAGE IIA                             2                             36
  STAGE IIB                            14                             41
  STAGE III                             1                              3
  STAGE IIIA                           21                             64
  STAGE IIIB                           12                             50
  STAGE IIIC                           10                             31
  STAGE IV                             12                             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 23(11P11.2) MUTATED     6  15  39  28
  AMP PEAK 23(11P11.2) WILD-TYPE  16  75 156  91
D23V4, multiclass
    clus
vv   AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE
  T1                            6                             16
  T2                           15                             75
  T3                           39                            156
  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    20  26  23  17
  AMP PEAK 23(11P11.2) WILD-TYPE 109  92  61  72
D23V5, multiclass
    clus
vv   AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE
  N0                           20                            109
  N1                           26                             92
  N2                           23                             61
  N3                           17                             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 308  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(11P11.2) MUTATED     79    6
  AMP PEAK 23(11P11.2) WILD-TYPE  308   24
   clus
vv  AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE
  0                           79                            308
  1                            6                             24
[1] 2 2
[1] FALSE
D23V7, binary
                                cls
clus                               0   1
  AMP PEAK 23(11P11.2) MUTATED    29  62
  AMP PEAK 23(11P11.2) WILD-TYPE 129 216
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(11P11.2) MUTATED     29   62
  AMP PEAK 23(11P11.2) WILD-TYPE  129  216
        clus
vv       AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE
  FEMALE                           29                            129
  MALE                             62                            216
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 23(11P11.2) MUTATED                                       9
  AMP PEAK 23(11P11.2) WILD-TYPE                                    62
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 23(11P11.2) MUTATED                                                       35
  AMP PEAK 23(11P11.2) WILD-TYPE                                                    127
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 23(11P11.2) MUTATED                                                                  17
  AMP PEAK 23(11P11.2) WILD-TYPE                                                                64
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 23(11P11.2) MUTATED                                                 23
  AMP PEAK 23(11P11.2) WILD-TYPE                                               55
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 23(11P11.2) MUTATED                                                          2
  AMP PEAK 23(11P11.2) WILD-TYPE                                                       19
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 23(11P11.2) MUTATED                                                           1
  AMP PEAK 23(11P11.2) WILD-TYPE                                                         7
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 23(11P11.2) MUTATED                                          3
  AMP PEAK 23(11P11.2) WILD-TYPE                                       10
D23V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 23(11P11.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      35
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            23
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     3
                                                                   clus
vv                                                                  AMP PEAK 23(11P11.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             64
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              55
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      10
[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"
D23V9, binary
                                cls
clus                               0   1
  AMP PEAK 23(11P11.2) MUTATED     2  89
  AMP PEAK 23(11P11.2) WILD-TYPE   4 341
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(11P11.2) MUTATED      2   89
  AMP PEAK 23(11P11.2) WILD-TYPE    4  341
     clus
vv    AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE
  NO                             2                              4
  YES                           89                            341
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 23(11P11.2) MUTATED    68   4   7   6
  AMP PEAK 23(11P11.2) WILD-TYPE 279  14  12  19
D23V10, multiclass
    clus
vv   AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE
  R0                           68                            279
  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                         8
                                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      56
  AMP PEAK 23(11P11.2) WILD-TYPE   218
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                                                               56
                                           clus
vv                                          AMP PEAK 23(11P11.2) WILD-TYPE
  ASIAN                                                                 71
  BLACK OR AFRICAN AMERICAN                                              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V13, binary
                                cls
clus                               0   1
  AMP PEAK 23(11P11.2) MUTATED     1  58
  AMP PEAK 23(11P11.2) WILD-TYPE   3 255
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(11P11.2) MUTATED      1   58
  AMP PEAK 23(11P11.2) WILD-TYPE    3  255
                        clus
vv                       AMP PEAK 23(11P11.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           58
                        clus
vv                       AMP PEAK 23(11P11.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            255
[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    63  39
  AMP PEAK 24(11Q13.3) WILD-TYPE 191 111
  AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE 
                           102                            302 
  AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE 
                            39                            111 
$`AMP PEAK 24(11Q13.3) MUTATED`
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-7704 TCGA-BR-7717 
       11.01         9.44        13.87        13.68        35.24        18.15 
TCGA-BR-7901 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8296 
        3.45        17.49        11.44         0.69         9.60        15.58 
TCGA-BR-8361 TCGA-BR-8365 TCGA-BR-8485 TCGA-BR-8589 TCGA-BR-8678 TCGA-BR-8686 
       19.50        17.52         9.21        15.81        11.54        15.68 
TCGA-BR-8687 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4PF TCGA-BR-A4QI 
        8.22        22.26         1.48        12.89         1.15        13.64 
TCGA-CD-5799 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-A487 
        3.25         0.07         0.10         0.10         0.13         9.34 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-4444 TCGA-CG-4449 
       11.61        12.20        20.02        54.08        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4472 TCGA-CG-5722 TCGA-CG-5724 TCGA-D7-8575 TCGA-D7-8576 
       12.03        12.00         0.99        12.03        18.21        14.66 
TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-8099 
       11.24         2.96        15.65         7.99        72.23        17.06 
TCGA-FP-8631 TCGA-HU-8243 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4GC TCGA-HU-A4GY 
        0.56         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        12.30         9.67        27.42         3.39         5.36 
TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU 
        5.19         1.41         6.44         6.74         5.56         1.81 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7ZI TCGA-RD-A7BT TCGA-RD-A7C1 
        5.56        37.64         9.86        61.25         8.61        16.67 
TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      122.30       115.69        57.44         8.94        35.61        19.04 
TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PJ 
        5.46        13.02        18.48        35.24        22.19         2.70 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91N 
       27.35        64.57        14.33        36.69        11.93        18.74 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91Y TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94T 
       22.68         1.71         9.73         4.54        64.18        11.24 
TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       40.08        32.94        29.98        21.11        12.43         0.79 

$`AMP PEAK 24(11Q13.3) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 
       26.70        11.70        19.56         9.47         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        4.64         7.43        18.35        30.90         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6563 
        6.61        34.68        15.95        17.29        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        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       12.82         9.21        24.76        23.93        15.42        28.01 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73        12.43         9.07        12.76        18.71 
TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       14.43        12.26        20.55         8.05         0.56        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 
        2.66        16.31         2.20         7.40         6.18        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        19.17        14.79         0.26        15.85 
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-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        9.34        13.45         6.28         7.53         0.49        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       16.44         9.86        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        6.08        13.41        13.51         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        12.82         0.66        19.36        13.51         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 
       20.65        20.42        11.57         5.13         2.83        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 
       13.18         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.13         0.16         0.10         0.13         0.10         3.42 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 
       11.31        12.43         6.58         0.10        12.62         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-4441 TCGA-CG-4443 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       14.01        29.98        21.99         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        0.99         6.02       105.07        15.02        28.96        79.07 
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        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        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        10.55        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        15.16        13.78        14.76        13.71 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.31        11.44         9.76         8.38         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62        16.24        14.47        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
        3.48        19.53        14.07        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       13.58         5.52         0.23        18.08        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       14.27        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        11.84        24.20        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-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 
        6.25        10.19         2.10        12.95        19.36         8.88 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RN 
        8.81        21.21         3.45        18.81        18.38        13.08 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 
       12.59         6.51         7.82        13.51         2.53        60.56 
TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       20.15         3.72        19.73        45.67        18.21         8.52 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MW 
        6.08         4.60         9.24        11.05         5.13        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL 
       40.64       116.38        71.38        16.87         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       48.79        13.25        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
        7.73        28.96        34.29        46.26        16.31         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       12.79        17.85         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q 
       13.35        26.24        65.16        11.70        61.22        20.81 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
       36.16         7.36         9.50        52.24         9.04         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-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       22.09        18.41        28.41        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-ZA-A8F6 
       16.14        10.62 

  AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE 
                          0.07                           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 
                        12.115                         13.015 
[1] "0.1 - 122.3 (12.1)" "0.0 - 116.4 (13.0)"
[1] "hr=" "1"  
D24V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 24(11Q13.3) MUTATED         1        4        9        8         7
  AMP PEAK 24(11Q13.3) WILD-TYPE       2       10       32       23        31
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 24(11Q13.3) MUTATED          14         0         22         18
  AMP PEAK 24(11Q13.3) WILD-TYPE        41         4         63         44
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 24(11Q13.3) MUTATED           15       12
  AMP PEAK 24(11Q13.3) WILD-TYPE         26       34
D24V3, multiclass
            clus
vv           AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE
  STAGE I                               1                              2
  STAGE IA                              4                             10
  STAGE IB                              9                             32
  STAGE II                              8                             23
  STAGE IIA                             7                             31
  STAGE IIB                            14                             41
  STAGE III                             0                              4
  STAGE IIIA                           22                             63
  STAGE IIIB                           18                             44
  STAGE IIIC                           15                             26
  STAGE IV                             12                             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 24(11Q13.3) MUTATED     6  21  47  37
  AMP PEAK 24(11Q13.3) WILD-TYPE  16  69 148  82
D24V4, multiclass
    clus
vv   AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE
  T1                            6                             16
  T2                           21                             69
  T3                           47                            148
  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 101  89  52  69
D24V5, multiclass
    clus
vv   AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE
  N0                           28                            101
  N1                           29                             89
  N2                           32                             52
  N3                           20                             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"
D24V6, binary
                                cls
clus                               0   1
  AMP PEAK 24(11Q13.3) MUTATED   105   5
  AMP PEAK 24(11Q13.3) WILD-TYPE 282  25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(11Q13.3) MUTATED    105    5
  AMP PEAK 24(11Q13.3) WILD-TYPE  282   25
   clus
vv  AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE
  0                          105                            282
  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 119 202
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(11Q13.3) MUTATED     39   76
  AMP PEAK 24(11Q13.3) WILD-TYPE  119  202
        clus
vv       AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE
  FEMALE                           39                            119
  MALE                             76                            202
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 24(11Q13.3) MUTATED                                      14
  AMP PEAK 24(11Q13.3) WILD-TYPE                                    57
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 24(11Q13.3) MUTATED                                                       45
  AMP PEAK 24(11Q13.3) WILD-TYPE                                                    117
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 24(11Q13.3) MUTATED                                                                  21
  AMP PEAK 24(11Q13.3) WILD-TYPE                                                                60
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 24(11Q13.3) MUTATED                                                 24
  AMP PEAK 24(11Q13.3) WILD-TYPE                                               54
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 24(11Q13.3) MUTATED                                                          7
  AMP PEAK 24(11Q13.3) WILD-TYPE                                                       14
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 24(11Q13.3) MUTATED                                                           1
  AMP PEAK 24(11Q13.3) WILD-TYPE                                                         7
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 24(11Q13.3) MUTATED                                          2
  AMP PEAK 24(11Q13.3) WILD-TYPE                                       11
D24V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 24(11Q13.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       14
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      45
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           21
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            24
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
                                                                   clus
vv                                                                  AMP PEAK 24(11Q13.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         57
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       117
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             60
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              54
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      11
[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"
D24V9, binary
                                cls
clus                               0   1
  AMP PEAK 24(11Q13.3) MUTATED     2 113
  AMP PEAK 24(11Q13.3) WILD-TYPE   4 317
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(11Q13.3) MUTATED      2  113
  AMP PEAK 24(11Q13.3) WILD-TYPE    4  317
     clus
vv    AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE
  NO                             2                              4
  YES                          113                            317
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 24(11Q13.3) MUTATED    91   5   7   6
  AMP PEAK 24(11Q13.3) WILD-TYPE 256  13  12  19
D24V10, multiclass
    clus
vv   AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE
  R0                           91                            256
  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                         6
                                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   207
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                                              6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                207
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V13, binary
                                cls
clus                               0   1
  AMP PEAK 24(11Q13.3) MUTATED     1  77
  AMP PEAK 24(11Q13.3) WILD-TYPE   3 236
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(11Q13.3) MUTATED      1   77
  AMP PEAK 24(11Q13.3) WILD-TYPE    3  236
                        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                                  3
  NOT HISPANIC OR LATINO                            236
[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    75  44
  AMP PEAK 25(12P12.1) WILD-TYPE 179 106
  AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE 
                           119                            285 
  AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE 
                            44                            106 
$`AMP PEAK 25(12P12.1) MUTATED`
TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6709 
        9.47         6.61        39.12        32.78        25.61        12.16 
TCGA-BR-6801 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8078 TCGA-BR-8295 
       21.11        28.73         3.45        18.71        12.26         2.20 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8369 
        7.40        19.50        13.08         0.26         0.95        14.04 
TCGA-BR-8370 TCGA-BR-8381 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8678 TCGA-BR-8687 
        3.32         0.26        20.22        15.81        11.54         8.22 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4PF 
        7.53        22.26         1.48         0.72        14.17         1.15 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 
        2.83         3.25         0.30         0.07         0.07         0.07 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-A48A TCGA-CD-A48C TCGA-CG-4300 TCGA-CG-4444 
        0.16         0.10        12.43        11.61        20.02        47.05 
TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5727 TCGA-D7-5578 
       21.99        12.00         0.99        12.03        79.07        12.66 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6817 TCGA-D7-6820 
       19.13        20.55        18.54        17.19        12.79        11.31 
TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-A4YV TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 
       19.50        18.21         5.92        11.31         2.96        15.65 
TCGA-D7-A747 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-A72C TCGA-FP-7735 
        8.38         7.40         0.62        16.24        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-A4BF TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8604 
       19.53        22.29         5.52         1.51        14.17        12.10 
TCGA-HU-A4G2 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GT 
       24.30         3.25        22.75        25.81         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 
        6.25        10.19         8.81        27.42         3.45         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V 
        5.36         6.44         6.74         6.51         1.81         7.82 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A7ZR 
        2.53        60.56        37.64        18.21        61.25         6.08 
TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       11.05        16.67         8.94         5.79         0.92        48.79 
TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PE 
       13.25        18.48        35.24        21.73         7.73        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91Q 
       17.85        14.33        36.69        11.93        18.74        20.81 
TCGA-VQ-A91V TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A94T TCGA-VQ-AA6K 
       36.16         4.54         5.72        11.24        12.43 

$`AMP PEAK 25(12P12.1) WILD-TYPE`
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-4267 TCGA-BR-4279 
        4.64         7.43        18.35        30.90         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-6564 TCGA-BR-6565 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       19.33        26.10         9.17        18.05        19.89         8.98 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
       12.43         9.07        12.76        17.49        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        20.55         8.05         0.56        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8365 
        2.66        16.31        15.58         6.18        22.19        17.52 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 
       26.33         4.31        11.80        19.17        14.79        15.85 
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-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        9.34        13.45         6.28         7.53         0.49        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       16.44         9.86        15.68        10.68        12.56        13.87 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J4 
        6.08        13.41        13.51        12.89         8.98         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
       12.82         0.66        19.36        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5800 TCGA-CD-5801 
       20.42        13.64        11.57         5.13        13.15        13.18 
TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 
        0.07         0.07         0.10         0.13         0.10         0.13 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG 
        0.13         0.10         3.42         9.34        11.31         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20         0.10        12.62         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        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-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99         6.02       105.07        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 
        4.01        69.04        21.07         7.99        12.36        11.93 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 
       18.84        18.61        17.85        13.35        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 
       15.98        10.55        12.33        24.72        16.80        17.19 
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        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        13.71        11.24        11.44         9.76 
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-FP-7916 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       14.07        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
        0.23        18.08        26.47         5.92        14.27        12.59 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       11.41        10.62         0.76         5.59        12.30        11.84 
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        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN 
        8.88        21.21        18.81        18.38         5.19        13.08 
TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A93G 
        1.41        12.59         5.56        13.51         5.56        20.15 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A804 
        3.72        19.73         9.86        45.67         8.52         4.60 
TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        9.24         8.61         5.13       122.30        37.91        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-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       19.04         5.46        13.02        34.45        27.88        32.48 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH 
       28.96        34.29        46.26        16.31         2.50        12.79 
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-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91K 
       26.24        27.35        64.57        65.16        11.70        61.22 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       22.68         1.71         7.36         9.50         9.73        52.24 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O 
        9.04         2.01        55.43         6.58        64.18        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
        2.66        42.54        22.09        18.41        40.08        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       32.94        29.98        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11        10.62         0.79 

  AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE 
                          0.07                           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 
                         11.61                          13.41 
[1] "0.1 - 79.1 (11.6)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.2"
D25V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 25(12P12.1) MUTATED         0        2       10        7        14
  AMP PEAK 25(12P12.1) WILD-TYPE       3       12       31       24        24
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 25(12P12.1) MUTATED          17         2         31         20
  AMP PEAK 25(12P12.1) WILD-TYPE        38         2         54         42
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 25(12P12.1) MUTATED           11       12
  AMP PEAK 25(12P12.1) WILD-TYPE         30       34
D25V3, multiclass
            clus
vv           AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE
  STAGE I                               0                              3
  STAGE IA                              2                             12
  STAGE IB                             10                             31
  STAGE II                              7                             24
  STAGE IIA                            14                             24
  STAGE IIB                            17                             38
  STAGE III                             2                              2
  STAGE IIIA                           31                             54
  STAGE IIIB                           20                             42
  STAGE IIIC                           11                             30
  STAGE IV                             12                             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 25(12P12.1) MUTATED     5  20  72  29
  AMP PEAK 25(12P12.1) WILD-TYPE  17  70 123  90
D25V4, multiclass
    clus
vv   AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE
  T1                            5                             17
  T2                           20                             70
  T3                           72                            123
  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 96 83 52 63
D25V5, multiclass
    clus
vv   AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE
  N0                           33                             96
  N1                           35                             83
  N2                           32                             52
  N3                           26                             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"
D25V6, binary
                                cls
clus                               0   1
  AMP PEAK 25(12P12.1) MUTATED   115   8
  AMP PEAK 25(12P12.1) WILD-TYPE 272  22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(12P12.1) MUTATED    115    8
  AMP PEAK 25(12P12.1) WILD-TYPE  272   22
   clus
vv  AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE
  0                          115                            272
  1                            8                             22
[1] 2 2
[1] FALSE
D25V7, binary
                                cls
clus                               0   1
  AMP PEAK 25(12P12.1) MUTATED    46  81
  AMP PEAK 25(12P12.1) WILD-TYPE 112 197
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(12P12.1) MUTATED     46   81
  AMP PEAK 25(12P12.1) WILD-TYPE  112  197
        clus
vv       AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE
  FEMALE                           46                            112
  MALE                             81                            197
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 25(12P12.1) MUTATED                                      24
  AMP PEAK 25(12P12.1) WILD-TYPE                                    47
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 25(12P12.1) MUTATED                                                       48
  AMP PEAK 25(12P12.1) WILD-TYPE                                                    114
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 25(12P12.1) MUTATED                                                                  17
  AMP PEAK 25(12P12.1) WILD-TYPE                                                                64
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 25(12P12.1) MUTATED                                                 29
  AMP PEAK 25(12P12.1) WILD-TYPE                                               49
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 25(12P12.1) MUTATED                                                          5
  AMP PEAK 25(12P12.1) WILD-TYPE                                                       16
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 25(12P12.1) MUTATED                                                           1
  AMP PEAK 25(12P12.1) WILD-TYPE                                                         7
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 25(12P12.1) MUTATED                                          2
  AMP PEAK 25(12P12.1) WILD-TYPE                                       11
D25V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 25(12P12.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       24
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      48
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            29
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
                                                                   clus
vv                                                                  AMP PEAK 25(12P12.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       114
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             64
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              49
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      11
[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"
D25V9, binary
                                cls
clus                               0   1
  AMP PEAK 25(12P12.1) MUTATED     2 125
  AMP PEAK 25(12P12.1) WILD-TYPE   4 305
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(12P12.1) MUTATED      2  125
  AMP PEAK 25(12P12.1) WILD-TYPE    4  305
     clus
vv    AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE
  NO                             2                              4
  YES                          125                            305
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 25(12P12.1) MUTATED   102   6   6   4
  AMP PEAK 25(12P12.1) WILD-TYPE 245  12  13  21
D25V10, multiclass
    clus
vv   AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE
  R0                          102                            245
  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                         8
                                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      80
  AMP PEAK 25(12P12.1) WILD-TYPE   194
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                                                               80
                                           clus
vv                                          AMP PEAK 25(12P12.1) WILD-TYPE
  ASIAN                                                                 59
  BLACK OR AFRICAN AMERICAN                                              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  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"
D25V13, binary
                                cls
clus                               0   1
  AMP PEAK 25(12P12.1) MUTATED     2  95
  AMP PEAK 25(12P12.1) WILD-TYPE   2 218
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(12P12.1) MUTATED      2   95
  AMP PEAK 25(12P12.1) WILD-TYPE    2  218
                        clus
vv                       AMP PEAK 25(12P12.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           95
                        clus
vv                       AMP PEAK 25(12P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            218
[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 191 110
  AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE 
                         103                          301 
  AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE 
                          40                          110 
$`AMP PEAK 26(12Q15) MUTATED`
TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6563 TCGA-BR-6566 
        9.47         6.61        18.35         6.18        39.12        32.78 
TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8295 
       28.73        18.71        11.44         0.69        12.26         2.20 
TCGA-BR-8297 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8370 TCGA-BR-8381 TCGA-BR-8484 
        7.40         0.26         0.95         3.32         0.26        25.18 
TCGA-BR-8589 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A4CS 
       15.81        15.68         8.22        12.56         7.53         1.48 
TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 
        0.72         0.53         0.66         1.15         2.83         3.25 
TCGA-CD-5802 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-A487 
        0.30         0.07         0.16         0.10         0.13         9.34 
TCGA-CD-A48A TCGA-CG-4301 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4472 
       12.43         3.02        47.05        12.03        21.99        12.00 
TCGA-CG-4475 TCGA-CG-5722 TCGA-CG-5725 TCGA-CG-5727 TCGA-CG-5732 TCGA-D7-5578 
       22.98         0.99        15.02        79.07        69.04        12.66 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6817 
       19.13        20.55        18.54        17.19        10.26        12.79 
TCGA-D7-8573 TCGA-D7-A4YV TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A74A TCGA-EQ-5647 
       19.50         5.92        15.65         8.38         7.40         0.62 
TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HU-8238 
       11.38        14.07        22.29         5.52         0.23         1.51 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4GT 
       14.17        12.10        24.30        22.75         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H4 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 
        6.25        10.19        23.84        27.42         3.45         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-AB1V TCGA-KB-A6F7 
        5.36        13.08         1.41         6.44         7.82        60.56 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-VQ-A8E0 TCGA-VQ-A8E2 
       61.25         6.08         5.13        16.67        18.48        35.24 
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 
       11.93        20.81         9.50         9.04         4.54         5.72 
TCGA-VQ-AA6K 
       12.43 

$`AMP PEAK 26(12Q15) WILD-TYPE`
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-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.64         7.43        30.90         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-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        9.17        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 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       24.76        35.24        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
       15.32        12.43         3.45         9.07        12.76        17.49 
TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       14.43         9.60        20.55         8.05         0.56        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        2.66        16.31        15.58         6.18        19.50        13.08 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 
       22.19        17.52        26.33         4.31        14.04        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 
       19.17        14.79        15.85         3.72         5.39         9.21 
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        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV 
       10.68        13.87         6.08        22.26        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 
       12.89         8.98        14.17        12.82        19.36        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
        0.46        20.65        20.42        13.64        11.57         5.13 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 
       13.15        13.18         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 
        0.10         0.13         0.10         0.13         0.10         3.42 
TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        11.61         6.58        12.20         0.10        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-4462 
       54.08         4.01        14.01        29.98        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-5723 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         6.02       105.07        12.03        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 
       65.10         4.01        21.07         7.99        12.36        11.93 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 
       18.84        18.61        17.85        13.35        15.22        15.98 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 
       10.55        11.31        12.33        24.72        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-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       15.16        13.78        14.76        13.71        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 
       11.44         9.76         2.96         4.34         7.13         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-A5NB 
       17.06        59.54         5.03        13.58         0.56        18.08 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 
       26.47         5.92        14.27        12.59        11.41        10.62 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GY 
       25.81        11.77        21.37        29.98         0.10         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        19.36        12.30         9.67         8.88 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RR 
        8.81        21.21        18.81        18.38         5.19         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 
       12.59         6.51         5.56         1.81        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        5.56        20.15        37.64         3.72        19.73         9.86 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       45.67        18.21         8.52         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        8.61       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-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        34.45        27.88        32.48        28.96        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
       46.26        16.31         2.50        17.85         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ 
       23.41        15.65        26.24        27.35        64.57        65.16 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U 
       36.69        11.70        61.22        18.74        22.68         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 
       36.16         7.36         9.73        52.24         2.01        55.43 
TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
        6.58        64.18        21.04         2.66        42.54        11.24 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       22.09        18.41        40.08        28.41        32.94        29.98 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       17.13        54.12        26.04        16.14        21.11        10.62 
TCGA-ZQ-A9CR 
        0.79 

  AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE 
                        0.07                         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 
                       10.19                        13.51 
[1] "0.1 - 79.1 (10.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D26V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 26(12Q15) MUTATED         0        2        9        7        12
  AMP PEAK 26(12Q15) WILD-TYPE       3       12       32       24        26
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 26(12Q15) MUTATED          14         2         23         14
  AMP PEAK 26(12Q15) WILD-TYPE        41         2         62         48
                              vv
clus                           STAGE IIIC STAGE IV
  AMP PEAK 26(12Q15) MUTATED           10       13
  AMP PEAK 26(12Q15) WILD-TYPE         31       33
D26V3, multiclass
            clus
vv           AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE
  STAGE I                             0                            3
  STAGE IA                            2                           12
  STAGE IB                            9                           32
  STAGE II                            7                           24
  STAGE IIA                          12                           26
  STAGE IIB                          14                           41
  STAGE III                           2                            2
  STAGE IIIA                         23                           62
  STAGE IIIB                         14                           48
  STAGE IIIC                         10                           31
  STAGE IV                           13                           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 26(12Q15) MUTATED     6  20  50  30
  AMP PEAK 26(12Q15) WILD-TYPE  16  70 145  89
D26V4, multiclass
    clus
vv   AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE
  T1                          6                           16
  T2                         20                           70
  T3                         50                          145
  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  25  19
  AMP PEAK 26(12Q15) WILD-TYPE 101  84  59  70
D26V5, multiclass
    clus
vv   AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE
  N0                         28                          101
  N1                         34                           84
  N2                         25                           59
  N3                         19                           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    96   8
  AMP PEAK 26(12Q15) WILD-TYPE 291  22
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(12Q15) MUTATED     96    8
  AMP PEAK 26(12Q15) WILD-TYPE  291   22
   clus
vv  AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE
  0                         96                          291
  1                          8                           22
[1] 2 2
[1] FALSE
D26V7, binary
                              cls
clus                             0   1
  AMP PEAK 26(12Q15) MUTATED    36  72
  AMP PEAK 26(12Q15) WILD-TYPE 122 206
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(12Q15) MUTATED     36   72
  AMP PEAK 26(12Q15) WILD-TYPE  122  206
        clus
vv       AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE
  FEMALE                         36                          122
  MALE                           72                          206
[1] 2 2
[1] FALSE
                              vv
clus                           STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 26(12Q15) MUTATED                                      22
  AMP PEAK 26(12Q15) WILD-TYPE                                    49
                              vv
clus                           STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 26(12Q15) MUTATED                                                       37
  AMP PEAK 26(12Q15) WILD-TYPE                                                    125
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 26(12Q15) MUTATED                                                                  13
  AMP PEAK 26(12Q15) WILD-TYPE                                                                68
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 26(12Q15) MUTATED                                                 26
  AMP PEAK 26(12Q15) WILD-TYPE                                               52
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 26(12Q15) MUTATED                                                          3
  AMP PEAK 26(12Q15) WILD-TYPE                                                       18
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 26(12Q15) MUTATED                                                           2
  AMP PEAK 26(12Q15) WILD-TYPE                                                         6
                              vv
clus                           STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 26(12Q15) MUTATED                                          3
  AMP PEAK 26(12Q15) WILD-TYPE                                       10
D26V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 26(12Q15) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     22
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    37
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                          26
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                  2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   3
                                                                   clus
vv                                                                  AMP PEAK 26(12Q15) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           68
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            52
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    10
[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"
D26V9, binary
                              cls
clus                             0   1
  AMP PEAK 26(12Q15) MUTATED     2 106
  AMP PEAK 26(12Q15) WILD-TYPE   4 324
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(12Q15) MUTATED      2  106
  AMP PEAK 26(12Q15) WILD-TYPE    4  324
     clus
vv    AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE
  NO                           2                            4
  YES                        106                          324
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 26(12Q15) MUTATED    83   5   7   5
  AMP PEAK 26(12Q15) WILD-TYPE 264  13  12  20
D26V10, multiclass
    clus
vv   AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE
  R0                         83                          264
  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                         9
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 26(12Q15) MUTATED                                           0    62
  AMP PEAK 26(12Q15) WILD-TYPE                                         1   212
D26V12, multiclass
                                           clus
vv                                          AMP PEAK 26(12Q15) MUTATED
  ASIAN                                                             28
  BLACK OR AFRICAN AMERICAN                                          2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          0
  WHITE                                                             62
                                           clus
vv                                          AMP PEAK 26(12Q15) WILD-TYPE
  ASIAN                                                               60
  BLACK OR AFRICAN AMERICAN                                            9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V13, binary
                              cls
clus                             0   1
  AMP PEAK 26(12Q15) MUTATED     2  78
  AMP PEAK 26(12Q15) WILD-TYPE   2 235
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(12Q15) MUTATED      2   78
  AMP PEAK 26(12Q15) WILD-TYPE    2  235
                        clus
vv                       AMP PEAK 26(12Q15) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         78
                        clus
vv                       AMP PEAK 26(12Q15) WILD-TYPE
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          235
[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   101  54
  AMP PEAK 27(13Q12.3) WILD-TYPE 153  96
  AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE 
                           155                            249 
  AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE 
                            54                             96 
$`AMP PEAK 27(13Q12.3) MUTATED`
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4279 TCGA-BR-4280 
       11.70        11.01         9.44         4.64         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6801 
       15.95        39.12         9.17        32.78        25.61        21.11 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 
        9.21        35.24        18.15        28.73         3.45        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8362 TCGA-BR-8373 
        0.69        12.26         9.60        12.95        13.08        14.79 
TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8682 
       15.85         5.39         9.21        20.22        12.79        16.44 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4J1 
       15.68         8.22        10.68        13.87        22.26         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
       14.17        12.82        13.51         0.46        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8525 TCGA-CD-8527 
        1.15         5.13         3.25        13.15         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH 
        0.10         0.13         3.42        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-4444 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5727 
       47.05         7.07        12.00         1.02        12.03        79.07 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 
        4.01        69.04         7.99        12.36        12.66        19.13 
TCGA-D7-6521 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       18.54        17.85        17.19        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YT 
       11.31        19.50        17.19        14.66        21.14        14.27 
TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-EQ-5647 
       14.76        11.24         2.96        15.65         8.38         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-A4BF 
        7.99        72.23         3.48        19.53        17.06         5.52 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GD 
       12.59        14.17        12.10        12.30        11.84        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        19.36        23.84        12.30 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RS 
       27.42         3.45        18.38         1.41         6.44        12.59 
TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
        1.81         5.56        37.64         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 
        8.52         8.61       122.30        37.91       115.69        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
        8.94        35.61         5.79        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PJ 
       13.02        21.73        34.45         7.73        22.19         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PP TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91Q TCGA-VQ-A91S 
       17.85        23.41        14.33        36.69        20.81        22.68 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-A94R 
        1.71        36.16        52.24         9.04        21.04        42.54 
TCGA-VQ-A94T TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       11.24        29.98        21.11        12.43         0.79 

$`AMP PEAK 27(13Q12.3) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 
       26.70        19.56         9.47         6.61         6.97         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6456 
       18.35        30.90         6.18        34.68        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       13.68        19.33        26.10        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        32.94        12.82        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 
       23.93        15.42        28.01        15.32        12.43         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8081 TCGA-BR-8284 
       12.76        18.71        17.49        14.43        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.56         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         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        19.17 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 
        0.26         3.72        25.18         1.12        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8683 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
        9.86        12.56         7.53         6.08         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
       13.51        12.89         8.98         0.53         0.66        19.36 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.64        11.57         2.83        13.18         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.07         0.13         0.16         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MI 
        0.13         0.10         9.34        11.31        11.61         0.10 
TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       12.62        27.02         1.02         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       19.07        12.03        21.99         0.00         9.01        18.97 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 
       22.98        30.97         6.97        36.00         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 
        0.99       105.07        15.02        28.96        65.10        21.07 
TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6527 
       11.93        20.55        18.84        18.61        13.35        10.26 
TCGA-D7-6528 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8575 TCGA-D7-8579 
       15.22        12.33        24.72        16.80        18.21        20.91 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EX 
       16.44         5.92        15.16        13.78        13.71        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-A4SO 
       11.44         9.76         4.34         7.40         7.13        16.24 
TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
       14.47        21.27        11.38        14.07        22.29        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 
        5.03        13.58         0.56         0.23        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
        1.51         5.92        14.27        11.41        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.30         5.59        24.20         3.25        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 
       29.98         8.98         0.10         6.25        10.19         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 
       12.95         9.67         8.88         8.81        21.21        18.81 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A7NR 
        3.39         5.36         5.19        13.08         6.74         6.51 
TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93G 
        5.56         7.82        13.51         2.53        60.56        20.15 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
        3.72        19.73        61.25         6.08         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-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P2 
       16.87        19.04         0.92        18.48        35.24        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
       32.48        28.96        34.29        46.26        16.31         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
       12.79         1.87         9.27        15.65        13.35        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       27.35        64.57        65.16        11.70        11.93        61.22 
TCGA-VQ-A91N TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 
       18.74         7.36         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-A94U 
        4.54         6.58         5.72        64.18         2.66        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6F 
       18.41        40.08        28.41        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-ZA-A8F6 
       26.04        16.14        10.62 

  AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE 
                          0.07                           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 
                         12.79                          12.89 
[1] "0.1 - 122.3 (12.8)" "0.0 - 116.4 (12.9)"
[1] "hr=" "1.2"
D27V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 27(13Q12.3) MUTATED         2        5       10       12        17
  AMP PEAK 27(13Q12.3) WILD-TYPE       1        9       31       19        21
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 27(13Q12.3) MUTATED          22         2         35         21
  AMP PEAK 27(13Q12.3) WILD-TYPE        33         2         50         41
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 27(13Q12.3) MUTATED           13       22
  AMP PEAK 27(13Q12.3) WILD-TYPE         28       24
D27V3, multiclass
            clus
vv           AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE
  STAGE I                               2                              1
  STAGE IA                              5                              9
  STAGE IB                             10                             31
  STAGE II                             12                             19
  STAGE IIA                            17                             21
  STAGE IIB                            22                             33
  STAGE III                             2                              2
  STAGE IIIA                           35                             50
  STAGE IIIB                           21                             41
  STAGE IIIC                           13                             28
  STAGE IV                             22                             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 27(13Q12.3) MUTATED     7  39  74  43
  AMP PEAK 27(13Q12.3) WILD-TYPE  15  51 121  76
D27V4, multiclass
    clus
vv   AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE
  T1                            7                             15
  T2                           39                             51
  T3                           74                            121
  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   46 43 34 37
  AMP PEAK 27(13Q12.3) WILD-TYPE 83 75 50 52
D27V5, multiclass
    clus
vv   AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE
  N0                           46                             83
  N1                           43                             75
  N2                           34                             50
  N3                           37                             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"
D27V6, binary
                                cls
clus                               0   1
  AMP PEAK 27(13Q12.3) MUTATED   151  12
  AMP PEAK 27(13Q12.3) WILD-TYPE 236  18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(13Q12.3) MUTATED    151   12
  AMP PEAK 27(13Q12.3) WILD-TYPE  236   18
   clus
vv  AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE
  0                          151                            236
  1                           12                             18
[1] 2 2
[1] FALSE
D27V7, binary
                                cls
clus                               0   1
  AMP PEAK 27(13Q12.3) MUTATED    56 112
  AMP PEAK 27(13Q12.3) WILD-TYPE 102 166
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(13Q12.3) MUTATED     56  112
  AMP PEAK 27(13Q12.3) WILD-TYPE  102  166
        clus
vv       AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE
  FEMALE                           56                            102
  MALE                            112                            166
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 27(13Q12.3) MUTATED                                      18
  AMP PEAK 27(13Q12.3) WILD-TYPE                                    53
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 27(13Q12.3) MUTATED                                                       64
  AMP PEAK 27(13Q12.3) WILD-TYPE                                                     98
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 27(13Q12.3) MUTATED                                                                  34
  AMP PEAK 27(13Q12.3) WILD-TYPE                                                                47
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 27(13Q12.3) MUTATED                                                 34
  AMP PEAK 27(13Q12.3) WILD-TYPE                                               44
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 27(13Q12.3) MUTATED                                                         10
  AMP PEAK 27(13Q12.3) WILD-TYPE                                                       11
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 27(13Q12.3) MUTATED                                                           4
  AMP PEAK 27(13Q12.3) WILD-TYPE                                                         4
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 27(13Q12.3) MUTATED                                          3
  AMP PEAK 27(13Q12.3) WILD-TYPE                                       10
D27V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 27(13Q12.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       18
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      64
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           34
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     3
                                                                   clus
vv                                                                  AMP PEAK 27(13Q12.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         53
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        98
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             47
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              44
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      10
[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"
D27V9, binary
                                cls
clus                               0   1
  AMP PEAK 27(13Q12.3) MUTATED     3 165
  AMP PEAK 27(13Q12.3) WILD-TYPE   3 265
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(13Q12.3) MUTATED      3  165
  AMP PEAK 27(13Q12.3) WILD-TYPE    3  265
     clus
vv    AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE
  NO                             3                              3
  YES                          165                            265
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 27(13Q12.3) MUTATED   129   9   8   9
  AMP PEAK 27(13Q12.3) WILD-TYPE 218   9  11  16
D27V10, multiclass
    clus
vv   AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE
  R0                          129                            218
  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                         4
                                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     100
  AMP PEAK 27(13Q12.3) WILD-TYPE   174
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                                                              100
                                           clus
vv                                          AMP PEAK 27(13Q12.3) WILD-TYPE
  ASIAN                                                                 55
  BLACK OR AFRICAN AMERICAN                                              4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  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"
D27V13, binary
                                cls
clus                               0   1
  AMP PEAK 27(13Q12.3) MUTATED     1 121
  AMP PEAK 27(13Q12.3) WILD-TYPE   3 192
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(13Q12.3) MUTATED      1  121
  AMP PEAK 27(13Q12.3) WILD-TYPE    3  192
                        clus
vv                       AMP PEAK 27(13Q12.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          121
                        clus
vv                       AMP PEAK 27(13Q12.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            192
[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   110  58
  AMP PEAK 28(13Q22.1) WILD-TYPE 144  92
  AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE 
                           168                            236 
  AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE 
                            58                             92 
$`AMP PEAK 28(13Q22.1) MUTATED`
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4279 
       11.70        11.01         9.44         4.64         7.43         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6801 
        6.61        15.95        39.12         9.17        32.78        21.11 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 
        9.21        35.24        15.42        28.01        18.15        28.73 
TCGA-BR-7901 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8362 TCGA-BR-8373 
        3.45         0.69        12.26         9.60        13.08        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8678 
        0.26        15.85         5.39         9.21        12.79        11.54 
TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4CQ 
       16.44        15.68         8.22        10.68        13.87        22.26 
TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4J9 
       12.89         0.72        14.17        12.82        13.51         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 
       20.65        20.42         1.15         5.13         3.25        13.15 
TCGA-CD-5802 TCGA-CD-8525 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A48A 
        0.30         0.07         0.13         0.13         3.42        12.43 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
        6.58        12.20        20.02        15.95         1.02         7.99 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4472 
       54.08         4.01        29.98        19.07         7.07        12.00 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 
       36.00         1.02       105.07        15.02         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 
        7.99        12.36        12.66        11.93        19.13        18.54 
TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 
       17.85        17.19        10.26        15.98        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-A4YT TCGA-D7-A4Z0 TCGA-D7-A6EV 
       12.33        19.50        17.19        14.27        14.76        11.24 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
        2.96        15.65         8.38         0.62         7.99        72.23 
TCGA-FP-7829 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
       19.53         0.56         5.52        12.59        14.17        12.10 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GT TCGA-HU-A4GU 
       12.30        11.84        22.75        25.81         6.51         6.25 
TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-8663 
        0.26        19.36        23.84        12.30        27.42         3.39 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-A7NU 
       18.38         5.19         1.41         6.44         6.51         1.81 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
        2.53         5.56        37.64         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 
        8.52         8.61       122.30        37.91       115.69        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
        8.94        35.61         5.79        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8PE TCGA-VQ-A8PH 
       13.02        35.24        21.73        34.45        22.19        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PP TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A91K 
        2.70        17.85        23.41        13.35        14.33        61.22 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Z 
       20.81        22.68         1.71        36.16         9.50        52.24 
TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T 
        9.04         4.54        64.18        21.04        42.54        11.24 
TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K 
       40.08        29.98        17.13        26.04        21.11        12.43 

$`AMP PEAK 28(13Q22.1) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4191 
       26.70        19.56         9.47         6.61         6.97        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
       30.90         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        32.94        12.82        24.76 
TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       23.93        15.32        12.43         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       17.49        14.43        11.44        20.55         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         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        19.17 
TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 
        3.72        25.18        20.22         1.12        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8683 
       13.45         6.28         7.53         0.49        15.81         9.86 
TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       12.56         7.53         6.08         1.48        13.41        13.51 
TCGA-BR-A4IZ TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4QI TCGA-BR-A4QL 
        8.98         0.53         0.66        19.36        13.64        11.57 
TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 
        2.83        13.18         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 
        0.10         0.13         0.16         0.10         0.10         0.10 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 
        9.34        11.31        11.61         0.10        12.62         3.02 
TCGA-CG-4304 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 
       27.02         8.05        14.01        47.05        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97        22.98        30.97         6.97 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         6.02         0.99        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6525 
       65.10        21.07        20.55        18.84        18.61        13.35 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8575 TCGA-D7-8576 
       15.22        12.79        24.72        16.80        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        16.44         5.92        15.16        13.78 
TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74A 
       13.71        11.31        11.44         9.76         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.13        16.24        14.47        21.27        11.38         3.48 
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-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        0.23        18.08        26.47         1.51         5.92        14.27 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G9 
       11.41        10.62         0.76        24.30         5.59        24.20 
TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       10.19         2.10        12.95         9.67         8.88         8.81 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR 
       21.21         3.45        18.81         5.36        13.08         6.74 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-KB-A93G 
       12.59         5.56         7.82        13.51        60.56        20.15 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
        3.72        19.73        61.25         6.08         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-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8E0 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       16.87        19.04         0.92        18.48        27.88        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
        7.73        28.96        34.29        46.26        16.31         2.50 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX 
        1.87         9.27        15.65        26.24        27.35        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91W 
       65.16        36.69        11.70        11.93        18.74         7.36 
TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P 
        9.73         2.01        55.43         6.58         5.72         2.66 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6I 
       22.09        18.41        28.41        32.94        54.12        16.14 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

  AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE 
                          0.07                           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 
                         12.79                          12.95 
[1] "0.1 - 122.3 (12.8)" "0.0 - 116.4 (12.9)"
[1] "hr=" "1.2"
D28V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 28(13Q22.1) MUTATED         2        4       12       14        17
  AMP PEAK 28(13Q22.1) WILD-TYPE       1       10       29       17        21
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 28(13Q22.1) MUTATED          26         1         38         22
  AMP PEAK 28(13Q22.1) WILD-TYPE        29         3         47         40
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 28(13Q22.1) MUTATED           13       22
  AMP PEAK 28(13Q22.1) WILD-TYPE         28       24
D28V3, multiclass
            clus
vv           AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE
  STAGE I                               2                              1
  STAGE IA                              4                             10
  STAGE IB                             12                             29
  STAGE II                             14                             17
  STAGE IIA                            17                             21
  STAGE IIB                            26                             29
  STAGE III                             1                              3
  STAGE IIIA                           38                             47
  STAGE IIIB                           22                             40
  STAGE IIIC                           13                             28
  STAGE IV                             22                             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 28(13Q22.1) MUTATED     6  41  83  43
  AMP PEAK 28(13Q22.1) WILD-TYPE  16  49 112  76
D28V4, multiclass
    clus
vv   AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE
  T1                            6                             16
  T2                           41                             49
  T3                           83                            112
  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   47 52 40 33
  AMP PEAK 28(13Q22.1) WILD-TYPE 82 66 44 56
D28V5, multiclass
    clus
vv   AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE
  N0                           47                             82
  N1                           52                             66
  N2                           40                             44
  N3                           33                             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"
D28V6, binary
                                cls
clus                               0   1
  AMP PEAK 28(13Q22.1) MUTATED   163  12
  AMP PEAK 28(13Q22.1) WILD-TYPE 224  18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(13Q22.1) MUTATED    163   12
  AMP PEAK 28(13Q22.1) WILD-TYPE  224   18
   clus
vv  AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE
  0                          163                            224
  1                           12                             18
[1] 2 2
[1] FALSE
D28V7, binary
                                cls
clus                               0   1
  AMP PEAK 28(13Q22.1) MUTATED    54 125
  AMP PEAK 28(13Q22.1) WILD-TYPE 104 153
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(13Q22.1) MUTATED     54  125
  AMP PEAK 28(13Q22.1) WILD-TYPE  104  153
        clus
vv       AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE
  FEMALE                           54                            104
  MALE                            125                            153
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 28(13Q22.1) MUTATED                                      16
  AMP PEAK 28(13Q22.1) WILD-TYPE                                    55
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 28(13Q22.1) MUTATED                                                       68
  AMP PEAK 28(13Q22.1) WILD-TYPE                                                     94
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 28(13Q22.1) MUTATED                                                                  38
  AMP PEAK 28(13Q22.1) WILD-TYPE                                                                43
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 28(13Q22.1) MUTATED                                                 38
  AMP PEAK 28(13Q22.1) WILD-TYPE                                               40
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 28(13Q22.1) MUTATED                                                         10
  AMP PEAK 28(13Q22.1) WILD-TYPE                                                       11
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 28(13Q22.1) MUTATED                                                           5
  AMP PEAK 28(13Q22.1) WILD-TYPE                                                         3
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 28(13Q22.1) MUTATED                                          3
  AMP PEAK 28(13Q22.1) WILD-TYPE                                       10
D28V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 28(13Q22.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       16
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      68
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     3
                                                                   clus
vv                                                                  AMP PEAK 28(13Q22.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         55
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        94
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             43
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              40
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      10
[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"
D28V9, binary
                                cls
clus                               0   1
  AMP PEAK 28(13Q22.1) MUTATED     1 178
  AMP PEAK 28(13Q22.1) WILD-TYPE   5 252
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(13Q22.1) MUTATED      1  178
  AMP PEAK 28(13Q22.1) WILD-TYPE    5  252
     clus
vv    AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE
  NO                             1                              5
  YES                          178                            252
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 28(13Q22.1) MUTATED   137  10   9  10
  AMP PEAK 28(13Q22.1) WILD-TYPE 210   8  10  15
D28V10, multiclass
    clus
vv   AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE
  R0                          137                            210
  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                         5
                                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     108
  AMP PEAK 28(13Q22.1) WILD-TYPE   166
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                                                              108
                                           clus
vv                                          AMP PEAK 28(13Q22.1) WILD-TYPE
  ASIAN                                                                 53
  BLACK OR AFRICAN AMERICAN                                              5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  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"
D28V13, binary
                                cls
clus                               0   1
  AMP PEAK 28(13Q22.1) MUTATED     1 123
  AMP PEAK 28(13Q22.1) WILD-TYPE   3 190
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(13Q22.1) MUTATED      1  123
  AMP PEAK 28(13Q22.1) WILD-TYPE    3  190
                        clus
vv                       AMP PEAK 28(13Q22.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          123
                        clus
vv                       AMP PEAK 28(13Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            190
[1] 2 2
[1] FALSE

Clustering(29) Variable = AMP PEAK 29(15Q26.1) MUTATION ANALYSIS
D29V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 29(15Q26.1) MUTATED    61  42
  AMP PEAK 29(15Q26.1) WILD-TYPE 193 108
  AMP PEAK 29(15Q26.1) MUTATED AMP PEAK 29(15Q26.1) WILD-TYPE 
                           103                            301 
  AMP PEAK 29(15Q26.1) MUTATED AMP PEAK 29(15Q26.1) WILD-TYPE 
                            42                            108 
$`AMP PEAK 29(15Q26.1) MUTATED`
TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6458 TCGA-BR-6709 TCGA-BR-7197 
        6.61        18.35         6.18        19.33        12.16         9.21 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8361 
       15.42        18.15        18.71        11.44         0.69        19.50 
TCGA-BR-8364 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4J4 
       22.19         9.86         8.22         7.53        22.26         0.53 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8525 TCGA-CD-8527 
        1.15        13.64         3.25        13.15         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A4MG TCGA-CG-4444 
        0.10         0.13         0.13         3.42         6.58        47.05 
TCGA-CG-4449 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5724 
       19.07        22.98        30.97         6.97         1.02        12.03 
TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 
       79.07         4.01        69.04        11.93        20.55        18.84 
TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8575 
       13.35        15.22        15.98        10.55        12.33        18.21 
TCGA-D7-A4YT TCGA-D7-A4YY TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-F1-6875 TCGA-F1-A72C 
       14.27        13.78        15.65         0.62        72.23        11.38 
TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 TCGA-HU-A4G8 TCGA-HU-A4GF 
       19.53        17.06        13.58         0.56        11.84        25.81 
TCGA-HU-A4GH TCGA-HU-A4GY TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 
       11.77         0.26        12.30        27.42         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RN TCGA-IN-A6RO TCGA-KB-A6F5 TCGA-KB-A6F7 
        3.39        18.38        13.08         1.41         5.56        60.56 
TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BT 
       37.64        45.67        18.21         6.08         9.24         8.61 
TCGA-RD-A8MV TCGA-RD-A8N6 TCGA-VQ-A8DL TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8P3 
      122.30         8.94         0.92        13.02        18.48        32.48 
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-A8PU TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A925 
       27.35        61.22        20.81         9.50         9.04         4.54 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6D 
       64.18        11.24        18.41        40.08        29.98        17.13 
TCGA-VQ-AA6F 
       54.12 

$`AMP PEAK 29(15Q26.1) WILD-TYPE`
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-4279 TCGA-BR-4280 
        6.97         4.64         7.43        30.90         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-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       24.76        35.24        23.93        28.01        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 
       12.43         3.45         9.07        12.76        17.49        14.43 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       12.26         9.60        20.55         8.05         0.56        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       13.08         0.26        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        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         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        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 
        7.53         0.49        11.54        15.81        16.44        15.68 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       10.68        12.56        13.87         6.08         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 
       13.51        12.89         8.98         0.72        14.17        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.66        19.36        13.51         0.46        20.65        20.42 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       11.57         5.13         2.83        13.18         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.07         0.07         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        0.10         9.34        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        12.03        21.99         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        7.07        12.00        36.00         0.99         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-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       12.36        12.66        19.13        18.54        18.61        17.85 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 
       17.19        10.26        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-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
        5.92        15.16        14.76        13.71        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.44         9.76         2.96         8.38         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 
        7.13         7.99        16.24        14.47        21.27         3.48 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF TCGA-FP-A8CX 
       14.07        22.29        59.54         5.03         5.52         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       18.08        26.47         1.51         5.92        14.27        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GJ 
        5.59        12.30        24.20         3.25        22.75        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         6.25        10.19 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        19.36        23.84         9.67         8.88 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR 
        8.81        21.21         5.36         5.19         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         5.56         1.81         7.82        13.51 
TCGA-IP-7968 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZF 
        2.53        20.15         3.72        19.73         9.86         8.52 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW 
       61.25         4.60        11.05         5.13        16.67        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-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       16.87        19.04         5.79        48.79         5.46        13.25 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       35.24        21.73        34.45        27.88        28.96        34.29 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       16.31         2.50         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        26.24        64.57        14.33        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       11.70        11.93        18.74        22.68         1.71        36.16 
TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
        7.36         9.73        52.24         2.01        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA69 
        5.72        21.04         2.66        42.54        22.09        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       32.94        26.04        16.14        21.11        12.43        10.62 
TCGA-ZQ-A9CR 
        0.79 

  AMP PEAK 29(15Q26.1) MUTATED AMP PEAK 29(15Q26.1) WILD-TYPE 
                          0.07                           0.00 
  AMP PEAK 29(15Q26.1) MUTATED AMP PEAK 29(15Q26.1) WILD-TYPE 
                        122.30                         116.38 
  AMP PEAK 29(15Q26.1) MUTATED AMP PEAK 29(15Q26.1) WILD-TYPE 
                         13.15                          12.79 
[1] "0.1 - 122.3 (13.2)" "0.0 - 116.4 (12.8)"
[1] "hr=" "1"  
D29V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 29(15Q26.1) MUTATED         2        3        8        9        10
  AMP PEAK 29(15Q26.1) WILD-TYPE       1       11       33       22        28
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 29(15Q26.1) MUTATED          11         2         27         15
  AMP PEAK 29(15Q26.1) WILD-TYPE        44         2         58         47
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 29(15Q26.1) MUTATED            6       15
  AMP PEAK 29(15Q26.1) WILD-TYPE         35       31
D29V3, multiclass
            clus
vv           AMP PEAK 29(15Q26.1) MUTATED AMP PEAK 29(15Q26.1) WILD-TYPE
  STAGE I                               2                              1
  STAGE IA                              3                             11
  STAGE IB                              8                             33
  STAGE II                              9                             22
  STAGE IIA                            10                             28
  STAGE IIB                            11                             44
  STAGE III                             2                              2
  STAGE IIIA                           27                             58
  STAGE IIIB                           15                             47
  STAGE IIIC                            6                             35
  STAGE IV                             15                             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 29(15Q26.1) MUTATED     6  26  52  25
  AMP PEAK 29(15Q26.1) WILD-TYPE  16  64 143  94
D29V4, multiclass
    clus
vv   AMP PEAK 29(15Q26.1) MUTATED AMP PEAK 29(15Q26.1) WILD-TYPE
  T1                            6                             16
  T2                           26                             64
  T3                           52                            143
  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 29(15Q26.1) MUTATED    29  32  29  18
  AMP PEAK 29(15Q26.1) WILD-TYPE 100  86  55  71
D29V5, multiclass
    clus
vv   AMP PEAK 29(15Q26.1) MUTATED AMP PEAK 29(15Q26.1) WILD-TYPE
  N0                           29                            100
  N1                           32                             86
  N2                           29                             55
  N3                           18                             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"
D29V6, binary
                                cls
clus                               0   1
  AMP PEAK 29(15Q26.1) MUTATED    96  10
  AMP PEAK 29(15Q26.1) WILD-TYPE 291  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(15Q26.1) MUTATED     96   10
  AMP PEAK 29(15Q26.1) WILD-TYPE  291   20
   clus
vv  AMP PEAK 29(15Q26.1) MUTATED AMP PEAK 29(15Q26.1) WILD-TYPE
  0                           96                            291
  1                           10                             20
[1] 2 2
[1] FALSE
D29V7, binary
                                cls
clus                               0   1
  AMP PEAK 29(15Q26.1) MUTATED    34  77
  AMP PEAK 29(15Q26.1) WILD-TYPE 124 201
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(15Q26.1) MUTATED     34   77
  AMP PEAK 29(15Q26.1) WILD-TYPE  124  201
        clus
vv       AMP PEAK 29(15Q26.1) MUTATED AMP PEAK 29(15Q26.1) WILD-TYPE
  FEMALE                           34                            124
  MALE                             77                            201
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 29(15Q26.1) MUTATED                                      14
  AMP PEAK 29(15Q26.1) WILD-TYPE                                    57
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 29(15Q26.1) MUTATED                                                       33
  AMP PEAK 29(15Q26.1) WILD-TYPE                                                    129
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 29(15Q26.1) MUTATED                                                                  24
  AMP PEAK 29(15Q26.1) WILD-TYPE                                                                57
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 29(15Q26.1) MUTATED                                                 28
  AMP PEAK 29(15Q26.1) WILD-TYPE                                               50
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 29(15Q26.1) MUTATED                                                          7
  AMP PEAK 29(15Q26.1) WILD-TYPE                                                       14
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 29(15Q26.1) MUTATED                                                           2
  AMP PEAK 29(15Q26.1) WILD-TYPE                                                         6
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 29(15Q26.1) MUTATED                                          2
  AMP PEAK 29(15Q26.1) WILD-TYPE                                       11
D29V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 29(15Q26.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       14
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      33
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           24
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            28
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
                                                                   clus
vv                                                                  AMP PEAK 29(15Q26.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         57
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             57
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              50
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      11
[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"
D29V9, binary
                                cls
clus                               0   1
  AMP PEAK 29(15Q26.1) MUTATED     2 109
  AMP PEAK 29(15Q26.1) WILD-TYPE   4 321
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(15Q26.1) MUTATED      2  109
  AMP PEAK 29(15Q26.1) WILD-TYPE    4  321
     clus
vv    AMP PEAK 29(15Q26.1) MUTATED AMP PEAK 29(15Q26.1) WILD-TYPE
  NO                             2                              4
  YES                          109                            321
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 29(15Q26.1) MUTATED    83   6   8   5
  AMP PEAK 29(15Q26.1) WILD-TYPE 264  12  11  20
D29V10, multiclass
    clus
vv   AMP PEAK 29(15Q26.1) MUTATED AMP PEAK 29(15Q26.1) WILD-TYPE
  R0                           83                            264
  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"
D29V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 29(15Q26.1) MUTATED      22                         5
  AMP PEAK 29(15Q26.1) WILD-TYPE    66                         6
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 29(15Q26.1) MUTATED                                           1
  AMP PEAK 29(15Q26.1) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 29(15Q26.1) MUTATED      63
  AMP PEAK 29(15Q26.1) WILD-TYPE   211
D29V12, multiclass
                                           clus
vv                                          AMP PEAK 29(15Q26.1) MUTATED
  ASIAN                                                               22
  BLACK OR AFRICAN AMERICAN                                            5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               63
                                           clus
vv                                          AMP PEAK 29(15Q26.1) WILD-TYPE
  ASIAN                                                                 66
  BLACK OR AFRICAN AMERICAN                                              6
  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"
D29V13, binary
                                cls
clus                               0   1
  AMP PEAK 29(15Q26.1) MUTATED     1  71
  AMP PEAK 29(15Q26.1) WILD-TYPE   3 242
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(15Q26.1) MUTATED      1   71
  AMP PEAK 29(15Q26.1) WILD-TYPE    3  242
                        clus
vv                       AMP PEAK 29(15Q26.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           71
                        clus
vv                       AMP PEAK 29(15Q26.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            242
[1] 2 2
[1] FALSE

Clustering(30) Variable = AMP PEAK 30(17Q12) MUTATION ANALYSIS
D30V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 30(17Q12) MUTATED    82  56
  AMP PEAK 30(17Q12) WILD-TYPE 172  94
  AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE 
                         138                          266 
  AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE 
                          56                           94 
$`AMP PEAK 30(17Q12) MUTATED`
TCGA-B7-5818 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7959 
       11.70         9.17         9.21        15.42        18.15        18.71 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 
       14.43        11.44         0.69        12.95         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        16.44 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY 
       15.68        10.68        13.87        22.26         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        13.64         3.25        13.15 
TCGA-CD-8525 TCGA-CD-8529 TCGA-CD-A486 TCGA-CD-A489 TCGA-CG-4300 TCGA-CG-4301 
        0.07         0.13         3.42        11.31        20.02         3.02 
TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
        7.99         4.01        47.05        19.07        12.03        21.99 
TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5724 
       18.97        22.98        30.97         1.02         0.99        12.03 
TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
        4.01        69.04        18.54        13.35        17.19        10.26 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8573 TCGA-D7-8576 
       15.98        12.79        11.31        12.33        19.50        14.66 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EV TCGA-D7-A6EY 
       20.91        14.27        16.44        15.16        11.24        11.44 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
        2.96        15.65         4.34         0.62         7.99        16.24 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HJ-7597 
       72.23         3.48        14.07         0.56         0.23        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-A4G6 TCGA-HU-A4GD 
        1.51         5.92        12.59        12.10        12.30        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4HD TCGA-IN-8462 
       25.81        11.77         2.10        12.95        27.42        18.81 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38         5.19        13.08         1.41         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-R5-A7ZE 
       12.59         5.56         1.81         7.82         2.53        18.21 
TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A8N6 TCGA-VQ-A8DL TCGA-VQ-A8DU 
        6.08         9.24         8.61         8.94         0.92         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PC 
       13.25        13.02        18.48        34.45         7.73        46.26 
TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PT 
       22.19        12.79         2.70        17.85         1.87        26.24 
TCGA-VQ-A8PZ TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A922 
       65.16        20.81        22.68        36.16         9.50         9.04 
TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA68 
        2.01         4.54        64.18        21.04        42.54        40.08 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       29.98        17.13        54.12        26.04        21.11         0.79 

$`AMP PEAK 30(17Q12) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        6.97         4.64         7.43        18.35        30.90         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-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        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        32.94        12.82        24.76        35.24        23.93 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       28.01        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       12.76        17.49        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        0.56        16.31         2.20         7.40         6.18        19.50 
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-8381 TCGA-BR-8382 
        4.31         3.32        11.80        19.17         0.26        15.85 
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        15.81 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU 
        9.86         8.22        12.56         7.53         6.08        13.41 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
       13.51         8.98        14.17        12.82         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM 
       13.51         0.46        20.65         1.15        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 
        2.83        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.07         0.10         0.16         0.10         0.10         0.13 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        0.13         0.10         9.34        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         0.10        12.62        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4462 TCGA-CG-4465 
        8.05        54.08        14.01        29.98         0.00         9.01 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 
        7.07        12.00         6.97        36.00         0.99         6.02 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5733 
      105.07        15.02        28.96        79.07        65.10        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-8570 
       18.84        18.61        17.85        15.22        10.55        24.72 
TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YV TCGA-D7-A4YY 
       16.80        17.19        18.21        21.14         5.92        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A74A 
       14.76        13.71        11.31         9.76         8.38         7.40 
TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7998 
        7.13        14.47        21.27        11.38        19.53        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-HF-A5NB 
       17.06        59.54         5.03        13.58         5.52        18.08 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.27        14.17        11.41        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GN 
        5.59        11.84        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         6.25        10.19         0.26 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       19.36        23.84        12.30         9.67         8.88         8.81 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A7NR TCGA-IN-AB1X 
       21.21         3.45         3.39         5.36         6.51        13.51 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        60.56        20.15        37.64         3.72        19.73 
TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS 
        9.86        45.67         8.52        61.25         4.60        11.05 
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-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44        35.61        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        5.79        48.79        35.24        21.73        27.88        32.48 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PP 
       28.96        34.29        16.31         2.50         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A 
       15.65        13.35        27.35        64.57        14.33        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91W 
       11.70        11.93        61.22        18.74         1.71         7.36 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P 
        9.73        52.24        55.43         6.58         5.72         2.66 
TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6I 
       11.24        22.09        18.41        28.41        32.94        16.14 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        10.62 

  AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE 
                        0.07                         0.00 
  AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE 
                       72.23                       122.30 
  AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE 
                       12.84                        12.82 
[1] "0.1 - 72.2 (12.8)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.3"
D30V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 30(17Q12) MUTATED         1        7       13        8        12
  AMP PEAK 30(17Q12) WILD-TYPE       2        7       28       23        26
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 30(17Q12) MUTATED          14         2         29         21
  AMP PEAK 30(17Q12) WILD-TYPE        41         2         56         41
                              vv
clus                           STAGE IIIC STAGE IV
  AMP PEAK 30(17Q12) MUTATED           13       22
  AMP PEAK 30(17Q12) WILD-TYPE         28       24
D30V3, multiclass
            clus
vv           AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE
  STAGE I                             1                            2
  STAGE IA                            7                            7
  STAGE IB                           13                           28
  STAGE II                            8                           23
  STAGE IIA                          12                           26
  STAGE IIB                          14                           41
  STAGE III                           2                            2
  STAGE IIIA                         29                           56
  STAGE IIIB                         21                           41
  STAGE IIIC                         13                           28
  STAGE IV                           22                           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 30(17Q12) MUTATED     9  33  61  40
  AMP PEAK 30(17Q12) WILD-TYPE  13  57 134  79
D30V4, multiclass
    clus
vv   AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE
  T1                          9                           13
  T2                         33                           57
  T3                         61                          134
  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 30(17Q12) MUTATED   43 34 31 33
  AMP PEAK 30(17Q12) WILD-TYPE 86 84 53 56
D30V5, multiclass
    clus
vv   AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE
  N0                         43                           86
  N1                         34                           84
  N2                         31                           53
  N3                         33                           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"
D30V6, binary
                              cls
clus                             0   1
  AMP PEAK 30(17Q12) MUTATED   119  15
  AMP PEAK 30(17Q12) WILD-TYPE 268  15
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 30(17Q12) MUTATED    119   15
  AMP PEAK 30(17Q12) WILD-TYPE  268   15
   clus
vv  AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE
  0                        119                          268
  1                         15                           15
[1] 2 2
[1] FALSE
D30V7, binary
                              cls
clus                             0   1
  AMP PEAK 30(17Q12) MUTATED    43 102
  AMP PEAK 30(17Q12) WILD-TYPE 115 176
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 30(17Q12) MUTATED     43  102
  AMP PEAK 30(17Q12) WILD-TYPE  115  176
        clus
vv       AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE
  FEMALE                         43                          115
  MALE                          102                          176
[1] 2 2
[1] FALSE
                              vv
clus                           STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 30(17Q12) MUTATED                                       9
  AMP PEAK 30(17Q12) WILD-TYPE                                    62
                              vv
clus                           STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 30(17Q12) MUTATED                                                       46
  AMP PEAK 30(17Q12) WILD-TYPE                                                    116
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 30(17Q12) MUTATED                                                                  35
  AMP PEAK 30(17Q12) WILD-TYPE                                                                46
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 30(17Q12) MUTATED                                                 38
  AMP PEAK 30(17Q12) WILD-TYPE                                               40
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 30(17Q12) MUTATED                                                          6
  AMP PEAK 30(17Q12) WILD-TYPE                                                       15
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 30(17Q12) MUTATED                                                           4
  AMP PEAK 30(17Q12) WILD-TYPE                                                         4
                              vv
clus                           STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 30(17Q12) MUTATED                                          6
  AMP PEAK 30(17Q12) WILD-TYPE                                        7
D30V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 30(17Q12) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    46
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                          38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                  4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   6
                                                                   clus
vv                                                                  AMP PEAK 30(17Q12) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     116
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           46
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            40
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     7
[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"
D30V9, binary
                              cls
clus                             0   1
  AMP PEAK 30(17Q12) MUTATED     2 143
  AMP PEAK 30(17Q12) WILD-TYPE   4 287
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 30(17Q12) MUTATED      2  143
  AMP PEAK 30(17Q12) WILD-TYPE    4  287
     clus
vv    AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE
  NO                           2                            4
  YES                        143                          287
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 30(17Q12) MUTATED   121   1  12   3
  AMP PEAK 30(17Q12) WILD-TYPE 226  17   7  22
D30V10, multiclass
    clus
vv   AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE
  R0                        121                          226
  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"
D30V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 30(17Q12) MUTATED      25                         8
  AMP PEAK 30(17Q12) WILD-TYPE    63                         3
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 30(17Q12) MUTATED                                           1    88
  AMP PEAK 30(17Q12) WILD-TYPE                                         0   186
D30V12, multiclass
                                           clus
vv                                          AMP PEAK 30(17Q12) MUTATED
  ASIAN                                                             25
  BLACK OR AFRICAN AMERICAN                                          8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                             88
                                           clus
vv                                          AMP PEAK 30(17Q12) WILD-TYPE
  ASIAN                                                               63
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              186
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V13, binary
                              cls
clus                             0   1
  AMP PEAK 30(17Q12) MUTATED     0  96
  AMP PEAK 30(17Q12) WILD-TYPE   4 217
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 30(17Q12) MUTATED      0   96
  AMP PEAK 30(17Q12) WILD-TYPE    4  217
                        clus
vv                       AMP PEAK 30(17Q12) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                         96
                        clus
vv                       AMP PEAK 30(17Q12) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          217
[1] 2 2
[1] FALSE

Clustering(31) Variable = AMP PEAK 31(18Q11.2) MUTATION ANALYSIS
D31V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 31(18Q11.2) MUTATED    74  51
  AMP PEAK 31(18Q11.2) WILD-TYPE 180  99
  AMP PEAK 31(18Q11.2) MUTATED AMP PEAK 31(18Q11.2) WILD-TYPE 
                           125                            279 
  AMP PEAK 31(18Q11.2) MUTATED AMP PEAK 31(18Q11.2) WILD-TYPE 
                            51                             99 
$`AMP PEAK 31(18Q11.2) MUTATED`
TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-6564 TCGA-BR-6565 
        9.44         6.97         7.43        18.35        26.10         9.17 
TCGA-BR-7715 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8077 TCGA-BR-8080 
       15.42        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        12.95         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 
       15.81         0.49        11.54        15.68         8.22        13.87 
TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD 
       22.26        12.89         0.72         0.66        13.51        20.65 
TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8526 TCGA-CD-8529 
        1.15         2.83         3.25        13.15         0.07         0.13 
TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4440 
        3.42        12.43        12.20        20.02         3.02         4.01 
TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5724 
       14.01        19.07        21.99         7.07        12.00        12.03 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       11.93        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         2.96         7.40         0.62        72.23        11.38 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        0.56         5.52         0.23        26.47         5.92        12.59 
TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.76        22.75         8.98        23.84        12.30         9.67 
TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO 
       27.42        18.81        18.38         5.19        13.08         1.41 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-KB-A6F7 TCGA-KB-A93H 
        6.44         6.74         1.81         7.82        60.56        37.64 
TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BW 
        9.86        45.67        61.25         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        65.16 
TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A922 TCGA-VQ-A92D 
       11.93        18.74         1.71        36.16         9.04        64.18 
TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-ZQ-A9CR 
       42.54        22.09        40.08        32.94         0.79 

$`AMP PEAK 31(18Q11.2) WILD-TYPE`
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-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.64        30.90         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-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 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7851 
       24.76        35.24        23.93        28.01        18.15        12.43 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        12.76        18.71        17.49        14.43        11.44 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8360 
       12.26        20.55         0.56         2.66        16.31         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         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        19.17         0.26        15.85 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        5.39         9.21        12.79         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44T 
        7.53        15.81        16.44         9.86        10.68        12.56 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
        7.53         6.08         1.48        13.41        13.51         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE 
       14.17         0.53        12.82        19.36         0.46        20.42 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.64        11.57         5.13        13.18         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.07         0.10         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.13         0.10         9.34        11.31 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 
       11.61         6.58         0.10        12.62        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4444 
        1.02         7.99         8.05        54.08        29.98        47.05 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 
       12.03         0.00         9.01        18.97        22.98        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-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        15.02        28.96        79.07        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        12.36        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        10.55        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        15.16 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       14.76        13.71         9.76        15.65         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 
        7.13         7.99        16.24        14.47        21.27         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-8211 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       13.58        18.08         1.51        14.27        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       12.10        10.62        24.30         5.59        12.30        11.84 
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-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       12.95        19.36         8.88         8.81        21.21         3.45 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1X 
        3.39         5.36        12.59         6.51         5.56        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZE 
        2.53         5.56        20.15         3.72        19.73        18.21 
TCGA-R5-A7ZF TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW 
        8.52         4.60        11.05         8.61       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-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       19.04        48.79        13.25        35.24        21.73        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       27.88        32.48         7.73        28.96        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PP 
       16.31        22.19         2.50        12.79        17.85        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       15.65        13.35        26.24        27.35        64.57        14.33 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91W 
       36.69        11.70        61.22        20.81        22.68         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.50         9.73        52.24         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        29.98        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       21.11        12.43        10.62 

  AMP PEAK 31(18Q11.2) MUTATED AMP PEAK 31(18Q11.2) WILD-TYPE 
                          0.07                           0.00 
  AMP PEAK 31(18Q11.2) MUTATED AMP PEAK 31(18Q11.2) WILD-TYPE 
                        115.69                         122.30 
  AMP PEAK 31(18Q11.2) MUTATED AMP PEAK 31(18Q11.2) WILD-TYPE 
                         11.93                          13.51 
[1] "0.1 - 115.7 (11.9)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D31V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 31(18Q11.2) MUTATED         1        5       10        8        12
  AMP PEAK 31(18Q11.2) WILD-TYPE       2        9       31       23        26
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 31(18Q11.2) MUTATED          14         1         29         16
  AMP PEAK 31(18Q11.2) WILD-TYPE        41         3         56         46
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 31(18Q11.2) MUTATED           16       18
  AMP PEAK 31(18Q11.2) WILD-TYPE         25       28
D31V3, multiclass
            clus
vv           AMP PEAK 31(18Q11.2) MUTATED AMP PEAK 31(18Q11.2) WILD-TYPE
  STAGE I                               1                              2
  STAGE IA                              5                              9
  STAGE IB                             10                             31
  STAGE II                              8                             23
  STAGE IIA                            12                             26
  STAGE IIB                            14                             41
  STAGE III                             1                              3
  STAGE IIIA                           29                             56
  STAGE IIIB                           16                             46
  STAGE IIIC                           16                             25
  STAGE IV                             18                             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 31(18Q11.2) MUTATED     8  25  56  42
  AMP PEAK 31(18Q11.2) WILD-TYPE  14  65 139  77
D31V4, multiclass
    clus
vv   AMP PEAK 31(18Q11.2) MUTATED AMP PEAK 31(18Q11.2) WILD-TYPE
  T1                            8                             14
  T2                           25                             65
  T3                           56                            139
  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 31(18Q11.2) MUTATED   38 34 28 31
  AMP PEAK 31(18Q11.2) WILD-TYPE 91 84 56 58
D31V5, multiclass
    clus
vv   AMP PEAK 31(18Q11.2) MUTATED AMP PEAK 31(18Q11.2) WILD-TYPE
  N0                           38                             91
  N1                           34                             84
  N2                           28                             56
  N3                           31                             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"
D31V6, binary
                                cls
clus                               0   1
  AMP PEAK 31(18Q11.2) MUTATED   119  11
  AMP PEAK 31(18Q11.2) WILD-TYPE 268  19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(18Q11.2) MUTATED    119   11
  AMP PEAK 31(18Q11.2) WILD-TYPE  268   19
   clus
vv  AMP PEAK 31(18Q11.2) MUTATED AMP PEAK 31(18Q11.2) WILD-TYPE
  0                          119                            268
  1                           11                             19
[1] 2 2
[1] FALSE
D31V7, binary
                                cls
clus                               0   1
  AMP PEAK 31(18Q11.2) MUTATED    51  86
  AMP PEAK 31(18Q11.2) WILD-TYPE 107 192
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(18Q11.2) MUTATED     51   86
  AMP PEAK 31(18Q11.2) WILD-TYPE  107  192
        clus
vv       AMP PEAK 31(18Q11.2) MUTATED AMP PEAK 31(18Q11.2) WILD-TYPE
  FEMALE                           51                            107
  MALE                             86                            192
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 31(18Q11.2) MUTATED                                      15
  AMP PEAK 31(18Q11.2) WILD-TYPE                                    56
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 31(18Q11.2) MUTATED                                                       57
  AMP PEAK 31(18Q11.2) WILD-TYPE                                                    105
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 31(18Q11.2) MUTATED                                                                  19
  AMP PEAK 31(18Q11.2) WILD-TYPE                                                                62
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 31(18Q11.2) MUTATED                                                 26
  AMP PEAK 31(18Q11.2) WILD-TYPE                                               52
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 31(18Q11.2) MUTATED                                                          7
  AMP PEAK 31(18Q11.2) WILD-TYPE                                                       14
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 31(18Q11.2) MUTATED                                                           4
  AMP PEAK 31(18Q11.2) WILD-TYPE                                                         4
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 31(18Q11.2) MUTATED                                          8
  AMP PEAK 31(18Q11.2) WILD-TYPE                                        5
D31V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 31(18Q11.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      57
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           19
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            26
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     8
                                                                   clus
vv                                                                  AMP PEAK 31(18Q11.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       105
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             62
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              52
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       5
[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"
D31V9, binary
                                cls
clus                               0   1
  AMP PEAK 31(18Q11.2) MUTATED     4 133
  AMP PEAK 31(18Q11.2) WILD-TYPE   2 297
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(18Q11.2) MUTATED      4  133
  AMP PEAK 31(18Q11.2) WILD-TYPE    2  297
     clus
vv    AMP PEAK 31(18Q11.2) MUTATED AMP PEAK 31(18Q11.2) WILD-TYPE
  NO                             4                              2
  YES                          133                            297
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 31(18Q11.2) MUTATED   104   8   8   8
  AMP PEAK 31(18Q11.2) WILD-TYPE 243  10  11  17
D31V10, multiclass
    clus
vv   AMP PEAK 31(18Q11.2) MUTATED AMP PEAK 31(18Q11.2) WILD-TYPE
  R0                          104                            243
  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"
D31V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 31(18Q11.2) MUTATED      26                         4
  AMP PEAK 31(18Q11.2) WILD-TYPE    62                         7
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 31(18Q11.2) MUTATED                                           0
  AMP PEAK 31(18Q11.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 31(18Q11.2) MUTATED      88
  AMP PEAK 31(18Q11.2) WILD-TYPE   186
D31V12, multiclass
                                           clus
vv                                          AMP PEAK 31(18Q11.2) MUTATED
  ASIAN                                                               26
  BLACK OR AFRICAN AMERICAN                                            4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               88
                                           clus
vv                                          AMP PEAK 31(18Q11.2) WILD-TYPE
  ASIAN                                                                 62
  BLACK OR AFRICAN AMERICAN                                              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                186
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V13, binary
                                cls
clus                               0   1
  AMP PEAK 31(18Q11.2) MUTATED     2 101
  AMP PEAK 31(18Q11.2) WILD-TYPE   2 212
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(18Q11.2) MUTATED      2  101
  AMP PEAK 31(18Q11.2) WILD-TYPE    2  212
                        clus
vv                       AMP PEAK 31(18Q11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          101
                        clus
vv                       AMP PEAK 31(18Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            212
[1] 2 2
[1] FALSE

Clustering(32) Variable = AMP PEAK 32(19P13.2) MUTATION ANALYSIS
D32V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 32(19P13.2) MUTATED    33   9
  AMP PEAK 32(19P13.2) WILD-TYPE 221 141
  AMP PEAK 32(19P13.2) MUTATED AMP PEAK 32(19P13.2) WILD-TYPE 
                            42                            362 
  AMP PEAK 32(19P13.2) MUTATED AMP PEAK 32(19P13.2) WILD-TYPE 
                             9                            141 
$`AMP PEAK 32(19P13.2) MUTATED`
TCGA-B7-A5TK TCGA-BR-6456 TCGA-BR-6801 TCGA-BR-7959 TCGA-BR-8370 TCGA-BR-A453 
        9.47        17.29        21.11        18.71         3.32         6.08 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-5801 TCGA-CD-8528 TCGA-CD-8533 
       13.51        20.65        13.64        13.18         0.10         0.13 
TCGA-CD-A486 TCGA-CG-4436 TCGA-CG-5722 TCGA-CG-5727 TCGA-D7-6518 TCGA-D7-6519 
        3.42         7.99         0.99        79.07        19.13        20.55 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-A4YU 
       18.54        13.35        17.19        15.22        15.98        16.44 
TCGA-D7-A6EV TCGA-EQ-A4SO TCGA-F1-A72C TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8249 
       11.24        16.24        11.38         0.56         5.52        14.17 
TCGA-HU-8604 TCGA-HU-A4GD TCGA-IN-7808 TCGA-IN-A6RP TCGA-IN-A7NT TCGA-RD-A7BT 
       12.10        22.75         3.45         6.44         5.56         8.61 
TCGA-VQ-A8DT TCGA-VQ-A8E3 TCGA-VQ-A91S TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-AA6A 
       48.79        21.73        22.68         4.54        64.18        32.94 

$`AMP PEAK 32(19P13.2) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        19.56        11.01         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        6.97         4.64         7.43        18.35        30.90         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-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-6802 TCGA-BR-6803 
       18.05        19.89        12.16         8.98        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       32.94        12.82         9.21        24.76        35.24        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        3.45         9.07        12.76        17.49        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        12.26         9.60        20.55         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         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        19.50        13.08         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        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         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        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       13.87         7.53        22.26         1.48        13.41        13.51 
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        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL 
        0.66        19.36         0.46        20.42         1.15        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13         2.83         3.25        13.15         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.07         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.10         0.13         0.10         9.34        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         0.10        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-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       12.03        21.99         0.00         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       12.00        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02       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        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6527 
       12.66        11.93        18.84        18.61        17.85        10.26 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        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-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44         9.76         2.96        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34         7.40         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-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A8CX TCGA-HF-A5NB 
       17.06        59.54         5.03        13.58         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       26.47         1.51         5.92        14.27        12.59        11.41 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
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         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 
        8.88         8.81        27.42        21.21        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR 
       18.38         5.36         5.19        13.08         1.41         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
       12.59         6.51         1.81         7.82        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        60.56        20.15        37.64         3.72        19.73 
TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
        9.86        45.67        18.21         8.52        61.25         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        4.60         9.24        11.05         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-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 
        5.46        13.25        13.02        18.48        35.24        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       27.88        32.48         7.73        28.96        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        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       27.35        64.57        14.33        65.16        36.69        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       11.93        61.22        18.74        20.81         1.71        36.16 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
        7.36         9.50         9.73        52.24         9.04         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-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B 
       11.24        22.09        18.41        40.08        28.41        29.98 
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        21.11        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

  AMP PEAK 32(19P13.2) MUTATED AMP PEAK 32(19P13.2) WILD-TYPE 
                           0.1                            0.0 
  AMP PEAK 32(19P13.2) MUTATED AMP PEAK 32(19P13.2) WILD-TYPE 
                         79.07                         122.30 
  AMP PEAK 32(19P13.2) MUTATED AMP PEAK 32(19P13.2) WILD-TYPE 
                        13.575                         12.790 
[1] "0.1 - 79.1 (13.6)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.8"
D32V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 32(19P13.2) MUTATED         0        0        3        2         6
  AMP PEAK 32(19P13.2) WILD-TYPE       3       14       38       29        32
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 32(19P13.2) MUTATED           5         1         14          7
  AMP PEAK 32(19P13.2) WILD-TYPE        50         3         71         55
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 32(19P13.2) MUTATED            3        4
  AMP PEAK 32(19P13.2) WILD-TYPE         38       42
D32V3, multiclass
            clus
vv           AMP PEAK 32(19P13.2) MUTATED AMP PEAK 32(19P13.2) WILD-TYPE
  STAGE I                               0                              3
  STAGE IA                              0                             14
  STAGE IB                              3                             38
  STAGE II                              2                             29
  STAGE IIA                             6                             32
  STAGE IIB                             5                             50
  STAGE III                             1                              3
  STAGE IIIA                           14                             71
  STAGE IIIB                            7                             55
  STAGE IIIC                            3                             38
  STAGE IV                              4                             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
  AMP PEAK 32(19P13.2) MUTATED     1  10  25  10
  AMP PEAK 32(19P13.2) WILD-TYPE  21  80 170 109
D32V4, multiclass
    clus
vv   AMP PEAK 32(19P13.2) MUTATED AMP PEAK 32(19P13.2) WILD-TYPE
  T1                            1                             21
  T2                           10                             80
  T3                           25                            170
  T4                           10                            109
[1] 4 2
[1] TRUE
[1] "dimension of 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(19P13.2) MUTATED    13  10  11  11
  AMP PEAK 32(19P13.2) WILD-TYPE 116 108  73  78
D32V5, multiclass
    clus
vv   AMP PEAK 32(19P13.2) MUTATED AMP PEAK 32(19P13.2) WILD-TYPE
  N0                           13                            116
  N1                           10                            108
  N2                           11                             73
  N3                           11                             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"
D32V6, binary
                                cls
clus                               0   1
  AMP PEAK 32(19P13.2) MUTATED    40   4
  AMP PEAK 32(19P13.2) WILD-TYPE 347  26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 32(19P13.2) MUTATED     40    4
  AMP PEAK 32(19P13.2) WILD-TYPE  347   26
   clus
vv  AMP PEAK 32(19P13.2) MUTATED AMP PEAK 32(19P13.2) WILD-TYPE
  0                           40                            347
  1                            4                             26
[1] 2 2
[1] FALSE
D32V7, binary
                                cls
clus                               0   1
  AMP PEAK 32(19P13.2) MUTATED    17  29
  AMP PEAK 32(19P13.2) WILD-TYPE 141 249
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 32(19P13.2) MUTATED     17   29
  AMP PEAK 32(19P13.2) WILD-TYPE  141  249
        clus
vv       AMP PEAK 32(19P13.2) MUTATED AMP PEAK 32(19P13.2) WILD-TYPE
  FEMALE                           17                            141
  MALE                             29                            249
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 32(19P13.2) MUTATED                                       8
  AMP PEAK 32(19P13.2) WILD-TYPE                                    63
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 32(19P13.2) MUTATED                                                       16
  AMP PEAK 32(19P13.2) WILD-TYPE                                                    146
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 32(19P13.2) MUTATED                                                                   9
  AMP PEAK 32(19P13.2) WILD-TYPE                                                                72
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 32(19P13.2) MUTATED                                                 10
  AMP PEAK 32(19P13.2) WILD-TYPE                                               68
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 32(19P13.2) MUTATED                                                          1
  AMP PEAK 32(19P13.2) WILD-TYPE                                                       20
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 32(19P13.2) MUTATED                                                           0
  AMP PEAK 32(19P13.2) WILD-TYPE                                                         8
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 32(19P13.2) MUTATED                                          2
  AMP PEAK 32(19P13.2) WILD-TYPE                                       11
D32V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 32(19P13.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      16
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            9
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
                                                                   clus
vv                                                                  AMP PEAK 32(19P13.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       146
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             72
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              68
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      11
[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"
D32V9, binary
                                cls
clus                               0   1
  AMP PEAK 32(19P13.2) MUTATED     0  46
  AMP PEAK 32(19P13.2) WILD-TYPE   6 384
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 32(19P13.2) MUTATED      0   46
  AMP PEAK 32(19P13.2) WILD-TYPE    6  384
     clus
vv    AMP PEAK 32(19P13.2) MUTATED AMP PEAK 32(19P13.2) WILD-TYPE
  NO                             0                              6
  YES                           46                            384
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 32(19P13.2) MUTATED    35   2   4   2
  AMP PEAK 32(19P13.2) WILD-TYPE 312  16  15  23
D32V10, multiclass
    clus
vv   AMP PEAK 32(19P13.2) MUTATED AMP PEAK 32(19P13.2) WILD-TYPE
  R0                           35                            312
  R1                            2                             16
  R2                            4                             15
  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"
D32V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 32(19P13.2) MUTATED       9                         1
  AMP PEAK 32(19P13.2) WILD-TYPE    79                        10
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 32(19P13.2) MUTATED                                           1
  AMP PEAK 32(19P13.2) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 32(19P13.2) MUTATED      30
  AMP PEAK 32(19P13.2) WILD-TYPE   244
D32V12, multiclass
                                           clus
vv                                          AMP PEAK 32(19P13.2) MUTATED
  ASIAN                                                                9
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               30
                                           clus
vv                                          AMP PEAK 32(19P13.2) WILD-TYPE
  ASIAN                                                                 79
  BLACK OR AFRICAN AMERICAN                                             10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  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"
D32V13, binary
                                cls
clus                               0   1
  AMP PEAK 32(19P13.2) MUTATED     0  36
  AMP PEAK 32(19P13.2) WILD-TYPE   4 277
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 32(19P13.2) MUTATED      0   36
  AMP PEAK 32(19P13.2) WILD-TYPE    4  277
                        clus
vv                       AMP PEAK 32(19P13.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           36
                        clus
vv                       AMP PEAK 32(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            277
[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    76  41
  AMP PEAK 33(19Q12) WILD-TYPE 178 109
  AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE 
                         117                          287 
  AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE 
                          41                          109 
$`AMP PEAK 33(19Q12) MUTATED`
TCGA-B7-A5TK TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 
        9.47        17.29        19.33         9.21        15.42        28.01 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8286 
       28.73         3.45        18.71        11.44         0.69        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8370 TCGA-BR-8373 TCGA-BR-8485 
        2.66        16.31         2.20         3.32        14.79         9.21 
TCGA-BR-8487 TCGA-BR-8590 TCGA-BR-8678 TCGA-BR-8690 TCGA-BR-A453 TCGA-BR-A4J1 
        1.12         9.34        11.54        10.68         6.08         0.72 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       13.51        20.65        13.64        13.15        13.18         0.30 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A486 
        0.07         0.07         0.07         0.16         0.13         3.42 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4438 TCGA-CG-4444 
        9.34        12.43        11.61        12.20        54.08        47.05 
TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5722 TCGA-CG-5730 TCGA-D7-5577 
       19.07        21.99        22.98         0.99         4.01        12.36 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 
       11.93        19.13        18.84        18.54        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A4YY 
       15.22        10.55        12.33        21.14        16.44        13.78 
TCGA-D7-A6F0 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 
        2.96         7.13         0.62         7.99        16.24        72.23 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8244 TCGA-HU-8245 
        3.48        14.07         0.56         5.52        14.27        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       14.17        12.10        24.30        22.75        25.81        11.77 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RI 
        2.10        12.95        12.30        27.42         3.45        18.38 
TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-R5-A7O7 
        5.19         1.41         6.44         5.56        60.56        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8N9 TCGA-SW-A7EB 
       18.21         6.08         8.61         5.13        35.61         5.79 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PE 
       48.79         5.46        13.25        35.24         7.73        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U 
       17.85         1.87        36.69        18.74        22.68         1.71 
TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A94O 
       36.16         9.50         9.04         2.01         4.54        21.04 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6K 
       17.13        54.12        12.43 

$`AMP PEAK 33(19Q12) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        19.56        11.01         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        6.97         4.64         7.43        18.35        30.90         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-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        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7717 
       32.94        12.82        24.76        35.24        23.93        18.15 
TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 
       15.32        12.43         9.07        12.76        17.49        14.43 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8296 
       12.26         9.60        20.55         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        19.50        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 
       17.52         0.95        26.33         4.31        14.04        11.80 
TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       19.17         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       20.22        12.79        15.81        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       12.56        13.87         7.53        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       13.51        12.89         8.98        14.17         0.53        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL 
        0.66        19.36         0.46        20.42         1.15        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5803 TCGA-CD-8527 TCGA-CD-8528 
        5.13         2.83         3.25         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A489 
        0.13         0.10         0.10         0.13         0.10        11.31 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58         0.10        12.62        20.02         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-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-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        6.02       105.07        12.03        15.02        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-6519 
       65.10        69.04        21.07         7.99        12.66        20.55 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 
       18.61        17.85        13.35        15.98        12.79        11.31 
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-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET 
       20.91        14.27         5.92        15.16        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        11.44         9.76        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 
        4.34         7.40        14.47        21.27        11.38        19.53 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A8CX 
       22.29        17.06        59.54         5.03        13.58         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8602 TCGA-HU-8608 
       18.08        26.47         1.51         5.92        11.41        10.62 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76         5.59        12.30        11.84        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         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
       10.19         0.26        19.36        23.84         9.67         8.88 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN 
        8.81        21.21        18.81         3.39         5.36        13.08 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51         5.56         1.81         7.82 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
       13.51         2.53        20.15        37.64         3.72        19.73 
TCGA-MX-A663 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        9.86         8.52        61.25         4.60         9.24        11.05 
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-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL 
       71.38        57.44         8.94        16.87        19.04         0.92 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.02        18.48        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH 
       28.96        34.29        46.26        16.31         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        2.70         9.27        23.41        15.65        13.35        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E 
       27.35        64.57        14.33        65.16        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A924 
       61.22        20.81         7.36         9.73        52.24        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
        6.58         5.72        64.18         2.66        42.54        11.24 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       22.09        18.41        40.08        28.41        32.94        29.98 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        21.11        10.62         0.79 

  AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE 
                        0.07                         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 
                       12.33                        13.08 
[1] "0.1 - 72.2 (12.3)"  "0.0 - 122.3 (13.1)"
[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        11
  AMP PEAK 33(19Q12) WILD-TYPE       2       10       30       22        27
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 33(19Q12) MUTATED          15         2         32         17
  AMP PEAK 33(19Q12) WILD-TYPE        40         2         53         45
                              vv
clus                           STAGE IIIC STAGE IV
  AMP PEAK 33(19Q12) MUTATED            8       14
  AMP PEAK 33(19Q12) WILD-TYPE         33       32
D33V3, multiclass
            clus
vv           AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE
  STAGE I                             1                            2
  STAGE IA                            4                           10
  STAGE IB                           11                           30
  STAGE II                            9                           22
  STAGE IIA                          11                           27
  STAGE IIB                          15                           40
  STAGE III                           2                            2
  STAGE IIIA                         32                           53
  STAGE IIIB                         17                           45
  STAGE IIIC                          8                           33
  STAGE IV                           14                           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 33(19Q12) MUTATED     6  25  69  26
  AMP PEAK 33(19Q12) WILD-TYPE  16  65 126  93
D33V4, multiclass
    clus
vv   AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE
  T1                          6                           16
  T2                         25                           65
  T3                         69                          126
  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 38 22 30
  AMP PEAK 33(19Q12) WILD-TYPE 95 80 62 59
D33V5, multiclass
    clus
vv   AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE
  N0                         34                           95
  N1                         38                           80
  N2                         22                           62
  N3                         30                           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"
D33V6, binary
                              cls
clus                             0   1
  AMP PEAK 33(19Q12) MUTATED   113   9
  AMP PEAK 33(19Q12) WILD-TYPE 274  21
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 33(19Q12) MUTATED    113    9
  AMP PEAK 33(19Q12) WILD-TYPE  274   21
   clus
vv  AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE
  0                        113                          274
  1                          9                           21
[1] 2 2
[1] FALSE
D33V7, binary
                              cls
clus                             0   1
  AMP PEAK 33(19Q12) MUTATED    45  84
  AMP PEAK 33(19Q12) WILD-TYPE 113 194
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 33(19Q12) MUTATED     45   84
  AMP PEAK 33(19Q12) WILD-TYPE  113  194
        clus
vv       AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE
  FEMALE                         45                          113
  MALE                           84                          194
[1] 2 2
[1] FALSE
                              vv
clus                           STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 33(19Q12) MUTATED                                      17
  AMP PEAK 33(19Q12) WILD-TYPE                                    54
                              vv
clus                           STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 33(19Q12) MUTATED                                                       46
  AMP PEAK 33(19Q12) WILD-TYPE                                                    116
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 33(19Q12) MUTATED                                                                  23
  AMP PEAK 33(19Q12) WILD-TYPE                                                                58
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 33(19Q12) MUTATED                                                 27
  AMP PEAK 33(19Q12) WILD-TYPE                                               51
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 33(19Q12) MUTATED                                                          7
  AMP PEAK 33(19Q12) WILD-TYPE                                                       14
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 33(19Q12) MUTATED                                                           4
  AMP PEAK 33(19Q12) WILD-TYPE                                                         4
                              vv
clus                           STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 33(19Q12) MUTATED                                          4
  AMP PEAK 33(19Q12) WILD-TYPE                                        9
D33V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 33(19Q12) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     17
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    46
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         23
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                          27
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                  4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   4
                                                                   clus
vv                                                                  AMP PEAK 33(19Q12) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       54
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     116
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           58
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            51
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     9
[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"
D33V9, binary
                              cls
clus                             0   1
  AMP PEAK 33(19Q12) MUTATED     4 125
  AMP PEAK 33(19Q12) WILD-TYPE   2 305
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 33(19Q12) MUTATED      4  125
  AMP PEAK 33(19Q12) WILD-TYPE    2  305
     clus
vv    AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE
  NO                           4                            2
  YES                        125                          305
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 33(19Q12) MUTATED    98   6   7   6
  AMP PEAK 33(19Q12) WILD-TYPE 249  12  12  19
D33V10, multiclass
    clus
vv   AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE
  R0                         98                          249
  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                         6
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 33(19Q12) MUTATED                                           1    73
  AMP PEAK 33(19Q12) WILD-TYPE                                         0   201
D33V12, multiclass
                                           clus
vv                                          AMP PEAK 33(19Q12) MUTATED
  ASIAN                                                             32
  BLACK OR AFRICAN AMERICAN                                          5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                             73
                                           clus
vv                                          AMP PEAK 33(19Q12) WILD-TYPE
  ASIAN                                                               56
  BLACK OR AFRICAN AMERICAN                                            6
  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"
D33V13, binary
                              cls
clus                             0   1
  AMP PEAK 33(19Q12) MUTATED     1  94
  AMP PEAK 33(19Q12) WILD-TYPE   3 219
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 33(19Q12) MUTATED      1   94
  AMP PEAK 33(19Q12) WILD-TYPE    3  219
                        clus
vv                       AMP PEAK 33(19Q12) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         94
                        clus
vv                       AMP PEAK 33(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          219
[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    64  34
  AMP PEAK 34(19Q13.32) WILD-TYPE 190 116
  AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE 
                             98                             306 
  AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE 
                             34                             116 
$`AMP PEAK 34(19Q13.32) MUTATED`
TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7716 
        9.47         6.61        19.33         9.17         9.21        28.01 
TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8286 
        3.45        12.76        18.71         0.69        12.26        12.95 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8370 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8690 
       16.31         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        13.64        13.18 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-A487 TCGA-CD-A48A 
        0.07         0.07         0.07         0.10         9.34        12.43 
TCGA-CD-A48C TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4472 
       11.61        54.08         4.01        47.05        21.99        12.00 
TCGA-CG-4475 TCGA-CG-5722 TCGA-CG-5730 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 
       22.98         0.99         4.01        12.36        11.93        19.13 
TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8578 
       18.54        17.19        10.55        12.33        24.72        21.14 
TCGA-D7-A4YU TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 
       16.44         7.99        16.24        72.23         3.48        14.07 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
        5.52         0.23        14.27        12.59        14.17        12.10 
TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 
       24.30        22.75        11.77         2.10        12.95        12.30 
TCGA-HU-A4H6 TCGA-IN-7808 TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-AB1V TCGA-KB-A6F7 
        9.67         3.45         5.19         6.44         7.82        60.56 
TCGA-R5-A7ZR TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT 
        6.08        11.05         8.61        35.61         5.79        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PE 
        5.46        13.25        35.24        32.48         7.73        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A91A TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X 
       12.79         1.87        36.69         1.71        36.16         9.50 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA6F 
        9.04         2.01        64.18        42.54        11.24        54.12 
TCGA-VQ-AA6I TCGA-VQ-AA6K 
       16.14        12.43 

$`AMP PEAK 34(19Q13.32) WILD-TYPE`
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-4267 TCGA-BR-4279 
        4.64         7.43        18.35        30.90         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-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10        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        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 
       12.82        24.76        35.24        23.93        15.42        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8059 
       15.32        28.73        12.43         9.07        17.49        14.43 
TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 
       11.44         9.60        20.55         8.05         0.56         2.66 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        19.50        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-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        5.39        25.18        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U 
       16.44         9.86        15.68         8.22        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        7.53        22.26         1.48        13.41        13.51        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        12.82         0.66        19.36 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.42         1.15        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8527 TCGA-CD-8529 
        3.25        13.15         0.30         0.07         0.07         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.16         0.10         0.10         0.13         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
        3.42        11.31         6.58        12.20         0.10        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-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-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-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         6.02       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07        65.10        69.04        21.07         7.99 
TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       12.66        20.55        18.84        18.61        17.85        13.35 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8572 
       10.26        15.22        15.98        12.79        11.31        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-A6EV 
        5.92        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44         9.76         2.96        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-A448 
        4.34         7.40         7.13         0.62        14.47        21.27 
TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       11.38        19.53        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       13.58         0.56        18.08        26.47         1.51         5.92 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       11.41        10.62         0.76         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       24.20         3.25        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-A4H3 
        0.10         6.51         6.25        10.19         0.26        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
       23.84         8.88         8.81        27.42        21.21        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR 
        3.39        18.38         5.36        13.08         1.41         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 
       12.59         6.51         5.56         1.81        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        5.56        20.15        37.64         3.72        19.73         9.86 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52        61.25         4.60         9.24 
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-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        16.87        19.04 
TCGA-VQ-A8DL TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        0.92        13.02        18.48        21.73        34.45        27.88 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PJ 
       28.96        34.29        46.26        16.31         2.50         2.70 
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        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E 
       27.35        64.57        14.33        65.16        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91Y 
       61.22        18.74        20.81        22.68         7.36         9.73 
TCGA-VQ-A91Z TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O 
       52.24        55.43         4.54         6.58         5.72        21.04 
TCGA-VQ-A94P TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
        2.66        22.09        18.41        40.08        28.41        32.94 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       29.98        17.13        26.04        21.11        10.62         0.79 

  AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE 
                           0.07                            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 
                          12.18                           13.43 
[1] "0.1 - 72.2 (12.2)"  "0.0 - 122.3 (13.4)"
[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         6
  AMP PEAK 34(19Q13.32) WILD-TYPE       3       10       33       27        32
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 34(19Q13.32) MUTATED          15         2         29         17
  AMP PEAK 34(19Q13.32) WILD-TYPE        40         2         56         45
                                 vv
clus                              STAGE IIIC STAGE IV
  AMP PEAK 34(19Q13.32) MUTATED            7       13
  AMP PEAK 34(19Q13.32) WILD-TYPE         34       33
D34V3, multiclass
            clus
vv           AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE
  STAGE I                                0                               3
  STAGE IA                               4                              10
  STAGE IB                               8                              33
  STAGE II                               4                              27
  STAGE IIA                              6                              32
  STAGE IIB                             15                              40
  STAGE III                              2                               2
  STAGE IIIA                            29                              56
  STAGE IIIB                            17                              45
  STAGE IIIC                             7                              34
  STAGE IV                              13                              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 34(19Q13.32) MUTATED     5  18  58  26
  AMP PEAK 34(19Q13.32) WILD-TYPE  17  72 137  93
D34V4, multiclass
    clus
vv   AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE
  T1                             5                              17
  T2                            18                              72
  T3                            58                             137
  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 103  83  67  62
D34V5, multiclass
    clus
vv   AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE
  N0                            26                             103
  N1                            35                              83
  N2                            17                              67
  N3                            27                              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"
D34V6, binary
                                 cls
clus                                0   1
  AMP PEAK 34(19Q13.32) MUTATED    95   7
  AMP PEAK 34(19Q13.32) WILD-TYPE 292  23
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 34(19Q13.32) MUTATED     95    7
  AMP PEAK 34(19Q13.32) WILD-TYPE  292   23
   clus
vv  AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE
  0                            95                             292
  1                             7                              23
[1] 2 2
[1] FALSE
D34V7, binary
                                 cls
clus                                0   1
  AMP PEAK 34(19Q13.32) MUTATED    37  72
  AMP PEAK 34(19Q13.32) WILD-TYPE 121 206
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 34(19Q13.32) MUTATED     37   72
  AMP PEAK 34(19Q13.32) WILD-TYPE  121  206
        clus
vv       AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE
  FEMALE                            37                             121
  MALE                              72                             206
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 34(19Q13.32) MUTATED                                      16
  AMP PEAK 34(19Q13.32) WILD-TYPE                                    55
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 34(19Q13.32) MUTATED                                                       37
  AMP PEAK 34(19Q13.32) WILD-TYPE                                                    125
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 34(19Q13.32) MUTATED                                                                  19
  AMP PEAK 34(19Q13.32) WILD-TYPE                                                                62
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 34(19Q13.32) MUTATED                                                 22
  AMP PEAK 34(19Q13.32) WILD-TYPE                                               56
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 34(19Q13.32) MUTATED                                                          6
  AMP PEAK 34(19Q13.32) WILD-TYPE                                                       15
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 34(19Q13.32) MUTATED                                                           2
  AMP PEAK 34(19Q13.32) WILD-TYPE                                                         6
                                 vv
clus                              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 34(19Q13.32) MUTATED                                          5
  AMP PEAK 34(19Q13.32) WILD-TYPE                                        8
D34V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 34(19Q13.32) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        16
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       37
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            19
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             22
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      5
                                                                   clus
vv                                                                  AMP PEAK 34(19Q13.32) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          55
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              62
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               56
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                        8
[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"
D34V9, binary
                                 cls
clus                                0   1
  AMP PEAK 34(19Q13.32) MUTATED     4 105
  AMP PEAK 34(19Q13.32) WILD-TYPE   2 325
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 34(19Q13.32) MUTATED      4  105
  AMP PEAK 34(19Q13.32) WILD-TYPE    2  325
     clus
vv    AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE
  NO                              4                               2
  YES                           105                             325
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 34(19Q13.32) MUTATED    83   7   6   6
  AMP PEAK 34(19Q13.32) WILD-TYPE 264  11  13  19
D34V10, multiclass
    clus
vv   AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE
  R0                            83                             264
  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                         8
                                 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      62
  AMP PEAK 34(19Q13.32) WILD-TYPE   212
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                                                                62
                                           clus
vv                                          AMP PEAK 34(19Q13.32) WILD-TYPE
  ASIAN                                                                  62
  BLACK OR AFRICAN AMERICAN                                               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               0
  WHITE                                                                 212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V13, binary
                                 cls
clus                                0   1
  AMP PEAK 34(19Q13.32) MUTATED     0  75
  AMP PEAK 34(19Q13.32) WILD-TYPE   4 238
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 34(19Q13.32) MUTATED      0   75
  AMP PEAK 34(19Q13.32) WILD-TYPE    4  238
                        clus
vv                       AMP PEAK 34(19Q13.32) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            75
                        clus
vv                       AMP PEAK 34(19Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             238
[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   170 104
  AMP PEAK 35(20Q13.2) WILD-TYPE  84  46
  AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE 
                           274                            130 
  AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE 
                           104                             46 
$`AMP PEAK 35(20Q13.2) MUTATED`
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-4191 TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
       18.35        30.90         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        21.11        32.94        12.82         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       15.42        28.01        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 
       12.76        18.71        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        16.31         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         0.26         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        15.81         9.34         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U 
       16.44         9.86        15.68         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        22.26         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        13.64 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        3.25        13.15        13.18         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 
        0.07         0.10         0.13         0.16         0.10         0.13 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        0.13         3.42         9.34        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20         0.10        20.02         3.02        27.02        15.95 
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-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4469 
       47.05        19.07        12.03        21.99        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5722 
       12.00        22.98        30.97        36.00         1.02         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        79.07         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
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-D7-6820 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-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       19.50        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
        5.92        15.16        13.71        11.24        11.31         9.76 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 
        2.96        15.65         8.38         7.40         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX 
       14.07        22.29        17.06         0.56         5.52         0.23 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
       26.47         1.51         5.92        14.27        12.59        14.17 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GC 
       12.10        10.62         0.76        24.30        12.30         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       22.75        25.81        11.77         8.98         0.10         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       10.19         0.26         2.10        12.95        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 
        9.67         8.81        27.42        21.21         3.45         3.39 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT 
       18.38         5.19         1.41         6.74        12.59         5.56 
TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G 
        1.81        13.51         2.53         5.56        60.56        20.15 
TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       37.64         9.86        45.67        18.21         8.52        61.25 
TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 
        6.08         8.61        16.67        37.91       115.69        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
        8.94        35.61         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-A8PC 
       13.25        13.02        18.48        35.24        21.73        46.26 
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-A8PQ TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        27.35        64.57        14.33        65.16        36.69 
TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       11.93        18.74        22.68         1.71        36.16         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 
        9.50         9.73        52.24         9.04         2.01         4.54 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
        5.72        64.18        21.04        42.54        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       40.08        32.94        29.98        17.13        54.12        26.04 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11        12.43        10.62         0.79 

$`AMP PEAK 35(20Q13.2) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-BR-4188 TCGA-BR-4267 TCGA-BR-4279 
       26.70        11.70        19.56         7.43         6.18         9.57 
TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 
       34.68        32.78        25.61        12.16         8.98        30.90 
TCGA-BR-6803 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-8058 
       31.20        24.76        23.93        12.43         9.07        17.49 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8360 TCGA-BR-8361 
       12.26        20.55         8.05        12.95         6.18        19.50 
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-8382 TCGA-BR-8384 
        4.31         3.32        11.80        19.17        15.85         3.72 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8680 TCGA-BR-A44T 
        1.12        12.79        13.45         6.28        15.81        12.56 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 
        6.08        13.41        13.51         8.98        14.17        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5802 
        0.66        19.36        11.57         5.13         2.83         0.30 
TCGA-CD-5803 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A4MJ TCGA-CG-4306 
        0.07         0.10         0.10        11.31        12.62         1.02 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 
        0.00         9.01         6.97         0.99         6.02       105.07 
TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6818 TCGA-D7-8574 
       65.10        21.07        18.61        17.85        10.55        17.19 
TCGA-D7-8575 TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6EY TCGA-D7-A748 TCGA-D7-A74B 
       18.21        13.78        14.76        11.44         4.34         7.13 
TCGA-F1-A448 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-A5NB TCGA-HU-8602 
       21.27        59.54         5.03        13.58        18.08        11.41 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT 
        5.59        11.84        24.20        21.37        29.98         6.51 
TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP 
       19.36         8.88        18.81         5.36        13.08         6.44 
TCGA-IN-A7NR TCGA-IN-AB1V TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A804 TCGA-R5-A805 
        6.51         7.82         3.72        19.73         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-A8NB TCGA-SW-A7EA TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       16.87        19.04        34.45        27.88        32.48         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PS 
       28.96        34.29        16.31         9.27        23.41        13.35 
TCGA-VQ-A8PT TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A924 TCGA-VQ-A927 
       26.24        11.70        61.22        20.81        55.43         6.58 
TCGA-VQ-A94P TCGA-VQ-A94U TCGA-VQ-AA69 TCGA-VQ-AA6I 
        2.66        22.09        28.41        16.14 

  AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE 
                          0.07                           0.00 
  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 
                        12.790                         13.015 
[1] "0.1 - 115.7 (12.8)" "0.0 - 122.3 (13.0)"
[1] "hr=" "1.1"
D35V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 35(20Q13.2) MUTATED         2       11       24       18        25
  AMP PEAK 35(20Q13.2) WILD-TYPE       1        3       17       13        13
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 35(20Q13.2) MUTATED          39         4         63         42
  AMP PEAK 35(20Q13.2) WILD-TYPE        16         0         22         20
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 35(20Q13.2) MUTATED           23       29
  AMP PEAK 35(20Q13.2) WILD-TYPE         18       17
D35V3, multiclass
            clus
vv           AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE
  STAGE I                               2                              1
  STAGE IA                             11                              3
  STAGE IB                             24                             17
  STAGE II                             18                             13
  STAGE IIA                            25                             13
  STAGE IIB                            39                             16
  STAGE III                             4                              0
  STAGE IIIA                           63                             22
  STAGE IIIB                           42                             20
  STAGE IIIC                           23                             18
  STAGE IV                             29                             17
[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    13  63 136  72
  AMP PEAK 35(20Q13.2) WILD-TYPE   9  27  59  47
D35V4, multiclass
    clus
vv   AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE
  T1                           13                              9
  T2                           63                             27
  T3                          136                             59
  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   78 87 60 54
  AMP PEAK 35(20Q13.2) WILD-TYPE 51 31 24 35
D35V5, multiclass
    clus
vv   AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE
  N0                           78                             51
  N1                           87                             31
  N2                           60                             24
  N3                           54                             35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                                cls
clus                               0   1
  AMP PEAK 35(20Q13.2) MUTATED   257  18
  AMP PEAK 35(20Q13.2) WILD-TYPE 130  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 35(20Q13.2) MUTATED    257   18
  AMP PEAK 35(20Q13.2) WILD-TYPE  130   12
   clus
vv  AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE
  0                          257                            130
  1                           18                             12
[1] 2 2
[1] FALSE
D35V7, binary
                                cls
clus                               0   1
  AMP PEAK 35(20Q13.2) MUTATED    93 197
  AMP PEAK 35(20Q13.2) WILD-TYPE  65  81
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 35(20Q13.2) MUTATED     93  197
  AMP PEAK 35(20Q13.2) WILD-TYPE   65   81
        clus
vv       AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE
  FEMALE                           93                             65
  MALE                            197                             81
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 35(20Q13.2) MUTATED                                      32
  AMP PEAK 35(20Q13.2) WILD-TYPE                                    39
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 35(20Q13.2) MUTATED                                                      101
  AMP PEAK 35(20Q13.2) WILD-TYPE                                                     61
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 35(20Q13.2) MUTATED                                                                  63
  AMP PEAK 35(20Q13.2) WILD-TYPE                                                                18
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 35(20Q13.2) MUTATED                                                 64
  AMP PEAK 35(20Q13.2) WILD-TYPE                                               14
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 35(20Q13.2) MUTATED                                                         13
  AMP PEAK 35(20Q13.2) WILD-TYPE                                                        8
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 35(20Q13.2) MUTATED                                                           6
  AMP PEAK 35(20Q13.2) WILD-TYPE                                                         2
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 35(20Q13.2) MUTATED                                          9
  AMP PEAK 35(20Q13.2) WILD-TYPE                                        4
D35V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 35(20Q13.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       32
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     101
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           63
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            64
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     9
                                                                   clus
vv                                                                  AMP PEAK 35(20Q13.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         39
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        61
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             18
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       4
[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"
D35V9, binary
                                cls
clus                               0   1
  AMP PEAK 35(20Q13.2) MUTATED     4 286
  AMP PEAK 35(20Q13.2) WILD-TYPE   2 144
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 35(20Q13.2) MUTATED      4  286
  AMP PEAK 35(20Q13.2) WILD-TYPE    2  144
     clus
vv    AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE
  NO                             4                              2
  YES                          286                            144
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 35(20Q13.2) MUTATED   236  10  13  14
  AMP PEAK 35(20Q13.2) WILD-TYPE 111   8   6  11
D35V10, multiclass
    clus
vv   AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE
  R0                          236                            111
  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                         2
                                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     174
  AMP PEAK 35(20Q13.2) WILD-TYPE   100
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                                                              174
                                           clus
vv                                          AMP PEAK 35(20Q13.2) WILD-TYPE
  ASIAN                                                                 27
  BLACK OR AFRICAN AMERICAN                                              2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                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"
D35V13, binary
                                cls
clus                               0   1
  AMP PEAK 35(20Q13.2) MUTATED     3 202
  AMP PEAK 35(20Q13.2) WILD-TYPE   1 111
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 35(20Q13.2) MUTATED      3  202
  AMP PEAK 35(20Q13.2) WILD-TYPE    1  111
                        clus
vv                       AMP PEAK 35(20Q13.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          202
                        clus
vv                       AMP PEAK 35(20Q13.2) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            111
[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    49  27
  AMP PEAK 36(XQ27.3) WILD-TYPE 205 123
  AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE 
                           76                           328 
  AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE 
                           27                           123 
$`AMP PEAK 36(XQ27.3) MUTATED`
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4191 
       11.70        11.01         9.44         6.61         4.64        18.35 
TCGA-BR-6458 TCGA-BR-6801 TCGA-BR-7717 TCGA-BR-8059 TCGA-BR-8362 TCGA-BR-8370 
       19.33        21.11        18.15        14.43        13.08         3.32 
TCGA-BR-8486 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-A44U TCGA-BR-A4CQ 
       20.22         0.49        15.81         9.86        13.87        22.26 
TCGA-BR-A4IY TCGA-BR-A4J2 TCGA-BR-A4QI TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-A4MG 
       12.89        14.17        13.64         0.07         0.07         6.58 
TCGA-CG-4300 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4460 TCGA-CG-4469 TCGA-CG-4472 
       20.02         8.05        54.08        21.99         7.07        12.00 
TCGA-CG-5727 TCGA-CG-5734 TCGA-D7-5579 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6528 
       79.07         7.99        11.93        18.54        17.19        15.22 
TCGA-D7-6815 TCGA-D7-6822 TCGA-D7-A4YX TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F2 
       15.98        12.33        15.16        11.24         9.76        15.65 
TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-A4BF 
        7.40         0.62         7.99        72.23         3.48         5.52 
TCGA-HU-8244 TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       14.27        12.10        24.30        12.30        11.84        24.20 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4H5 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RL 
       22.75        25.81        12.30         3.45         3.39         5.19 
TCGA-IN-A6RP TCGA-R5-A7O7 TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PU 
        6.44        45.67        35.24         7.73        46.26        27.35 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       14.33        65.16        11.93        20.81        22.68         1.71 
TCGA-VQ-A91Z TCGA-VQ-A92D TCGA-VQ-AA68 TCGA-VQ-AA6A 
       52.24        64.18        40.08        32.94 

$`AMP PEAK 36(XQ27.3) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4201 
       26.70        19.56         9.47         6.97         7.43        30.90 
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        32.94        12.82         9.21        24.76        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       23.93        15.42        28.01        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 
        3.45         9.07        12.76        18.71        17.49        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        12.26         9.60        20.55         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33         4.31        14.04        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
        7.53        11.54        16.44        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       12.56         7.53         6.08         1.48        13.41        13.51 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72         0.53        12.82         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL 
       13.51         0.46        20.65        20.42         1.15        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.10         0.10         0.13         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        11.31        12.43        11.61        12.20         0.10 
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-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97        22.98        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-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       21.07        12.36        12.66        19.13        20.55        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 
       18.61        17.85        13.35        10.26        12.79        10.55 
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-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 
       13.78        14.76        13.71        11.31        11.44         2.96 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 
        8.38         4.34         7.13        16.24        14.47        21.27 
TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       11.38        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 
        5.03        13.58         0.56         0.23        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 
        1.51         5.92        12.59        14.17        11.41        10.62 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        0.76         5.59         3.25        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         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        19.36        23.84         9.67         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ 
        8.81        27.42        21.21        18.81        18.38         5.36 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       13.08         1.41         6.74        12.59         6.51         5.56 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        1.81         7.82        13.51         2.53         5.56        60.56 
TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZE 
       20.15        37.64         3.72        19.73         9.86        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        61.25         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-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.25        13.02        18.48        21.73        34.45        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       32.48        28.96        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-A91A TCGA-VQ-A91D 
       15.65        13.35        26.24        64.57        36.69        11.70 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       61.22        18.74        36.16         7.36         9.50         9.73 
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-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 
       21.04         2.66        42.54        11.24        22.09        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        29.98        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11        12.43        10.62         0.79 

  AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE 
                         0.07                          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 
                       13.755                        12.790 
[1] "0.1 - 79.1 (13.8)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.2"
D36V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 36(XQ27.3) MUTATED         1        5        8        5         6
  AMP PEAK 36(XQ27.3) WILD-TYPE       2        9       33       26        32
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 36(XQ27.3) MUTATED          13         2         15          9
  AMP PEAK 36(XQ27.3) WILD-TYPE        42         2         70         53
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 36(XQ27.3) MUTATED            4       11
  AMP PEAK 36(XQ27.3) WILD-TYPE         37       35
D36V3, multiclass
            clus
vv           AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE
  STAGE I                              1                             2
  STAGE IA                             5                             9
  STAGE IB                             8                            33
  STAGE II                             5                            26
  STAGE IIA                            6                            32
  STAGE IIB                           13                            42
  STAGE III                            2                             2
  STAGE IIIA                          15                            70
  STAGE IIIB                           9                            53
  STAGE IIIC                           4                            37
  STAGE IV                            11                            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 36(XQ27.3) MUTATED     6  18  36  20
  AMP PEAK 36(XQ27.3) WILD-TYPE  16  72 159  99
D36V4, multiclass
    clus
vv   AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE
  T1                           6                            16
  T2                          18                            72
  T3                          36                           159
  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    26  25  16  12
  AMP PEAK 36(XQ27.3) WILD-TYPE 103  93  68  77
D36V5, multiclass
    clus
vv   AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE
  N0                          26                           103
  N1                          25                            93
  N2                          16                            68
  N3                          12                            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"
D36V6, binary
                               cls
clus                              0   1
  AMP PEAK 36(XQ27.3) MUTATED    76   5
  AMP PEAK 36(XQ27.3) WILD-TYPE 311  25
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 36(XQ27.3) MUTATED     76    5
  AMP PEAK 36(XQ27.3) WILD-TYPE  311   25
   clus
vv  AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE
  0                          76                           311
  1                           5                            25
[1] 2 2
[1] FALSE
D36V7, binary
                               cls
clus                              0   1
  AMP PEAK 36(XQ27.3) MUTATED    30  53
  AMP PEAK 36(XQ27.3) WILD-TYPE 128 225
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 36(XQ27.3) MUTATED     30   53
  AMP PEAK 36(XQ27.3) WILD-TYPE  128  225
        clus
vv       AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE
  FEMALE                          30                           128
  MALE                            53                           225
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 36(XQ27.3) MUTATED                                       8
  AMP PEAK 36(XQ27.3) WILD-TYPE                                    63
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 36(XQ27.3) MUTATED                                                       28
  AMP PEAK 36(XQ27.3) WILD-TYPE                                                    134
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 36(XQ27.3) MUTATED                                                                  16
  AMP PEAK 36(XQ27.3) WILD-TYPE                                                                65
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 36(XQ27.3) MUTATED                                                 23
  AMP PEAK 36(XQ27.3) WILD-TYPE                                               55
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 36(XQ27.3) MUTATED                                                          2
  AMP PEAK 36(XQ27.3) WILD-TYPE                                                       19
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 36(XQ27.3) MUTATED                                                           2
  AMP PEAK 36(XQ27.3) WILD-TYPE                                                         6
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 36(XQ27.3) MUTATED                                          3
  AMP PEAK 36(XQ27.3) WILD-TYPE                                       10
D36V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 36(XQ27.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     28
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          16
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           23
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    3
                                                                   clus
vv                                                                  AMP PEAK 36(XQ27.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            65
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             55
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     10
[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"
D36V9, binary
                               cls
clus                              0   1
  AMP PEAK 36(XQ27.3) MUTATED     1  82
  AMP PEAK 36(XQ27.3) WILD-TYPE   5 348
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 36(XQ27.3) MUTATED      1   82
  AMP PEAK 36(XQ27.3) WILD-TYPE    5  348
     clus
vv    AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE
  NO                            1                             5
  YES                          82                           348
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 36(XQ27.3) MUTATED    64   4   2   6
  AMP PEAK 36(XQ27.3) WILD-TYPE 283  14  17  19
D36V10, multiclass
    clus
vv   AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE
  R0                          64                           283
  R1                           4                            14
  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"
D36V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 36(XQ27.3) MUTATED      19                         3
  AMP PEAK 36(XQ27.3) WILD-TYPE    69                         8
                               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   224
D36V12, multiclass
                                           clus
vv                                          AMP PEAK 36(XQ27.3) MUTATED
  ASIAN                                                              19
  BLACK OR AFRICAN AMERICAN                                           3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              50
                                           clus
vv                                          AMP PEAK 36(XQ27.3) WILD-TYPE
  ASIAN                                                                69
  BLACK OR AFRICAN AMERICAN                                             8
  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"
D36V13, binary
                               cls
clus                              0   1
  AMP PEAK 36(XQ27.3) MUTATED     1  58
  AMP PEAK 36(XQ27.3) WILD-TYPE   3 255
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 36(XQ27.3) MUTATED      1   58
  AMP PEAK 36(XQ27.3) WILD-TYPE    3  255
                        clus
vv                       AMP PEAK 36(XQ27.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          58
                        clus
vv                       AMP PEAK 36(XQ27.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           255
[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  51
  DEL PEAK  1(1P36.11) WILD-TYPE 182  99
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           123                            281 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            51                             99 
$`DEL PEAK  1(1P36.11) MUTATED`
TCGA-B7-5816 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 
       26.70        11.01         9.44        18.35         6.18         9.57 
TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7704 TCGA-BR-7959 TCGA-BR-8060 
       17.29        19.33         9.17        35.24        18.71        11.44 
TCGA-BR-8289 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8677 TCGA-BR-8678 
        2.66         5.39        25.18         9.21         0.49        11.54 
TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4PD TCGA-BR-A4PE 
        9.86        10.68         7.53        22.26        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8529 
        1.15        13.64         3.25         0.07         0.07         0.13 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.13         3.42         9.34        11.31 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4437 
       11.61        12.20        20.02         3.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4469 
       54.08        14.01        29.98        47.05        19.07         7.07 
TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-D7-5579 
       30.97         1.02        12.03        15.02         4.01        11.93 
TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6822 
       20.55        17.19        10.26        15.22        12.79        12.33 
TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-A4YY TCGA-D7-A6EX TCGA-D7-A6F0 
       24.72        19.50        18.21        13.78        11.31         2.96 
TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-A72C TCGA-FP-8099 
        7.40         0.62         7.99        16.24        11.38        17.06 
TCGA-FP-8211 TCGA-FP-A4BF TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8604 
       13.58         5.52         1.51         5.92        14.17        12.10 
TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4HD 
       25.81         8.98        12.95        23.84        12.30        27.42 
TCGA-IN-AB1V TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZR 
        7.82        60.56        37.64         9.86        18.21         6.08 
TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N9 TCGA-VQ-A8DL 
        9.24         8.61        16.67       122.30        35.61         0.92 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE 
       13.25        13.02        18.48         7.73        46.26        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A8PU 
       12.79         2.70        17.85         1.87        13.35        27.35 
TCGA-VQ-A91A TCGA-VQ-A91Q TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-A92D 
       36.69        20.81         9.73        52.24         4.54        64.18 
TCGA-VQ-A94O TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       21.04        11.24        18.41        40.08        32.94        29.98 
TCGA-VQ-AA6D TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       17.13        12.43         0.79 

$`DEL PEAK  1(1P36.11) WILD-TYPE`
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-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        7.43        30.90         6.61        34.68        15.95        13.87 
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        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
        9.07        12.76        17.49        14.43         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 
        9.60        20.55         8.05         0.56        12.95        16.31 
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        19.50        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        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       15.85         3.72        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 
        9.34        13.45         6.28         7.53        15.81        16.44 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CS 
       15.68         8.22        12.56        13.87         6.08         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        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        12.82         0.66        19.36        13.51         0.46 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       11.57         5.13         2.83        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.07         0.10         0.16         0.10 
TCGA-CD-8536 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 
        0.10        12.43         6.58         0.10        12.62        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4440 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       15.95         1.02         4.01        12.03        21.99         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97        12.00        22.98         6.97        36.00 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 
        0.99         6.02         0.99       105.07        28.96        79.07 
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        12.36        12.66 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 
       15.98        10.55        11.31        16.80        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        15.16 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 
       14.76        13.71        11.24        11.44         9.76        15.65 
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-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
        3.48        19.53        14.07        22.29        59.54         5.03 
TCGA-FP-8631 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8245 
        0.56         0.23        18.08        26.47        14.27        12.59 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       11.41        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ 
       11.84        24.20         3.25        22.75        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         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
        2.10        19.36         9.67         8.88         8.81        21.21 
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         5.36         5.19 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.08         1.41         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93G 
        5.56         1.81        13.51         2.53         5.56        20.15 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
        3.72        19.73        45.67         8.52        61.25         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        35.24        21.73        34.45        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PO 
       32.48        28.96        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        26.24        64.57        14.33        65.16 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U 
       11.70        11.93        61.22        18.74        22.68         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
       36.16         7.36         9.50         9.04         2.01        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA69 
        6.58         5.72         2.66        42.54        22.09        28.41 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       54.12        26.04        16.14        21.11        10.62 

  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                          0.07                           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 
                         12.33                          13.08 
[1] "0.1 - 122.3 (12.3)" "0.0 - 116.4 (13.1)"
[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       14       11        14
  DEL PEAK  1(1P36.11) WILD-TYPE       3       12       27       20        24
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  1(1P36.11) MUTATED          14         1         30         18
  DEL PEAK  1(1P36.11) WILD-TYPE        41         3         55         44
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK  1(1P36.11) MUTATED            8       15
  DEL PEAK  1(1P36.11) WILD-TYPE         33       31
D37V3, multiclass
            clus
vv           DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  STAGE I                               0                              3
  STAGE IA                              2                             12
  STAGE IB                             14                             27
  STAGE II                             11                             20
  STAGE IIA                            14                             24
  STAGE IIB                            14                             41
  STAGE III                             1                              3
  STAGE IIIA                           30                             55
  STAGE IIIB                           18                             44
  STAGE IIIC                            8                             33
  STAGE IV                             15                             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  1(1P36.11) MUTATED     3  30  65  31
  DEL PEAK  1(1P36.11) WILD-TYPE  19  60 130  88
D37V4, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  T1                            3                             19
  T2                           30                             60
  T3                           65                            130
  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   37 34 27 27
  DEL PEAK  1(1P36.11) WILD-TYPE 92 84 57 62
D37V5, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  N0                           37                             92
  N1                           34                             84
  N2                           27                             57
  N3                           27                             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"
D37V6, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED   118   9
  DEL PEAK  1(1P36.11) WILD-TYPE 269  21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    118    9
  DEL PEAK  1(1P36.11) WILD-TYPE  269   21
   clus
vv  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  0                          118                            269
  1                            9                             21
[1] 2 2
[1] FALSE
D37V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED    45  88
  DEL PEAK  1(1P36.11) WILD-TYPE 113 190
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     45   88
  DEL PEAK  1(1P36.11) WILD-TYPE  113  190
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  FEMALE                           45                            113
  MALE                             88                            190
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK  1(1P36.11) MUTATED                                      11
  DEL PEAK  1(1P36.11) WILD-TYPE                                    60
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  1(1P36.11) MUTATED                                                       42
  DEL PEAK  1(1P36.11) WILD-TYPE                                                    120
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  1(1P36.11) MUTATED                                                                  31
  DEL PEAK  1(1P36.11) WILD-TYPE                                                                50
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  1(1P36.11) MUTATED                                                 35
  DEL PEAK  1(1P36.11) WILD-TYPE                                               43
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK  1(1P36.11) MUTATED                                                          7
  DEL PEAK  1(1P36.11) WILD-TYPE                                                       14
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK  1(1P36.11) MUTATED                                                           2
  DEL PEAK  1(1P36.11) WILD-TYPE                                                         6
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK  1(1P36.11) MUTATED                                          5
  DEL PEAK  1(1P36.11) WILD-TYPE                                        8
D37V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  1(1P36.11) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       11
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      42
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           31
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     5
                                                                   clus
vv                                                                  DEL PEAK  1(1P36.11) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         60
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       120
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             50
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              43
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       8
[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"
D37V9, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED     3 130
  DEL PEAK  1(1P36.11) WILD-TYPE   3 300
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      3  130
  DEL PEAK  1(1P36.11) WILD-TYPE    3  300
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  NO                             3                              3
  YES                          130                            300
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  1(1P36.11) MUTATED    96   8   9   9
  DEL PEAK  1(1P36.11) WILD-TYPE 251  10  10  16
D37V10, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  R0                           96                            251
  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                         7
                                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      78
  DEL PEAK  1(1P36.11) WILD-TYPE   196
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                                                               78
                                           clus
vv                                          DEL PEAK  1(1P36.11) WILD-TYPE
  ASIAN                                                                 60
  BLACK OR AFRICAN AMERICAN                                              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                196
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V13, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED     0  87
  DEL PEAK  1(1P36.11) WILD-TYPE   4 226
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      0   87
  DEL PEAK  1(1P36.11) WILD-TYPE    4  226
                        clus
vv                       DEL PEAK  1(1P36.11) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           87
                        clus
vv                       DEL PEAK  1(1P36.11) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            226
[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    57  32
  DEL PEAK  2(1P13.2) WILD-TYPE 197 118
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           89                           315 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           32                           118 
$`DEL PEAK  2(1P13.2) MUTATED`
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-6456 TCGA-BR-7704 TCGA-BR-7901 TCGA-BR-7959 
       11.01         9.44        17.29        35.24         3.45        18.71 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8369 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8678 
        2.66         2.20        14.04         5.39         9.21        11.54 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J6 TCGA-BR-A4PE 
        9.86         8.22        22.26        12.89         0.66        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-8527 TCGA-CD-8531 
        1.15        13.64         3.25         0.30         0.07         0.10 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A4MH TCGA-CG-4301 
        0.13         0.13         3.42        11.31        12.20         3.02 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-5724 
        7.99        54.08        29.98        18.97        22.98        12.03 
TCGA-CG-5730 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 
        4.01        11.93        20.55        18.54        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-A6EX TCGA-D7-A6EZ 
       15.22        12.79        24.72        19.50        11.31         9.76 
TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-FP-7829 
       15.65         7.40         0.62         7.99        16.24        19.53 
TCGA-FP-A4BF TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4HD 
        5.52         1.51        14.17        12.10        22.75        27.42 
TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IP-7968 TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7ZE 
        5.19         1.41         2.53        37.64         9.86        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 
       36.69        18.74        36.16        52.24         4.54        21.04 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6K 
       11.24        18.41        32.94        29.98        12.43 

$`DEL PEAK  2(1P13.2) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 
       26.70        11.70        19.56         9.47         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        4.64         7.43        18.35        30.90         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        6.61        34.68        15.95        13.87        13.68        19.33 
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        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 
       28.01        18.15        15.32        28.73        12.43         9.07 
TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       12.76        17.49        14.43        11.44         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 
        9.60        20.55         8.05         0.56        12.95        16.31 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        19.50        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 
       22.19        17.52         0.95        26.33         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        15.81        16.44 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
       15.68        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        1.48        13.41        13.51         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        12.82        19.36        13.51         0.46        20.65 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 
       11.57         5.13         2.83        13.15        13.18         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        0.10         0.10         9.34        12.43        11.61         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        12.62        20.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        8.05         4.01        14.01        47.05        19.07        12.03 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
       21.99         0.00         9.01         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-5727 TCGA-CG-5728 TCGA-CG-5732 
      105.07        15.02        28.96        79.07        65.10        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6520 
       21.07         7.99        12.36        12.66        19.13        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 
       18.61        17.85        13.35        15.98        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       12.33        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-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A747 
       14.76        13.71        11.24        11.44         2.96         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        4.34         7.13        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-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56         0.23        18.08        26.47         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.27        12.59        11.41        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
        5.59        12.30        11.84        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 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       23.84        12.30         9.67         8.88         8.81        21.21 
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         5.36        13.08 
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         5.56         1.81 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG 
        7.82        13.51         5.56        60.56        20.15         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        61.25         6.08         4.60 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         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-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       16.87        19.04         5.79        18.48        35.24        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       34.45        27.88        32.48        28.96        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       16.31         2.50        12.79         1.87        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       13.35        26.24        27.35        64.57        14.33        65.16 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       11.70        11.93        61.22        20.81        22.68         1.71 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
        7.36         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-A94U 
        6.58         5.72        64.18         2.66        42.54        22.09 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       40.08        28.41        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11        10.62         0.79 

  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                         0.07                          0.00 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                        54.08                        122.30 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                        11.93                         13.15 
[1] "0.1 - 54.1 (11.9)"  "0.0 - 122.3 (13.2)"
[1] "hr=" "1.1"
D38V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  2(1P13.2) MUTATED         0        2        7        7        11
  DEL PEAK  2(1P13.2) WILD-TYPE       3       12       34       24        27
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  2(1P13.2) MUTATED          12         0         23         14
  DEL PEAK  2(1P13.2) WILD-TYPE        43         4         62         48
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  2(1P13.2) MUTATED            5       10
  DEL PEAK  2(1P13.2) WILD-TYPE         36       36
D38V3, multiclass
            clus
vv           DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  STAGE I                              0                             3
  STAGE IA                             2                            12
  STAGE IB                             7                            34
  STAGE II                             7                            24
  STAGE IIA                           11                            27
  STAGE IIB                           12                            43
  STAGE III                            0                             4
  STAGE IIIA                          23                            62
  STAGE IIIB                          14                            48
  STAGE IIIC                           5                            36
  STAGE IV                            10                            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  2(1P13.2) MUTATED     2  16  52  22
  DEL PEAK  2(1P13.2) WILD-TYPE  20  74 143  97
D38V4, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  T1                           2                            20
  T2                          16                            74
  T3                          52                           143
  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    27  20  25  17
  DEL PEAK  2(1P13.2) WILD-TYPE 102  98  59  72
D38V5, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  N0                          27                           102
  N1                          20                            98
  N2                          25                            59
  N3                          17                            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"
D38V6, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED    84   7
  DEL PEAK  2(1P13.2) WILD-TYPE 303  23
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     84    7
  DEL PEAK  2(1P13.2) WILD-TYPE  303   23
   clus
vv  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  0                          84                           303
  1                           7                            23
[1] 2 2
[1] FALSE
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED    29  65
  DEL PEAK  2(1P13.2) WILD-TYPE 129 213
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     29   65
  DEL PEAK  2(1P13.2) WILD-TYPE  129  213
        clus
vv       DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  FEMALE                          29                           129
  MALE                            65                           213
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK  2(1P13.2) MUTATED                                       7
  DEL PEAK  2(1P13.2) WILD-TYPE                                    64
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  2(1P13.2) MUTATED                                                       30
  DEL PEAK  2(1P13.2) WILD-TYPE                                                    132
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  2(1P13.2) MUTATED                                                                  23
  DEL PEAK  2(1P13.2) WILD-TYPE                                                                58
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  2(1P13.2) MUTATED                                                 24
  DEL PEAK  2(1P13.2) WILD-TYPE                                               54
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK  2(1P13.2) MUTATED                                                          4
  DEL PEAK  2(1P13.2) WILD-TYPE                                                       17
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK  2(1P13.2) MUTATED                                                           1
  DEL PEAK  2(1P13.2) WILD-TYPE                                                         7
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK  2(1P13.2) MUTATED                                          4
  DEL PEAK  2(1P13.2) WILD-TYPE                                        9
D38V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  2(1P13.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     30
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          23
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           24
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    4
                                                                   clus
vv                                                                  DEL PEAK  2(1P13.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        64
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            58
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             54
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      9
[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"
D38V9, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED     1  93
  DEL PEAK  2(1P13.2) WILD-TYPE   5 337
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      1   93
  DEL PEAK  2(1P13.2) WILD-TYPE    5  337
     clus
vv    DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  NO                            1                             5
  YES                          93                           337
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  2(1P13.2) MUTATED    69   4   8   3
  DEL PEAK  2(1P13.2) WILD-TYPE 278  14  11  22
D38V10, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  R0                          69                           278
  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                         9
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  2(1P13.2) MUTATED                                           1    59
  DEL PEAK  2(1P13.2) WILD-TYPE                                         0   215
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                                                              59
                                           clus
vv                                          DEL PEAK  2(1P13.2) WILD-TYPE
  ASIAN                                                                69
  BLACK OR AFRICAN AMERICAN                                             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  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"
D38V13, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED     0  64
  DEL PEAK  2(1P13.2) WILD-TYPE   4 249
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      0   64
  DEL PEAK  2(1P13.2) WILD-TYPE    4  249
                        clus
vv                       DEL PEAK  2(1P13.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          64
                        clus
vv                       DEL PEAK  2(1P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           249
[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    17  11
  DEL PEAK  3(1Q44) WILD-TYPE 237 139
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         28                         376 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         11                         139 
$`DEL PEAK  3(1Q44) MUTATED`
TCGA-B7-A5TN TCGA-BR-6456 TCGA-BR-7704 TCGA-BR-8362 TCGA-BR-A452 TCGA-BR-A4PD 
        9.44        17.29        35.24        13.08         7.53        20.65 
TCGA-CD-5801 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4306 TCGA-CG-4441 
       13.18         3.42        12.43        12.20         1.02        14.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5724 TCGA-D7-6519 TCGA-D7-8576 TCGA-D7-A6F2 
       18.97         7.07        12.03        20.55        14.66        15.65 
TCGA-HU-8604 TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-IN-8663 TCGA-IN-A7NU TCGA-IP-7968 
       12.10         8.98         2.10         3.39         1.81         2.53 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-VQ-A8PM TCGA-VQ-A91V 
        5.56        37.64         1.87        36.16 

$`DEL PEAK  3(1Q44) WILD-TYPE`
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-4191 TCGA-BR-4201 TCGA-BR-4267 
        6.97         4.64         7.43        18.35        30.90         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-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        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.56        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         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 
       19.17        14.79         0.26        15.85         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        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       12.56        13.87         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        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 
       12.82         0.66        19.36        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        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.15         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C 
        0.13         0.13         0.10         9.34        11.31        11.61 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 
       15.95         7.99         8.05        54.08         4.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       47.05        19.07        12.03        21.99         0.00         9.01 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       12.00        22.98        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-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        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 
       12.36        12.66        11.93        19.13        18.84        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-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        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        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       13.71        11.24        11.31        11.44         9.76         2.96 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34         7.40         7.13         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
       16.24        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-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 
       13.58         0.56         5.52         0.23        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        1.51         5.92        14.27        12.59        14.17        11.41 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
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-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI 
        8.81        27.42        21.21         3.45        18.81        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR 
        5.36         5.19        13.08         1.41         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F7 
       12.59         6.51         5.56         7.82        13.51        60.56 
TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       20.15         3.72        19.73         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        61.25         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        35.24        21.73        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       27.88        32.48         7.73        28.96        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-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU 
        9.27        23.41        15.65        13.35        26.24        27.35 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        65.16        36.69        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W 
       61.22        18.74        20.81        22.68         1.71         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
        9.50         9.73        52.24         9.04         2.01        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P 
        4.54         6.58         5.72        64.18        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.54        11.24        22.09        18.41        40.08        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       32.94        29.98        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11        12.43        10.62         0.79 

  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                       1.02                        0.00 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                      37.64                      122.30 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                      12.15                       12.92 
[1] "1.0 - 37.6 (12.1)"  "0.0 - 122.3 (12.9)"
[1] "hr=" "1.3"
D39V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  3(1Q44) MUTATED         0        0        2        1         5
  DEL PEAK  3(1Q44) WILD-TYPE       3       14       39       30        33
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  3(1Q44) MUTATED           5         0          5          3
  DEL PEAK  3(1Q44) WILD-TYPE        50         4         80         59
                             vv
clus                          STAGE IIIC STAGE IV
  DEL PEAK  3(1Q44) MUTATED            4        4
  DEL PEAK  3(1Q44) WILD-TYPE         37       42
D39V3, multiclass
            clus
vv           DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  STAGE I                            0                           3
  STAGE IA                           0                          14
  STAGE IB                           2                          39
  STAGE II                           1                          30
  STAGE IIA                          5                          33
  STAGE IIB                          5                          50
  STAGE III                          0                           4
  STAGE IIIA                         5                          80
  STAGE IIIB                         3                          59
  STAGE IIIC                         4                          37
  STAGE IV                           4                          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  3(1Q44) MUTATED     0   6  16   7
  DEL PEAK  3(1Q44) WILD-TYPE  22  84 179 112
D39V4, multiclass
    clus
vv   DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  T1                         0                          22
  T2                         6                          84
  T3                        16                         179
  T4                         7                         112
[1] 4 2
[1] TRUE
[1] "dimension of 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     8   6   6   8
  DEL PEAK  3(1Q44) WILD-TYPE 121 112  78  81
D39V5, multiclass
    clus
vv   DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  N0                         8                         121
  N1                         6                         112
  N2                         6                          78
  N3                         8                          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    27   2
  DEL PEAK  3(1Q44) WILD-TYPE 360  28
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED     27    2
  DEL PEAK  3(1Q44) WILD-TYPE  360   28
   clus
vv  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  0                        27                         360
  1                         2                          28
[1] 2 2
[1] FALSE
D39V7, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED    11  19
  DEL PEAK  3(1Q44) WILD-TYPE 147 259
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED     11   19
  DEL PEAK  3(1Q44) WILD-TYPE  147  259
        clus
vv       DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  FEMALE                        11                         147
  MALE                          19                         259
[1] 2 2
[1] FALSE
                             vv
clus                          STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK  3(1Q44) MUTATED                                       4
  DEL PEAK  3(1Q44) WILD-TYPE                                    67
                             vv
clus                          STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  3(1Q44) MUTATED                                                       14
  DEL PEAK  3(1Q44) WILD-TYPE                                                    148
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  3(1Q44) MUTATED                                                                   5
  DEL PEAK  3(1Q44) WILD-TYPE                                                                76
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  3(1Q44) MUTATED                                                  6
  DEL PEAK  3(1Q44) WILD-TYPE                                               72
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK  3(1Q44) MUTATED                                                          0
  DEL PEAK  3(1Q44) WILD-TYPE                                                       21
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK  3(1Q44) MUTATED                                                           0
  DEL PEAK  3(1Q44) WILD-TYPE                                                         8
                             vv
clus                          STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK  3(1Q44) MUTATED                                          1
  DEL PEAK  3(1Q44) WILD-TYPE                                       12
D39V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  3(1Q44) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                   14
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                          6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                  0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                 0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                  1
                                                                   clus
vv                                                                  DEL PEAK  3(1Q44) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      67
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    148
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          76
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           72
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   12
[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"
D39V9, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED     0  30
  DEL PEAK  3(1Q44) WILD-TYPE   6 400
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED      0   30
  DEL PEAK  3(1Q44) WILD-TYPE    6  400
     clus
vv    DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  NO                          0                           6
  YES                        30                         400
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  3(1Q44) MUTATED    22   1   2   1
  DEL PEAK  3(1Q44) WILD-TYPE 325  17  17  24
D39V10, multiclass
    clus
vv   DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  R0                        22                         325
  R1                         1                          17
  R2                         2                          17
  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"
D39V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  3(1Q44) MUTATED       9                         0
  DEL PEAK  3(1Q44) WILD-TYPE    79                        11
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  3(1Q44) MUTATED                                           0    14
  DEL PEAK  3(1Q44) WILD-TYPE                                         1   260
D39V12, multiclass
                                           clus
vv                                          DEL PEAK  3(1Q44) MUTATED
  ASIAN                                                             9
  BLACK OR AFRICAN AMERICAN                                         0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         0
  WHITE                                                            14
                                           clus
vv                                          DEL PEAK  3(1Q44) WILD-TYPE
  ASIAN                                                              79
  BLACK OR AFRICAN AMERICAN                                          11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             260
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V13, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED     0  21
  DEL PEAK  3(1Q44) WILD-TYPE   4 292
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED      0   21
  DEL PEAK  3(1Q44) WILD-TYPE    4  292
                        clus
vv                       DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  HISPANIC OR LATINO                             0                           4
  NOT HISPANIC OR LATINO                        21                         292
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK  4(1Q44) MUTATION ANALYSIS
D40V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  4(1Q44) MUTATED    16   9
  DEL PEAK  4(1Q44) WILD-TYPE 238 141
  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE 
                         25                         379 
  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE 
                          9                         141 
$`DEL PEAK  4(1Q44) MUTATED`
TCGA-B7-A5TN TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6705 TCGA-BR-7704 TCGA-BR-8077 
        9.44        17.29        19.33        25.61        35.24         0.69 
TCGA-BR-8362 TCGA-BR-A4PD TCGA-CD-A486 TCGA-CD-A48A TCGA-CG-4441 TCGA-CG-5724 
       13.08        20.65         3.42        12.43        14.01        12.03 
TCGA-D7-6519 TCGA-D7-8576 TCGA-D7-A6F2 TCGA-HU-8604 TCGA-HU-A4GP TCGA-HU-A4H0 
       20.55        14.66        15.65        12.10         8.98         2.10 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IP-7968 TCGA-KB-A93H TCGA-VQ-A8P3 TCGA-VQ-A91V 
        3.39        18.38         2.53        37.64        32.48        36.16 
TCGA-VQ-A928 
        5.72 

$`DEL PEAK  4(1Q44) WILD-TYPE`
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-4191 TCGA-BR-4201 TCGA-BR-4267 
        6.97         4.64         7.43        18.35        30.90         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-6565 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        32.78        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        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       12.82         9.21        24.76        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       18.15        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 
       12.76        18.71        17.49        14.43        11.44        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        20.55         8.05         0.56        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
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        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         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        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51         0.46        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.30         0.07         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG 
        0.13         0.10         9.34        11.31        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         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-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       29.98        47.05        19.07        12.03        21.99         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
        9.01        18.97         7.07        12.00        22.98        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-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        15.02        28.96        79.07        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        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        18.84        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        10.55 
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-D7-8578 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 
       15.16        13.78        14.76        13.71        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.44         9.76         2.96         8.38         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
        7.13         0.62         7.99        16.24        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-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        0.23        18.08        26.47         1.51         5.92        14.27 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       12.59        14.17        11.41        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        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-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.25        10.19         0.26        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       12.30         9.67         8.88         8.81        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO 
        3.45        18.81         5.36         5.19        13.08         1.41 
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         5.56         1.81 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG 
        7.82        13.51         5.56        60.56        20.15         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73         9.86        45.67        18.21         8.52        61.25 
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-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P5 
       18.48        35.24        21.73        34.45        27.88         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       28.96        34.29        46.26        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-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       15.65        13.35        26.24        27.35        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       65.16        36.69        11.70        11.93        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       20.81        22.68         1.71         7.36         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       52.24         9.04         2.01        55.43         4.54         6.58 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U 
       64.18        21.04         2.66        42.54        11.24        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       18.41        40.08        28.41        32.94        29.98        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        21.11        12.43        10.62 
TCGA-ZQ-A9CR 
        0.79 

  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE 
                       0.69                        0.00 
  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE 
                      37.64                      122.30 
  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE 
                      14.01                       12.79 
[1] "0.7 - 37.6 (14.0)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1"  
D40V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  4(1Q44) MUTATED         1        0        1        1         4
  DEL PEAK  4(1Q44) WILD-TYPE       2       14       40       30        34
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  4(1Q44) MUTATED           6         0          3          5
  DEL PEAK  4(1Q44) WILD-TYPE        49         4         82         57
                             vv
clus                          STAGE IIIC STAGE IV
  DEL PEAK  4(1Q44) MUTATED            3        2
  DEL PEAK  4(1Q44) WILD-TYPE         38       44
D40V3, multiclass
            clus
vv           DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  STAGE I                            1                           2
  STAGE IA                           0                          14
  STAGE IB                           1                          40
  STAGE II                           1                          30
  STAGE IIA                          4                          34
  STAGE IIB                          6                          49
  STAGE III                          0                           4
  STAGE IIIA                         3                          82
  STAGE IIIB                         5                          57
  STAGE IIIC                         3                          38
  STAGE IV                           2                          44
[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(1Q44) MUTATED     1   5  13   7
  DEL PEAK  4(1Q44) WILD-TYPE  21  85 182 112
D40V4, multiclass
    clus
vv   DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  T1                         1                          21
  T2                         5                          85
  T3                        13                         182
  T4                         7                         112
[1] 4 2
[1] TRUE
[1] "dimension of 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(1Q44) MUTATED     7   7   4   7
  DEL PEAK  4(1Q44) WILD-TYPE 122 111  80  82
D40V5, multiclass
    clus
vv   DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  N0                         7                         122
  N1                         7                         111
  N2                         4                          80
  N3                         7                          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"
D40V6, binary
                             cls
clus                            0   1
  DEL PEAK  4(1Q44) MUTATED    24   1
  DEL PEAK  4(1Q44) WILD-TYPE 363  29
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(1Q44) MUTATED     24    1
  DEL PEAK  4(1Q44) WILD-TYPE  363   29
   clus
vv  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  0                        24                         363
  1                         1                          29
[1] 2 2
[1] FALSE
D40V7, binary
                             cls
clus                            0   1
  DEL PEAK  4(1Q44) MUTATED    12  14
  DEL PEAK  4(1Q44) WILD-TYPE 146 264
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(1Q44) MUTATED     12   14
  DEL PEAK  4(1Q44) WILD-TYPE  146  264
        clus
vv       DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  FEMALE                        12                         146
  MALE                          14                         264
[1] 2 2
[1] FALSE
                             vv
clus                          STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK  4(1Q44) MUTATED                                       4
  DEL PEAK  4(1Q44) WILD-TYPE                                    67
                             vv
clus                          STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  4(1Q44) MUTATED                                                       12
  DEL PEAK  4(1Q44) WILD-TYPE                                                    150
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  4(1Q44) MUTATED                                                                   3
  DEL PEAK  4(1Q44) WILD-TYPE                                                                78
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  4(1Q44) MUTATED                                                  6
  DEL PEAK  4(1Q44) WILD-TYPE                                               72
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK  4(1Q44) MUTATED                                                          0
  DEL PEAK  4(1Q44) WILD-TYPE                                                       21
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK  4(1Q44) MUTATED                                                           1
  DEL PEAK  4(1Q44) WILD-TYPE                                                         7
                             vv
clus                          STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK  4(1Q44) MUTATED                                          0
  DEL PEAK  4(1Q44) WILD-TYPE                                       13
D40V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  4(1Q44) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                   12
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                          6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                  0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                 1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                  0
                                                                   clus
vv                                                                  DEL PEAK  4(1Q44) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      67
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    150
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          78
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           72
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   13
[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"
D40V9, binary
                             cls
clus                            0   1
  DEL PEAK  4(1Q44) MUTATED     0  26
  DEL PEAK  4(1Q44) WILD-TYPE   6 404
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(1Q44) MUTATED      0   26
  DEL PEAK  4(1Q44) WILD-TYPE    6  404
     clus
vv    DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  NO                          0                           6
  YES                        26                         404
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  4(1Q44) MUTATED    22   0   1   0
  DEL PEAK  4(1Q44) WILD-TYPE 325  18  18  25
D40V10, multiclass
    clus
vv   DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  R0                        22                         325
  R1                         0                          18
  R2                         1                          18
  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"
D40V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  4(1Q44) MUTATED       6                         0
  DEL PEAK  4(1Q44) WILD-TYPE    82                        11
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  4(1Q44) MUTATED                                           0    17
  DEL PEAK  4(1Q44) WILD-TYPE                                         1   257
D40V12, multiclass
                                           clus
vv                                          DEL PEAK  4(1Q44) MUTATED
  ASIAN                                                             6
  BLACK OR AFRICAN AMERICAN                                         0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         0
  WHITE                                                            17
                                           clus
vv                                          DEL PEAK  4(1Q44) WILD-TYPE
  ASIAN                                                              82
  BLACK OR AFRICAN AMERICAN                                          11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             257
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V13, binary
                             cls
clus                            0   1
  DEL PEAK  4(1Q44) MUTATED     0  20
  DEL PEAK  4(1Q44) WILD-TYPE   4 293
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(1Q44) MUTATED      0   20
  DEL PEAK  4(1Q44) WILD-TYPE    4  293
                        clus
vv                       DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  HISPANIC OR LATINO                             0                           4
  NOT HISPANIC OR LATINO                        20                         293
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK  5(2Q32.1) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(2Q32.1) MUTATED    30  27
  DEL PEAK  5(2Q32.1) WILD-TYPE 224 123
  DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE 
                           57                           347 
  DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE 
                           27                           123 
$`DEL PEAK  5(2Q32.1) MUTATED`
TCGA-BR-4188 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-8058 TCGA-BR-8077 
        7.43        17.29        19.33         9.17        17.49         0.69 
TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
        9.60        12.95        26.33         4.31        14.04         3.32 
TCGA-BR-8676 TCGA-BR-8682 TCGA-BR-8687 TCGA-BR-A4PD TCGA-CD-8525 TCGA-CD-8532 
        7.53        16.44         8.22        20.65         0.07         0.10 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CG-4300 TCGA-CG-4444 TCGA-CG-4462 TCGA-CG-4472 
        0.13         3.42        20.02        47.05         0.00        12.00 
TCGA-CG-5720 TCGA-CG-5724 TCGA-CG-5725 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6526 
        0.99        12.03        15.02        12.66        11.93        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A6F0 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-A4G3 
       18.21        14.66         2.96        26.47         5.92         5.59 
TCGA-HU-A4GD TCGA-HU-A4GU TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-AB1V TCGA-MX-A663 
       22.75         6.25        27.42        18.38         7.82         9.86 
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        32.48 
TCGA-VQ-A8PK TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A91Y TCGA-VQ-A94O TCGA-VQ-A94U 
       17.85        27.35        14.33         9.73        21.04        22.09 
TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-ZA-A8F6 
       40.08        32.94        10.62 

$`DEL PEAK  5(2Q32.1) WILD-TYPE`
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-4187 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        6.61         6.97         4.64        18.35        30.90         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-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10        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        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       12.82         9.21        24.76        35.24        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 
        9.07        12.76        18.71        14.43        11.44        12.26 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05         0.56         2.66        16.31         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        19.50        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       22.19        17.52         0.95        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         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        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 
        6.28         0.49        11.54        15.81         9.86        15.68 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        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        12.82         0.66        19.36        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
        0.46        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.10         0.13         0.10         9.34        11.31        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         0.10        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-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
        4.01        14.01        29.98        19.07        12.03        21.99 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 
       36.00         1.02         6.02         0.99       105.07        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.36        19.13        20.55        18.84        18.54        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-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        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-A6EX 
       15.16        13.78        14.76        13.71        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.44         9.76        15.65         8.38         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
        7.13         0.62         7.99        16.24        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-A8CX TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
        0.23        18.08         1.51        14.27        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 
       11.41        12.10        10.62         0.76        24.30        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       11.84        24.20         3.25        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        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88         8.81        21.21         3.45        18.81         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR 
        5.36         5.19        13.08         1.41         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 
       12.59         6.51         5.56         1.81        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        60.56        20.15        37.64         3.72        19.73 
TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67         8.52        61.25         6.08         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-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-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E0 
       16.87        19.04         5.79        48.79         5.46        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       35.24        21.73        34.45        27.88         7.73        28.96 
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-A8PS 
        2.70         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       26.24        64.57        65.16        36.69        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       61.22        18.74        20.81        22.68         1.71        36.16 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
        7.36         9.50        52.24         9.04         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        64.18         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       11.24        18.41        28.41        29.98        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       26.04        16.14        21.11        12.43         0.79 

  DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE 
                         0.00                          0.07 
  DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE 
                        47.05                        122.30 
  DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE 
                        13.02                         12.79 
[1] "0.0 - 47.0 (13.0)"  "0.1 - 122.3 (12.8)"
[1] "hr=" "1.5"
D41V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  5(2Q32.1) MUTATED         1        1        8        3         3
  DEL PEAK  5(2Q32.1) WILD-TYPE       2       13       33       28        35
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  5(2Q32.1) MUTATED           9         0         11         10
  DEL PEAK  5(2Q32.1) WILD-TYPE        46         4         74         52
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  5(2Q32.1) MUTATED            8        5
  DEL PEAK  5(2Q32.1) WILD-TYPE         33       41
D41V3, multiclass
            clus
vv           DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE
  STAGE I                              1                             2
  STAGE IA                             1                            13
  STAGE IB                             8                            33
  STAGE II                             3                            28
  STAGE IIA                            3                            35
  STAGE IIB                            9                            46
  STAGE III                            0                             4
  STAGE IIIA                          11                            74
  STAGE IIIB                          10                            52
  STAGE IIIC                           8                            33
  STAGE IV                             5                            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  5(2Q32.1) MUTATED     2  11  29  18
  DEL PEAK  5(2Q32.1) WILD-TYPE  20  79 166 101
D41V4, multiclass
    clus
vv   DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE
  T1                           2                            20
  T2                          11                            79
  T3                          29                           166
  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  5(2Q32.1) MUTATED    20  11  12  17
  DEL PEAK  5(2Q32.1) WILD-TYPE 109 107  72  72
D41V5, multiclass
    clus
vv   DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE
  N0                          20                           109
  N1                          11                           107
  N2                          12                            72
  N3                          17                            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"
D41V6, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q32.1) MUTATED    56   3
  DEL PEAK  5(2Q32.1) WILD-TYPE 331  27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q32.1) MUTATED     56    3
  DEL PEAK  5(2Q32.1) WILD-TYPE  331   27
   clus
vv  DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE
  0                          56                           331
  1                           3                            27
[1] 2 2
[1] FALSE
D41V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q32.1) MUTATED    22  40
  DEL PEAK  5(2Q32.1) WILD-TYPE 136 238
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q32.1) MUTATED     22   40
  DEL PEAK  5(2Q32.1) WILD-TYPE  136  238
        clus
vv       DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE
  FEMALE                          22                           136
  MALE                            40                           238
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK  5(2Q32.1) MUTATED                                       8
  DEL PEAK  5(2Q32.1) WILD-TYPE                                    63
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  5(2Q32.1) MUTATED                                                       22
  DEL PEAK  5(2Q32.1) WILD-TYPE                                                    140
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  5(2Q32.1) MUTATED                                                                   8
  DEL PEAK  5(2Q32.1) WILD-TYPE                                                                73
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  5(2Q32.1) MUTATED                                                 15
  DEL PEAK  5(2Q32.1) WILD-TYPE                                               63
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK  5(2Q32.1) MUTATED                                                          5
  DEL PEAK  5(2Q32.1) WILD-TYPE                                                       16
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK  5(2Q32.1) MUTATED                                                           0
  DEL PEAK  5(2Q32.1) WILD-TYPE                                                         8
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK  5(2Q32.1) MUTATED                                          3
  DEL PEAK  5(2Q32.1) WILD-TYPE                                       10
D41V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  5(2Q32.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     22
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           8
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    3
                                                                   clus
vv                                                                  DEL PEAK  5(2Q32.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      140
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            73
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             63
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     10
[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"
D41V9, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q32.1) MUTATED     1  61
  DEL PEAK  5(2Q32.1) WILD-TYPE   5 369
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q32.1) MUTATED      1   61
  DEL PEAK  5(2Q32.1) WILD-TYPE    5  369
     clus
vv    DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE
  NO                            1                             5
  YES                          61                           369
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  5(2Q32.1) MUTATED    50   3   4   3
  DEL PEAK  5(2Q32.1) WILD-TYPE 297  15  15  22
D41V10, multiclass
    clus
vv   DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE
  R0                          50                           297
  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"
D41V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  5(2Q32.1) MUTATED      11                         2
  DEL PEAK  5(2Q32.1) WILD-TYPE    77                         9
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  5(2Q32.1) MUTATED                                           0    40
  DEL PEAK  5(2Q32.1) WILD-TYPE                                         1   234
D41V12, multiclass
                                           clus
vv                                          DEL PEAK  5(2Q32.1) MUTATED
  ASIAN                                                              11
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              40
                                           clus
vv                                          DEL PEAK  5(2Q32.1) WILD-TYPE
  ASIAN                                                                77
  BLACK OR AFRICAN AMERICAN                                             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V13, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q32.1) MUTATED     0  41
  DEL PEAK  5(2Q32.1) WILD-TYPE   4 272
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q32.1) MUTATED      0   41
  DEL PEAK  5(2Q32.1) WILD-TYPE    4  272
                        clus
vv                       DEL PEAK  5(2Q32.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          41
                        clus
vv                       DEL PEAK  5(2Q32.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           272
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK  6(2Q33.3) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(2Q33.3) MUTATED    24  21
  DEL PEAK  6(2Q33.3) WILD-TYPE 230 129
  DEL PEAK  6(2Q33.3) MUTATED DEL PEAK  6(2Q33.3) WILD-TYPE 
                           45                           359 
  DEL PEAK  6(2Q33.3) MUTATED DEL PEAK  6(2Q33.3) WILD-TYPE 
                           21                           129 
$`DEL PEAK  6(2Q33.3) MUTATED`
TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7901 TCGA-BR-8058 TCGA-BR-8080 
       19.33         9.17        12.16         3.45        17.49         9.60 
TCGA-BR-8286 TCGA-BR-8369 TCGA-BR-8687 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8535 
       12.95        14.04         8.22         0.07         0.07         0.13 
TCGA-CD-A486 TCGA-CG-4300 TCGA-CG-4462 TCGA-CG-5720 TCGA-CG-5724 TCGA-D7-5578 
        3.42        20.02         0.00         0.99        12.03        12.66 
TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-8573 TCGA-D7-8576 TCGA-HJ-7597 
       11.93        17.19        15.22        19.50        14.66        26.47 
TCGA-HU-8243 TCGA-HU-A4G8 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GU TCGA-HU-A4H0 
        5.92        11.84        22.75        25.81         6.25         2.10 
TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RO TCGA-IN-AB1V TCGA-VQ-A8DU TCGA-VQ-A8DV 
       27.42        18.38         1.41         7.82         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8PC TCGA-VQ-A8PK TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A94U 
       13.02        46.26        17.85        27.35        14.33        22.09 
TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6J 
       40.08        32.94        21.11 

$`DEL PEAK  6(2Q33.3) WILD-TYPE`
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-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
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-6566 TCGA-BR-6705 
       17.29        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        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       32.94        12.82         9.21        24.76        35.24        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        9.07        12.76        18.71        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 
       12.26        20.55         8.05         0.56         2.66        16.31 
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        19.50        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        19.17        14.79         0.26        15.85 
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        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        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        12.82         0.66        19.36        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        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.10         0.13         0.10         9.34        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         0.10        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-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03        21.99         9.01        18.97         7.07        12.00 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5721 
       22.98        30.97         6.97        36.00         1.02         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        15.02        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 
        4.01        69.04        21.07         7.99        12.36        19.13 
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-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 
       24.72        16.80        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        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       13.71        11.24        11.31        11.44         9.76         2.96 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34         7.40         7.13         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.99        16.24        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-A4BF TCGA-FP-A8CX TCGA-HF-A5NB 
        5.03        13.58         0.56         5.52         0.23        18.08 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51        14.27        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       10.62         0.76        24.30         5.59        12.30        24.20 
TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.51        10.19         0.26        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88         8.81        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
       18.81         3.39         5.36         5.19        13.08         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         5.56         1.81        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG 
        2.53         5.56        60.56        20.15        37.64         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73         9.86        45.67        18.21         8.52        61.25 
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-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        5.79         0.92        48.79        18.48        35.24        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       34.45        27.88        32.48         7.73        28.96        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        26.24        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       65.16        36.69        11.70        11.93        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       20.81        22.68         1.71        36.16         7.36         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.73        52.24         9.04         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
        6.58         5.72        64.18        21.04         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       11.24        18.41        28.41        29.98        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        12.43        10.62         0.79 

  DEL PEAK  6(2Q33.3) MUTATED DEL PEAK  6(2Q33.3) WILD-TYPE 
                         0.00                          0.07 
  DEL PEAK  6(2Q33.3) MUTATED DEL PEAK  6(2Q33.3) WILD-TYPE 
                        46.26                        122.30 
  DEL PEAK  6(2Q33.3) MUTATED DEL PEAK  6(2Q33.3) WILD-TYPE 
                        13.02                         12.79 
[1] "0.0 - 46.3 (13.0)"  "0.1 - 122.3 (12.8)"
[1] "hr=" "1.4"
D42V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  6(2Q33.3) MUTATED         1        2        5        2         3
  DEL PEAK  6(2Q33.3) WILD-TYPE       2       12       36       29        35
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  6(2Q33.3) MUTATED           7         0         10          8
  DEL PEAK  6(2Q33.3) WILD-TYPE        48         4         75         54
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  6(2Q33.3) MUTATED            7        4
  DEL PEAK  6(2Q33.3) WILD-TYPE         34       42
D42V3, multiclass
            clus
vv           DEL PEAK  6(2Q33.3) MUTATED DEL PEAK  6(2Q33.3) WILD-TYPE
  STAGE I                              1                             2
  STAGE IA                             2                            12
  STAGE IB                             5                            36
  STAGE II                             2                            29
  STAGE IIA                            3                            35
  STAGE IIB                            7                            48
  STAGE III                            0                             4
  STAGE IIIA                          10                            75
  STAGE IIIB                           8                            54
  STAGE IIIC                           7                            34
  STAGE IV                             4                            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  6(2Q33.3) MUTATED     3   6  27  13
  DEL PEAK  6(2Q33.3) WILD-TYPE  19  84 168 106
D42V4, multiclass
    clus
vv   DEL PEAK  6(2Q33.3) MUTATED DEL PEAK  6(2Q33.3) WILD-TYPE
  T1                           3                            19
  T2                           6                            84
  T3                          27                           168
  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  6(2Q33.3) MUTATED    15  10  10  14
  DEL PEAK  6(2Q33.3) WILD-TYPE 114 108  74  75
D42V5, multiclass
    clus
vv   DEL PEAK  6(2Q33.3) MUTATED DEL PEAK  6(2Q33.3) WILD-TYPE
  N0                          15                           114
  N1                          10                           108
  N2                          10                            74
  N3                          14                            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"
D42V6, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q33.3) MUTATED    44   3
  DEL PEAK  6(2Q33.3) WILD-TYPE 343  27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q33.3) MUTATED     44    3
  DEL PEAK  6(2Q33.3) WILD-TYPE  343   27
   clus
vv  DEL PEAK  6(2Q33.3) MUTATED DEL PEAK  6(2Q33.3) WILD-TYPE
  0                          44                           343
  1                           3                            27
[1] 2 2
[1] FALSE
D42V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q33.3) MUTATED    19  30
  DEL PEAK  6(2Q33.3) WILD-TYPE 139 248
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q33.3) MUTATED     19   30
  DEL PEAK  6(2Q33.3) WILD-TYPE  139  248
        clus
vv       DEL PEAK  6(2Q33.3) MUTATED DEL PEAK  6(2Q33.3) WILD-TYPE
  FEMALE                          19                           139
  MALE                            30                           248
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK  6(2Q33.3) MUTATED                                       7
  DEL PEAK  6(2Q33.3) WILD-TYPE                                    64
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  6(2Q33.3) MUTATED                                                       16
  DEL PEAK  6(2Q33.3) WILD-TYPE                                                    146
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  6(2Q33.3) MUTATED                                                                   5
  DEL PEAK  6(2Q33.3) WILD-TYPE                                                                76
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  6(2Q33.3) MUTATED                                                 13
  DEL PEAK  6(2Q33.3) WILD-TYPE                                               65
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK  6(2Q33.3) MUTATED                                                          4
  DEL PEAK  6(2Q33.3) WILD-TYPE                                                       17
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK  6(2Q33.3) MUTATED                                                           0
  DEL PEAK  6(2Q33.3) WILD-TYPE                                                         8
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK  6(2Q33.3) MUTATED                                          4
  DEL PEAK  6(2Q33.3) WILD-TYPE                                        9
D42V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  6(2Q33.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     16
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    4
                                                                   clus
vv                                                                  DEL PEAK  6(2Q33.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        64
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      146
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            76
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             65
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      9
[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"
D42V9, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q33.3) MUTATED     2  47
  DEL PEAK  6(2Q33.3) WILD-TYPE   4 383
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q33.3) MUTATED      2   47
  DEL PEAK  6(2Q33.3) WILD-TYPE    4  383
     clus
vv    DEL PEAK  6(2Q33.3) MUTATED DEL PEAK  6(2Q33.3) WILD-TYPE
  NO                            2                             4
  YES                          47                           383
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  6(2Q33.3) MUTATED    40   4   3   0
  DEL PEAK  6(2Q33.3) WILD-TYPE 307  14  16  25
D42V10, multiclass
    clus
vv   DEL PEAK  6(2Q33.3) MUTATED DEL PEAK  6(2Q33.3) WILD-TYPE
  R0                          40                           307
  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"
D42V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  6(2Q33.3) MUTATED      13                         2
  DEL PEAK  6(2Q33.3) WILD-TYPE    75                         9
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  6(2Q33.3) MUTATED                                           0    27
  DEL PEAK  6(2Q33.3) WILD-TYPE                                         1   247
D42V12, multiclass
                                           clus
vv                                          DEL PEAK  6(2Q33.3) MUTATED
  ASIAN                                                              13
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              27
                                           clus
vv                                          DEL PEAK  6(2Q33.3) WILD-TYPE
  ASIAN                                                                75
  BLACK OR AFRICAN AMERICAN                                             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               247
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V13, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q33.3) MUTATED     0  31
  DEL PEAK  6(2Q33.3) WILD-TYPE   4 282
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q33.3) MUTATED      0   31
  DEL PEAK  6(2Q33.3) WILD-TYPE    4  282
                        clus
vv                       DEL PEAK  6(2Q33.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          31
                        clus
vv                       DEL PEAK  6(2Q33.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           282
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK  7(2Q37.2) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(2Q37.2) MUTATED    39  29
  DEL PEAK  7(2Q37.2) WILD-TYPE 215 121
  DEL PEAK  7(2Q37.2) MUTATED DEL PEAK  7(2Q37.2) WILD-TYPE 
                           68                           336 
  DEL PEAK  7(2Q37.2) MUTATED DEL PEAK  7(2Q37.2) WILD-TYPE 
                           29                           121 
$`DEL PEAK  7(2Q37.2) MUTATED`
TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7704 TCGA-BR-7901 TCGA-BR-8058 TCGA-BR-8059 
        9.17        12.16        35.24         3.45        17.49        14.43 
TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8361 TCGA-BR-8373 TCGA-BR-8381 
       11.44         9.60        12.95        19.50        14.79         0.26 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8677 TCGA-BR-8687 TCGA-BR-A4PD TCGA-CD-5800 
       25.18         9.21         0.49         8.22        20.65        13.15 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 
        0.07         0.07         0.13         0.13         3.42        11.31 
TCGA-CG-4300 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-4472 
       20.02         8.05        14.01        19.07        18.97        12.00 
TCGA-CG-5719 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 
        1.02        12.66        20.55        17.19        15.22        15.98 
TCGA-D7-6818 TCGA-D7-8576 TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-HJ-7597 TCGA-HU-8243 
       10.55        14.66        11.24         2.96        26.47         5.92 
TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4H2 TCGA-HU-A4HD TCGA-IN-A6RO TCGA-IN-A6RR 
       22.75         8.98        12.95        27.42         1.41         6.74 
TCGA-IN-AB1V TCGA-R5-A7ZE TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8PE TCGA-VQ-A8PU 
        7.82        18.21        13.25        13.02        22.19        27.35 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A922 
       64.57        14.33        18.74        20.81        22.68         9.04 
TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A 
        4.54         5.72        22.09        18.41        40.08        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6I 
       54.12        16.14 

$`DEL PEAK  7(2Q37.2) WILD-TYPE`
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-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
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-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        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 
        9.07        12.76        18.71         0.69        12.26        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56         2.66        16.31         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 
       19.17        15.85         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        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 
       11.54        15.81        16.44         9.86        15.68        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        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        12.82         0.66        19.36        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        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8527 
        3.25        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 
        0.10         0.13         0.16         0.10         0.10         0.10 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        12.43        11.61         6.58        12.20         0.10 
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-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 
       54.08         4.01        29.98        47.05        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 
       21.07         7.99        12.36        11.93        19.13        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6817 
       18.54        18.61        17.85        13.35        10.26        12.79 
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-D7-8578 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-A6EX TCGA-D7-A6EY 
       15.16        13.78        14.76        13.71        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
        9.76        15.65         8.38         4.34         7.40         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        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-A8CX 
       59.54         5.03        13.58         0.56         5.52         0.23 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       18.08         1.51        14.27        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       11.84        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         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
        8.81        21.21         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR 
        5.36         5.19        13.08         6.44        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        5.56         1.81        13.51         2.53         5.56        60.56 
TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 
       20.15        37.64         3.72        19.73         9.86        45.67 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        61.25         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-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       18.48        35.24        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
        7.73        28.96        34.29        46.26        16.31         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-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       15.65        13.35        26.24        65.16        36.69        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       11.93        61.22         1.71        36.16         7.36         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A92D 
        9.73        52.24         2.01        55.43         6.58        64.18 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA69 TCGA-VQ-AA6B 
       21.04         2.66        42.54        11.24        28.41        29.98 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.13        26.04        21.11        12.43        10.62         0.79 

  DEL PEAK  7(2Q37.2) MUTATED DEL PEAK  7(2Q37.2) WILD-TYPE 
                         0.07                          0.00 
  DEL PEAK  7(2Q37.2) MUTATED DEL PEAK  7(2Q37.2) WILD-TYPE 
                        64.57                        122.30 
  DEL PEAK  7(2Q37.2) MUTATED DEL PEAK  7(2Q37.2) WILD-TYPE 
                       13.200                        12.775 
[1] "0.1 - 64.6 (13.2)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.2"
D43V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  7(2Q37.2) MUTATED         1        3        6        7         3
  DEL PEAK  7(2Q37.2) WILD-TYPE       2       11       35       24        35
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  7(2Q37.2) MUTATED          10         1         14         12
  DEL PEAK  7(2Q37.2) WILD-TYPE        45         3         71         50
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  7(2Q37.2) MUTATED            8        7
  DEL PEAK  7(2Q37.2) WILD-TYPE         33       39
D43V3, multiclass
            clus
vv           DEL PEAK  7(2Q37.2) MUTATED DEL PEAK  7(2Q37.2) WILD-TYPE
  STAGE I                              1                             2
  STAGE IA                             3                            11
  STAGE IB                             6                            35
  STAGE II                             7                            24
  STAGE IIA                            3                            35
  STAGE IIB                           10                            45
  STAGE III                            1                             3
  STAGE IIIA                          14                            71
  STAGE IIIB                          12                            50
  STAGE IIIC                           8                            33
  STAGE IV                             7                            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  7(2Q37.2) MUTATED     4  15  31  22
  DEL PEAK  7(2Q37.2) WILD-TYPE  18  75 164  97
D43V4, multiclass
    clus
vv   DEL PEAK  7(2Q37.2) MUTATED DEL PEAK  7(2Q37.2) WILD-TYPE
  T1                           4                            18
  T2                          15                            75
  T3                          31                           164
  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  7(2Q37.2) MUTATED    21  19  15  17
  DEL PEAK  7(2Q37.2) WILD-TYPE 108  99  69  72
D43V5, multiclass
    clus
vv   DEL PEAK  7(2Q37.2) MUTATED DEL PEAK  7(2Q37.2) WILD-TYPE
  N0                          21                           108
  N1                          19                            99
  N2                          15                            69
  N3                          17                            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"
D43V6, binary
                               cls
clus                              0   1
  DEL PEAK  7(2Q37.2) MUTATED    68   2
  DEL PEAK  7(2Q37.2) WILD-TYPE 319  28
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(2Q37.2) MUTATED     68    2
  DEL PEAK  7(2Q37.2) WILD-TYPE  319   28
   clus
vv  DEL PEAK  7(2Q37.2) MUTATED DEL PEAK  7(2Q37.2) WILD-TYPE
  0                          68                           319
  1                           2                            28
[1] 2 2
[1] FALSE
D43V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(2Q37.2) MUTATED    32  40
  DEL PEAK  7(2Q37.2) WILD-TYPE 126 238
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(2Q37.2) MUTATED     32   40
  DEL PEAK  7(2Q37.2) WILD-TYPE  126  238
        clus
vv       DEL PEAK  7(2Q37.2) MUTATED DEL PEAK  7(2Q37.2) WILD-TYPE
  FEMALE                          32                           126
  MALE                            40                           238
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK  7(2Q37.2) MUTATED                                       6
  DEL PEAK  7(2Q37.2) WILD-TYPE                                    65
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  7(2Q37.2) MUTATED                                                       22
  DEL PEAK  7(2Q37.2) WILD-TYPE                                                    140
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  7(2Q37.2) MUTATED                                                                  16
  DEL PEAK  7(2Q37.2) WILD-TYPE                                                                65
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  7(2Q37.2) MUTATED                                                 19
  DEL PEAK  7(2Q37.2) WILD-TYPE                                               59
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK  7(2Q37.2) MUTATED                                                          3
  DEL PEAK  7(2Q37.2) WILD-TYPE                                                       18
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK  7(2Q37.2) MUTATED                                                           2
  DEL PEAK  7(2Q37.2) WILD-TYPE                                                         6
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK  7(2Q37.2) MUTATED                                          3
  DEL PEAK  7(2Q37.2) WILD-TYPE                                       10
D43V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  7(2Q37.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     22
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          16
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    3
                                                                   clus
vv                                                                  DEL PEAK  7(2Q37.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        65
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      140
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            65
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             59
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     10
[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"
D43V9, binary
                               cls
clus                              0   1
  DEL PEAK  7(2Q37.2) MUTATED     2  70
  DEL PEAK  7(2Q37.2) WILD-TYPE   4 360
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(2Q37.2) MUTATED      2   70
  DEL PEAK  7(2Q37.2) WILD-TYPE    4  360
     clus
vv    DEL PEAK  7(2Q37.2) MUTATED DEL PEAK  7(2Q37.2) WILD-TYPE
  NO                            2                             4
  YES                          70                           360
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  7(2Q37.2) MUTATED    65   2   2   0
  DEL PEAK  7(2Q37.2) WILD-TYPE 282  16  17  25
D43V10, multiclass
    clus
vv   DEL PEAK  7(2Q37.2) MUTATED DEL PEAK  7(2Q37.2) WILD-TYPE
  R0                          65                           282
  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"
D43V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  7(2Q37.2) MUTATED      14                         2
  DEL PEAK  7(2Q37.2) WILD-TYPE    74                         9
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  7(2Q37.2) MUTATED                                           0    42
  DEL PEAK  7(2Q37.2) WILD-TYPE                                         1   232
D43V12, multiclass
                                           clus
vv                                          DEL PEAK  7(2Q37.2) MUTATED
  ASIAN                                                              14
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              42
                                           clus
vv                                          DEL PEAK  7(2Q37.2) WILD-TYPE
  ASIAN                                                                74
  BLACK OR AFRICAN AMERICAN                                             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V13, binary
                               cls
clus                              0   1
  DEL PEAK  7(2Q37.2) MUTATED     0  44
  DEL PEAK  7(2Q37.2) WILD-TYPE   4 269
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(2Q37.2) MUTATED      0   44
  DEL PEAK  7(2Q37.2) WILD-TYPE    4  269
                        clus
vv                       DEL PEAK  7(2Q37.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          44
                        clus
vv                       DEL PEAK  7(2Q37.2) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           269
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK  8(3P26.1) MUTATION ANALYSIS
D44V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(3P26.1) MUTATED    81  51
  DEL PEAK  8(3P26.1) WILD-TYPE 173  99
  DEL PEAK  8(3P26.1) MUTATED DEL PEAK  8(3P26.1) WILD-TYPE 
                          132                           272 
  DEL PEAK  8(3P26.1) MUTATED DEL PEAK  8(3P26.1) WILD-TYPE 
                           51                            99 
$`DEL PEAK  8(3P26.1) MUTATED`
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4191 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6705 
       11.01         9.44        18.35        19.33         9.17        25.61 
TCGA-BR-6803 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7957 TCGA-BR-7959 
       31.20        35.24        15.42        28.01         9.07        18.71 
TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8362 
       17.49         0.69         2.66        16.31         7.40        13.08 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8680 
        5.39        25.18         9.21        20.22        11.54        15.81 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
       15.68         8.22        10.68         7.53        22.26         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-5801 TCGA-CD-8526 TCGA-CD-8527 
        1.15        13.64         3.25        13.18         0.07         0.07 
TCGA-CD-8533 TCGA-CD-A487 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4437 
        0.13         9.34        20.02         3.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4466 
       54.08         4.01        14.01        47.05        12.03        18.97 
TCGA-CG-5718 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5730 TCGA-D7-5578 TCGA-D7-6521 
       36.00       105.07        15.02         4.01        12.66        18.54 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-A6EX TCGA-D7-A6EZ 
       13.35        17.19        15.22        12.79        11.31         9.76 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-FP-7829 TCGA-FP-7916 
        2.96        15.65         0.62         7.99        19.53        14.07 
TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4G6 
       17.06         0.56         5.52        12.59        14.17        12.30 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H5 
        3.25        22.75         6.25         2.10        23.84        12.30 
TCGA-IN-7806 TCGA-IN-A6RI TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR 
       21.21        18.38         1.41         6.44        12.59         6.51 
TCGA-IN-A7NT TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7O7 
        5.56         5.56        60.56        37.64         9.86        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 
       34.45         7.73        22.19        12.79         2.70        17.85 
TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y 
       27.35        14.33        36.69        36.16         9.50         9.73 
TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA64 
        2.01         4.54        21.04        42.54        22.09        18.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       32.94        29.98        54.12        21.11        12.43         0.79 

$`DEL PEAK  8(3P26.1) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 
       26.70        11.70        19.56         9.47         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.64         7.43        30.90         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-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       26.10        32.78        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 
       21.11        30.90        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       23.93        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       12.76        14.43        11.44        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 
        8.05         0.56        12.95         2.20        15.58         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         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        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        0.26        15.85         3.72         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8682 
        9.34        13.45         6.28         7.53         0.49        16.44 
TCGA-BR-8683 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
        9.86        12.56        13.87         6.08        13.41        13.51 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 
        8.98        14.17        12.82         0.66        19.36         0.46 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
       11.57         5.13         2.83        13.15         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A 
        0.10         0.13         0.10         3.42        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 
       11.61         6.58        12.20         0.10        12.62        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 
       15.95         1.02        29.98        19.07        21.99         0.00 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01         7.07        12.00        22.98        30.97         6.97 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         6.02         0.99        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10        69.04        21.07         7.99        12.36 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
       11.93        19.13        20.55        18.84        18.61        17.85 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       10.26        15.98        10.55        11.31        12.33        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        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A747 TCGA-D7-A748 
       14.76        13.71        11.24        11.44         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.40         7.13        16.24        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-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        0.23        18.08        26.47         1.51         5.92        14.27 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       11.84        24.20        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-A4H2 
        8.98         0.10         6.51        10.19         0.26        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 
       19.36         9.67         8.88         8.81        27.42         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR 
       18.81         3.39         5.36         5.19        13.08         6.74 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A93G TCGA-MX-A5UG 
        1.81         7.82        13.51         2.53        20.15         3.72 
TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       19.73        61.25         6.08         4.60         9.24        11.05 
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-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DT TCGA-VQ-A8DZ TCGA-VQ-A8E2 
       35.61        16.87        19.04        48.79        13.02        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       21.73        27.88        32.48        28.96        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       16.31         2.50         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E 
       13.35        26.24        64.57        65.16        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W 
       61.22        18.74        20.81        22.68         1.71         7.36 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
       52.24         9.04        55.43         6.58         5.72        64.18 
TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G 
        2.66        11.24        40.08        28.41        17.13        26.04 
TCGA-VQ-AA6I TCGA-ZA-A8F6 
       16.14        10.62 

  DEL PEAK  8(3P26.1) MUTATED DEL PEAK  8(3P26.1) WILD-TYPE 
                         0.07                          0.00 
  DEL PEAK  8(3P26.1) MUTATED DEL PEAK  8(3P26.1) WILD-TYPE 
                       115.69                        122.30 
  DEL PEAK  8(3P26.1) MUTATED DEL PEAK  8(3P26.1) WILD-TYPE 
                       12.985                        12.805 
[1] "0.1 - 115.7 (13.0)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D44V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  8(3P26.1) MUTATED         1        4       14        8         8
  DEL PEAK  8(3P26.1) WILD-TYPE       2       10       27       23        30
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  8(3P26.1) MUTATED          18         0         34         20
  DEL PEAK  8(3P26.1) WILD-TYPE        37         4         51         42
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  8(3P26.1) MUTATED           14       15
  DEL PEAK  8(3P26.1) WILD-TYPE         27       31
D44V3, multiclass
            clus
vv           DEL PEAK  8(3P26.1) MUTATED DEL PEAK  8(3P26.1) WILD-TYPE
  STAGE I                              1                             2
  STAGE IA                             4                            10
  STAGE IB                            14                            27
  STAGE II                             8                            23
  STAGE IIA                            8                            30
  STAGE IIB                           18                            37
  STAGE III                            0                             4
  STAGE IIIA                          34                            51
  STAGE IIIB                          20                            42
  STAGE IIIC                          14                            27
  STAGE IV                            15                            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  8(3P26.1) MUTATED     7  27  63  40
  DEL PEAK  8(3P26.1) WILD-TYPE  15  63 132  79
D44V4, multiclass
    clus
vv   DEL PEAK  8(3P26.1) MUTATED DEL PEAK  8(3P26.1) WILD-TYPE
  T1                           7                            15
  T2                          27                            63
  T3                          63                           132
  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  8(3P26.1) MUTATED   32 38 38 27
  DEL PEAK  8(3P26.1) WILD-TYPE 97 80 46 62
D44V5, multiclass
    clus
vv   DEL PEAK  8(3P26.1) MUTATED DEL PEAK  8(3P26.1) WILD-TYPE
  N0                          32                            97
  N1                          38                            80
  N2                          38                            46
  N3                          27                            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"
D44V6, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P26.1) MUTATED   121  12
  DEL PEAK  8(3P26.1) WILD-TYPE 266  18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P26.1) MUTATED    121   12
  DEL PEAK  8(3P26.1) WILD-TYPE  266   18
   clus
vv  DEL PEAK  8(3P26.1) MUTATED DEL PEAK  8(3P26.1) WILD-TYPE
  0                         121                           266
  1                          12                            18
[1] 2 2
[1] FALSE
D44V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P26.1) MUTATED    45  95
  DEL PEAK  8(3P26.1) WILD-TYPE 113 183
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P26.1) MUTATED     45   95
  DEL PEAK  8(3P26.1) WILD-TYPE  113  183
        clus
vv       DEL PEAK  8(3P26.1) MUTATED DEL PEAK  8(3P26.1) WILD-TYPE
  FEMALE                          45                           113
  MALE                            95                           183
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK  8(3P26.1) MUTATED                                      15
  DEL PEAK  8(3P26.1) WILD-TYPE                                    56
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  8(3P26.1) MUTATED                                                       48
  DEL PEAK  8(3P26.1) WILD-TYPE                                                    114
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  8(3P26.1) MUTATED                                                                  38
  DEL PEAK  8(3P26.1) WILD-TYPE                                                                43
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  8(3P26.1) MUTATED                                                 28
  DEL PEAK  8(3P26.1) WILD-TYPE                                               50
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK  8(3P26.1) MUTATED                                                          5
  DEL PEAK  8(3P26.1) WILD-TYPE                                                       16
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK  8(3P26.1) MUTATED                                                           3
  DEL PEAK  8(3P26.1) WILD-TYPE                                                         5
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK  8(3P26.1) MUTATED                                          3
  DEL PEAK  8(3P26.1) WILD-TYPE                                       10
D44V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  8(3P26.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     48
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           28
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    3
                                                                   clus
vv                                                                  DEL PEAK  8(3P26.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      114
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            43
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             50
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     10
[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"
D44V9, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P26.1) MUTATED     2 138
  DEL PEAK  8(3P26.1) WILD-TYPE   4 292
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P26.1) MUTATED      2  138
  DEL PEAK  8(3P26.1) WILD-TYPE    4  292
     clus
vv    DEL PEAK  8(3P26.1) MUTATED DEL PEAK  8(3P26.1) WILD-TYPE
  NO                            2                             4
  YES                         138                           292
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  8(3P26.1) MUTATED   114   5   8   5
  DEL PEAK  8(3P26.1) WILD-TYPE 233  13  11  20
D44V10, multiclass
    clus
vv   DEL PEAK  8(3P26.1) MUTATED DEL PEAK  8(3P26.1) WILD-TYPE
  R0                         114                           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"
D44V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  8(3P26.1) MUTATED      25                         4
  DEL PEAK  8(3P26.1) WILD-TYPE    63                         7
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  8(3P26.1) MUTATED                                           1    90
  DEL PEAK  8(3P26.1) WILD-TYPE                                         0   184
D44V12, multiclass
                                           clus
vv                                          DEL PEAK  8(3P26.1) MUTATED
  ASIAN                                                              25
  BLACK OR AFRICAN AMERICAN                                           4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              90
                                           clus
vv                                          DEL PEAK  8(3P26.1) WILD-TYPE
  ASIAN                                                                63
  BLACK OR AFRICAN AMERICAN                                             7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               184
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V13, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P26.1) MUTATED     1  93
  DEL PEAK  8(3P26.1) WILD-TYPE   3 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P26.1) MUTATED      1   93
  DEL PEAK  8(3P26.1) WILD-TYPE    3  220
                        clus
vv                       DEL PEAK  8(3P26.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          93
                        clus
vv                       DEL PEAK  8(3P26.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           220
[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    90  60
  DEL PEAK  9(3P14.2) WILD-TYPE 164  90
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                          150                           254 
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                           60                            90 
$`DEL PEAK  9(3P14.2) MUTATED`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6458 
       26.70        19.56        11.01         6.61        17.29        19.33 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7704 TCGA-BR-7715 
        9.17        25.61        31.20        32.94        35.24        15.42 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 
       28.01        15.32         3.45         9.07        18.71        17.49 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       11.44         0.69         2.66         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ 
       20.22        15.68         8.22        13.87         7.53        22.26 
TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4PD 
        1.48        12.89         0.72         0.53        13.51        20.65 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-8524 
        1.15        13.64         3.25        13.15        13.18         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A487 TCGA-CG-4300 
        0.07         0.07         0.13         0.13         9.34        20.02 
TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
        3.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-5718 TCGA-CG-5719 
       14.01        47.05        12.03        18.97        36.00         1.02 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6520 
       12.03        15.02         4.01        12.36        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 
       18.54        13.35        17.19        10.26        15.22        12.79 
TCGA-D7-6822 TCGA-D7-A4YT TCGA-D7-A4YY TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       12.33        14.27        13.78        11.31        11.44         9.76 
TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 
        7.40         0.62         7.99        19.53        14.07        17.06 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        0.56         5.52        26.47         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       11.41        12.10        12.30         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H4 
       11.77         8.98         0.10         6.25         2.10        23.84 
TCGA-HU-A4H8 TCGA-IN-7806 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP 
        8.88        21.21        18.38         5.19         1.41         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1X TCGA-KB-A6F5 
        6.74        12.59         6.51         5.56        13.51         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       60.56        37.64         9.86        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DU 
       61.25        16.67        37.91         8.94         5.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       13.25        34.45         7.73        22.19         2.70        17.85 
TCGA-VQ-A8PO TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A91N TCGA-VQ-A91V TCGA-VQ-A91X 
        9.27        13.35        14.33        18.74        36.16         9.50 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A94U TCGA-VQ-AA64 
        9.04         2.01        55.43         4.54        22.09        18.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       32.94        29.98        54.12        26.04        12.43         0.79 

$`DEL PEAK  9(3P14.2) WILD-TYPE`
TCGA-B7-5818 TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       11.70         9.47         9.44         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         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-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        21.11        30.90 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7723 
       12.82         9.21        24.76        23.93        18.15        28.73 
TCGA-BR-7851 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       12.43        12.76        14.43        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56        12.95        16.31         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        19.50        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        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
       10.68        12.56         6.08        13.41        13.51         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE 
       14.17        12.82         0.66        19.36         0.46        20.42 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 
       11.57         5.13         2.83         0.30         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 
        0.10         0.13         0.16         0.10         0.10         0.10 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        3.42        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 
        0.10        12.62        27.02         1.02        29.98        19.07 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
       21.99         0.00         9.01         7.07        12.00        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       30.97         6.97         0.99         6.02         0.99       105.07 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07        65.10        69.04        21.07         7.99 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6815 
       12.66        11.93        19.13        18.61        17.85        15.98 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       10.55        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-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-D7-A6F2 
       15.16        14.76        13.71        11.24         2.96        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
        8.38         4.34         7.13        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
       21.27        11.38         3.48        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8608 
       13.58         0.23        18.08         1.51        14.27        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ 
        0.76        24.30         5.59        11.84        24.20        21.37 
TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 
       29.98         6.51        10.19         0.26        12.95        19.36 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 
       12.30         9.67         8.81        27.42         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 
        3.39         5.36        13.08         1.81         7.82         2.53 
TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       20.15         3.72        19.73         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 
       11.05         8.61         5.13       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-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        0.92        48.79        13.02        18.48        35.24        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       27.88        32.48        28.96        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        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       27.35        64.57        65.16        36.69        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y 
       61.22        20.81        22.68         1.71         7.36         9.73 
TCGA-VQ-A91Z TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P 
       52.24         6.58         5.72        64.18        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6I 
       42.54        11.24        40.08        28.41        17.13        16.14 
TCGA-VQ-AA6J TCGA-ZA-A8F6 
       21.11        10.62 

  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                         0.07                          0.00 
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                        61.25                        122.30 
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                        12.59                         12.95 
[1] "0.1 - 61.2 (12.6)"  "0.0 - 122.3 (12.9)"
[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       12        13
  DEL PEAK  9(3P14.2) WILD-TYPE       2        9       29       19        25
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  9(3P14.2) MUTATED          23         0         40         19
  DEL PEAK  9(3P14.2) WILD-TYPE        32         4         45         43
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  9(3P14.2) MUTATED           13       17
  DEL PEAK  9(3P14.2) WILD-TYPE         28       29
D45V3, multiclass
            clus
vv           DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  STAGE I                              1                             2
  STAGE IA                             5                             9
  STAGE IB                            12                            29
  STAGE II                            12                            19
  STAGE IIA                           13                            25
  STAGE IIB                           23                            32
  STAGE III                            0                             4
  STAGE IIIA                          40                            45
  STAGE IIIB                          19                            43
  STAGE IIIC                          13                            28
  STAGE IV                            17                            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  9(3P14.2) MUTATED     9  32  73  41
  DEL PEAK  9(3P14.2) WILD-TYPE  13  58 122  78
D45V4, multiclass
    clus
vv   DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  T1                           9                            13
  T2                          32                            58
  T3                          73                           122
  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 49 36 28
  DEL PEAK  9(3P14.2) WILD-TYPE 88 69 48 61
D45V5, multiclass
    clus
vv   DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  N0                          41                            88
  N1                          49                            69
  N2                          36                            48
  N3                          28                            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"
D45V6, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P14.2) MUTATED   135  14
  DEL PEAK  9(3P14.2) WILD-TYPE 252  16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P14.2) MUTATED    135   14
  DEL PEAK  9(3P14.2) WILD-TYPE  252   16
   clus
vv  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  0                         135                           252
  1                          14                            16
[1] 2 2
[1] FALSE
D45V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P14.2) MUTATED    58  98
  DEL PEAK  9(3P14.2) WILD-TYPE 100 180
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P14.2) MUTATED     58   98
  DEL PEAK  9(3P14.2) WILD-TYPE  100  180
        clus
vv       DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  FEMALE                          58                           100
  MALE                            98                           180
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK  9(3P14.2) MUTATED                                      19
  DEL PEAK  9(3P14.2) WILD-TYPE                                    52
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  9(3P14.2) MUTATED                                                       52
  DEL PEAK  9(3P14.2) WILD-TYPE                                                    110
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  9(3P14.2) MUTATED                                                                  36
  DEL PEAK  9(3P14.2) WILD-TYPE                                                                45
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  9(3P14.2) MUTATED                                                 36
  DEL PEAK  9(3P14.2) WILD-TYPE                                               42
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK  9(3P14.2) MUTATED                                                          4
  DEL PEAK  9(3P14.2) WILD-TYPE                                                       17
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK  9(3P14.2) MUTATED                                                           4
  DEL PEAK  9(3P14.2) WILD-TYPE                                                         4
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK  9(3P14.2) MUTATED                                          5
  DEL PEAK  9(3P14.2) WILD-TYPE                                        8
D45V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  9(3P14.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      19
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     52
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    5
                                                                   clus
vv                                                                  DEL PEAK  9(3P14.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        52
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      110
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            45
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             42
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      8
[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"
D45V9, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P14.2) MUTATED     2 154
  DEL PEAK  9(3P14.2) WILD-TYPE   4 276
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P14.2) MUTATED      2  154
  DEL PEAK  9(3P14.2) WILD-TYPE    4  276
     clus
vv    DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  NO                            2                             4
  YES                         154                           276
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  9(3P14.2) MUTATED   135   3   7   3
  DEL PEAK  9(3P14.2) WILD-TYPE 212  15  12  22
D45V10, multiclass
    clus
vv   DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  R0                         135                           212
  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      34                         1
  DEL PEAK  9(3P14.2) WILD-TYPE    54                        10
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  9(3P14.2) MUTATED                                           0    96
  DEL PEAK  9(3P14.2) WILD-TYPE                                         1   178
D45V12, multiclass
                                           clus
vv                                          DEL PEAK  9(3P14.2) MUTATED
  ASIAN                                                              34
  BLACK OR AFRICAN AMERICAN                                           1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              96
                                           clus
vv                                          DEL PEAK  9(3P14.2) WILD-TYPE
  ASIAN                                                                54
  BLACK OR AFRICAN AMERICAN                                            10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               178
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V13, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P14.2) MUTATED     2 109
  DEL PEAK  9(3P14.2) WILD-TYPE   2 204
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P14.2) MUTATED      2  109
  DEL PEAK  9(3P14.2) WILD-TYPE    2  204
                        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                                 2
  NOT HISPANIC OR LATINO                           204
[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    28  15
  DEL PEAK 10(3Q26.31) WILD-TYPE 226 135
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                            43                            361 
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                            15                            135 
$`DEL PEAK 10(3Q26.31) MUTATED`
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7959 TCGA-BR-8077 TCGA-BR-8485 TCGA-BR-8486 
       35.24        15.42        18.71         0.69         9.21        20.22 
TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PF 
       10.68        13.87        12.89         0.72        13.51         1.15 
TCGA-CD-8533 TCGA-CD-A487 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4466 TCGA-D7-5578 
        0.13         9.34        54.08        14.01        18.97        12.66 
TCGA-D7-6526 TCGA-D7-8573 TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-EQ-8122 
       17.19        19.50        11.31        11.44         2.96         7.99 
TCGA-FP-A4BF TCGA-HU-8249 TCGA-HU-A4GF TCGA-HU-A4GU TCGA-IN-7806 TCGA-KB-A6F5 
        5.52        14.17        25.81         6.25        21.21         5.56 
TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7ZF TCGA-RD-A7C1 TCGA-VQ-A8DU TCGA-VQ-A8DV 
       37.64         9.86         8.52        16.67         5.46        13.25 
TCGA-VQ-A8PE TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94U 
       22.19        36.16         9.50        21.04        42.54        22.09 
TCGA-VQ-AA6B 
       29.98 

$`DEL PEAK 10(3Q26.31) WILD-TYPE`
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-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
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-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 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       24.76        23.93        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 
       12.43         3.45         9.07        12.76        17.49        14.43 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44        12.26         9.60        20.55         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         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        19.50        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 
       19.17        14.79         0.26        15.85         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        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 
        9.86        15.68         8.22        12.56         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 
       22.26         1.48        13.41        13.51         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD 
        0.53        12.82         0.66        19.36         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 
       13.15        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A 
        0.10         0.13         0.10         3.42        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
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-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
        4.01        29.98        47.05        19.07        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01         7.07        12.00        22.98        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-5727 TCGA-CG-5728 
      105.07        12.03        15.02        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 
        4.01        69.04        21.07         7.99        12.36        11.93 
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-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       13.35        10.26        15.22        15.98        12.79        10.55 
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-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 
       15.16        13.78        14.76        13.71        11.24         9.76 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34         7.40         7.13         0.62 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
       16.24        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-8211 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       13.58         0.56         0.23        18.08        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        14.27        12.59        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        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-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       19.36        23.84        12.30         9.67         8.88         8.81 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       27.42         3.45        18.81         3.39        18.38         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
        5.19        13.08         1.41         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         5.56         1.81         7.82        13.51         2.53 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE 
       60.56        20.15         3.72        19.73        45.67        18.21 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       61.25         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        5.13       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-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
        5.79         0.92        48.79        13.02        18.48        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        34.45        27.88        32.48         7.73        28.96 
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-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       26.24        27.35        64.57        14.33        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       11.70        11.93        61.22        18.74        20.81        22.68 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
        1.71         7.36         9.73        52.24         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        64.18         2.66 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D 
       11.24        18.41        40.08        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        21.11        12.43        10.62 
TCGA-ZQ-A9CR 
        0.79 

  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                          0.13                           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 
                         13.51                          12.79 
[1] "0.1 - 54.1 (13.5)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D46V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 10(3Q26.31) MUTATED         0        1        5        2         4
  DEL PEAK 10(3Q26.31) WILD-TYPE       3       13       36       29        34
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 10(3Q26.31) MUTATED           7         0         12          8
  DEL PEAK 10(3Q26.31) WILD-TYPE        48         4         73         54
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 10(3Q26.31) MUTATED            3        3
  DEL PEAK 10(3Q26.31) WILD-TYPE         38       43
D46V3, multiclass
            clus
vv           DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  STAGE I                               0                              3
  STAGE IA                              1                             13
  STAGE IB                              5                             36
  STAGE II                              2                             29
  STAGE IIA                             4                             34
  STAGE IIB                             7                             48
  STAGE III                             0                              4
  STAGE IIIA                           12                             73
  STAGE IIIB                            8                             54
  STAGE IIIC                            3                             38
  STAGE IV                              3                             43
[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   6  27  12
  DEL PEAK 10(3Q26.31) WILD-TYPE  21  84 168 107
D46V4, multiclass
    clus
vv   DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  T1                            1                             21
  T2                            6                             84
  T3                           27                            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    14   9  14   8
  DEL PEAK 10(3Q26.31) WILD-TYPE 115 109  70  81
D46V5, multiclass
    clus
vv   DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  N0                           14                            115
  N1                            9                            109
  N2                           14                             70
  N3                            8                             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"
D46V6, binary
                                cls
clus                               0   1
  DEL PEAK 10(3Q26.31) MUTATED    43   1
  DEL PEAK 10(3Q26.31) WILD-TYPE 344  29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q26.31) MUTATED     43    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                           43                            344
  1                            1                             29
[1] 2 2
[1] FALSE
D46V7, binary
                                cls
clus                               0   1
  DEL PEAK 10(3Q26.31) MUTATED    16  31
  DEL PEAK 10(3Q26.31) WILD-TYPE 142 247
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q26.31) MUTATED     16   31
  DEL PEAK 10(3Q26.31) WILD-TYPE  142  247
        clus
vv       DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  FEMALE                           16                            142
  MALE                             31                            247
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 10(3Q26.31) MUTATED                                       4
  DEL PEAK 10(3Q26.31) WILD-TYPE                                    67
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 10(3Q26.31) MUTATED                                                       16
  DEL PEAK 10(3Q26.31) WILD-TYPE                                                    146
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 10(3Q26.31) MUTATED                                                                  13
  DEL PEAK 10(3Q26.31) WILD-TYPE                                                                68
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 10(3Q26.31) MUTATED                                                 11
  DEL PEAK 10(3Q26.31) WILD-TYPE                                               67
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 10(3Q26.31) MUTATED                                                          1
  DEL PEAK 10(3Q26.31) WILD-TYPE                                                       20
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 10(3Q26.31) MUTATED                                                           0
  DEL PEAK 10(3Q26.31) WILD-TYPE                                                         8
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 10(3Q26.31) MUTATED                                          2
  DEL PEAK 10(3Q26.31) WILD-TYPE                                       11
D46V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 10(3Q26.31) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      16
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
                                                                   clus
vv                                                                  DEL PEAK 10(3Q26.31) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         67
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       146
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             68
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              67
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      11
[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"
D46V9, binary
                                cls
clus                               0   1
  DEL PEAK 10(3Q26.31) MUTATED     1  46
  DEL PEAK 10(3Q26.31) WILD-TYPE   5 384
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q26.31) MUTATED      1   46
  DEL PEAK 10(3Q26.31) WILD-TYPE    5  384
     clus
vv    DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  NO                             1                              5
  YES                           46                            384
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 10(3Q26.31) MUTATED    42   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                           42                            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       8                         2
  DEL PEAK 10(3Q26.31) WILD-TYPE    80                         9
                                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      31
  DEL PEAK 10(3Q26.31) WILD-TYPE   243
D46V12, multiclass
                                           clus
vv                                          DEL PEAK 10(3Q26.31) MUTATED
  ASIAN                                                                8
  BLACK OR AFRICAN AMERICAN                                            2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               31
                                           clus
vv                                          DEL PEAK 10(3Q26.31) WILD-TYPE
  ASIAN                                                                 80
  BLACK OR AFRICAN AMERICAN                                              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                243
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V13, binary
                                cls
clus                               0   1
  DEL PEAK 10(3Q26.31) MUTATED     0  32
  DEL PEAK 10(3Q26.31) WILD-TYPE   4 281
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q26.31) MUTATED      0   32
  DEL PEAK 10(3Q26.31) WILD-TYPE    4  281
                        clus
vv                       DEL PEAK 10(3Q26.31) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           32
                        clus
vv                       DEL PEAK 10(3Q26.31) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            281
[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    97  59
  DEL PEAK 11(4P16.3) WILD-TYPE 157  91
  DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE 
                          156                           248 
  DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE 
                           59                            91 
$`DEL PEAK 11(4P16.3) MUTATED`
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-6456 
       11.01         9.44         6.61         7.43        18.35        17.29 
TCGA-BR-6565 TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 
        9.17        31.20         9.21        24.76        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 
       18.15        28.73         3.45         9.07        18.71        17.49 
TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        9.60        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8384 
        7.40        22.19        17.52        14.04        14.79         3.72 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8683 
        5.39         9.21        20.22         0.49        11.54         9.86 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 
       15.68        10.68         7.53        22.26         1.48         0.72 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-CD-5802 TCGA-CD-5803 
        0.66        13.51         0.46        13.64         0.30         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
        0.07         0.07         0.13         0.10         0.13         0.13 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 
        9.34        11.31        11.61        12.20        20.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        8.05        54.08         4.01        47.05        19.07        12.03 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5725 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       18.97         7.07        15.02        19.13        20.55        18.84 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8573 
       17.19        10.26        15.22        11.31        24.72        19.50 
TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A74A 
       18.21        21.14        16.44        11.31         2.96         7.40 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-A4BF 
        7.99        72.23        11.38        14.07        17.06         5.52 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       18.08        26.47         1.51         5.92        12.59        14.17 
TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY 
       12.10        22.75        25.81         8.98         6.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 
        2.10        12.95        23.84         9.67        27.42        21.21 
TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IP-7968 TCGA-KB-A6F5 
       18.81         5.36         1.41         6.44         2.53         5.56 
TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR 
       60.56         3.72         9.86        45.67        18.21         6.08 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 
        9.24        11.05        16.67        37.91       115.69         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       35.61         5.79         5.46        13.25        35.24        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH 
       34.45        32.48         7.73        46.26        22.19        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91V 
        2.70         1.87        27.35        65.16        36.69        36.16 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A94O 
        9.50         9.73        52.24         9.04         4.54        21.04 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       42.54        11.24        22.09        32.94        29.98        54.12 

$`DEL PEAK 11(4P16.3) WILD-TYPE`
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-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         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-6566 
       13.87        13.68        19.33        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        21.11 
TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7722 
       30.90        32.94        12.82        35.24        23.93        15.32 
TCGA-BR-7851 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       12.43        12.76        14.43        11.44         0.69        12.26 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       20.55         8.05         0.56         6.18        19.50        13.08 
TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
        0.26         0.95        26.33         4.31         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 
       19.17         0.26        15.85        25.18         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 
       15.81         9.34        13.45         6.28         7.53        15.81 
TCGA-BR-8682 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU 
       16.44         8.22        12.56        13.87         6.08        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       13.51        12.89         8.98        14.17         0.53        12.82 
TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM 
       19.36        20.65        20.42         1.15        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8527 
        2.83         3.25        13.15        13.18         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A48A 
        0.10         0.16         0.10         0.10         3.42        12.43 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        6.58         0.10        12.62         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
        1.02        14.01        29.98        21.99         0.00         9.01 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       12.00        22.98        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-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       12.36        12.66        11.93        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8572 
       13.35        15.98        12.79        10.55        12.33        16.80 
TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX 
       17.19        14.66        20.91        14.27         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        13.71        11.24        11.44         9.76 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO 
       15.65         8.38         4.34         7.13         0.62        16.24 
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-8631 TCGA-FP-A8CX TCGA-HU-8244 TCGA-HU-8602 
        5.03        13.58         0.56         0.23        14.27        11.41 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
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        10.19        19.36        12.30         8.88         8.81 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR 
        3.45         3.39        18.38         5.19        13.08         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51         5.56         1.81         7.82        13.51 
TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
       20.15        37.64        19.73         8.52        61.25         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        27.88        28.96        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        26.24 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       64.57        14.33        11.70        11.93        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A924 
       20.81        22.68         1.71         7.36         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        64.18         2.66        18.41        40.08 
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        21.11        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

  DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE 
                         0.07                          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 
                       12.395                        12.955 
[1] "0.1 - 115.7 (12.4)" "0.0 - 122.3 (13.0)"
[1] "hr=" "1"  
D47V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 11(4P16.3) MUTATED         0        4       12       13        18
  DEL PEAK 11(4P16.3) WILD-TYPE       3       10       29       18        20
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 11(4P16.3) MUTATED          19         1         39         23
  DEL PEAK 11(4P16.3) WILD-TYPE        36         3         46         39
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 11(4P16.3) MUTATED           17       14
  DEL PEAK 11(4P16.3) WILD-TYPE         24       32
D47V3, multiclass
            clus
vv           DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE
  STAGE I                              0                             3
  STAGE IA                             4                            10
  STAGE IB                            12                            29
  STAGE II                            13                            18
  STAGE IIA                           18                            20
  STAGE IIB                           19                            36
  STAGE III                            1                             3
  STAGE IIIA                          39                            46
  STAGE IIIB                          23                            39
  STAGE IIIC                          17                            24
  STAGE IV                            14                            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 11(4P16.3) MUTATED     6  27  89  40
  DEL PEAK 11(4P16.3) WILD-TYPE  16  63 106  79
D47V4, multiclass
    clus
vv   DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE
  T1                           6                            16
  T2                          27                            63
  T3                          89                           106
  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   44 47 37 32
  DEL PEAK 11(4P16.3) WILD-TYPE 85 71 47 57
D47V5, multiclass
    clus
vv   DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE
  N0                          44                            85
  N1                          47                            71
  N2                          37                            47
  N3                          32                            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"
D47V6, binary
                               cls
clus                              0   1
  DEL PEAK 11(4P16.3) MUTATED   154   7
  DEL PEAK 11(4P16.3) WILD-TYPE 233  23
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P16.3) MUTATED    154    7
  DEL PEAK 11(4P16.3) WILD-TYPE  233   23
   clus
vv  DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE
  0                         154                           233
  1                           7                            23
[1] 2 2
[1] FALSE
D47V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(4P16.3) MUTATED    55 112
  DEL PEAK 11(4P16.3) WILD-TYPE 103 166
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P16.3) MUTATED     55  112
  DEL PEAK 11(4P16.3) WILD-TYPE  103  166
        clus
vv       DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE
  FEMALE                          55                           103
  MALE                           112                           166
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 11(4P16.3) MUTATED                                      23
  DEL PEAK 11(4P16.3) WILD-TYPE                                    48
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 11(4P16.3) MUTATED                                                       56
  DEL PEAK 11(4P16.3) WILD-TYPE                                                    106
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 11(4P16.3) MUTATED                                                                  30
  DEL PEAK 11(4P16.3) WILD-TYPE                                                                51
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 11(4P16.3) MUTATED                                                 39
  DEL PEAK 11(4P16.3) WILD-TYPE                                               39
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 11(4P16.3) MUTATED                                                         10
  DEL PEAK 11(4P16.3) WILD-TYPE                                                       11
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 11(4P16.3) MUTATED                                                           3
  DEL PEAK 11(4P16.3) WILD-TYPE                                                         5
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 11(4P16.3) MUTATED                                          6
  DEL PEAK 11(4P16.3) WILD-TYPE                                        7
D47V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 11(4P16.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      23
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     56
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          30
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           39
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    6
                                                                   clus
vv                                                                  DEL PEAK 11(4P16.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      106
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            51
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             39
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      7
[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"
D47V9, binary
                               cls
clus                              0   1
  DEL PEAK 11(4P16.3) MUTATED     2 165
  DEL PEAK 11(4P16.3) WILD-TYPE   4 265
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P16.3) MUTATED      2  165
  DEL PEAK 11(4P16.3) WILD-TYPE    4  265
     clus
vv    DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE
  NO                            2                             4
  YES                         165                           265
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 11(4P16.3) MUTATED   133   8   4   9
  DEL PEAK 11(4P16.3) WILD-TYPE 214  10  15  16
D47V10, multiclass
    clus
vv   DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE
  R0                         133                           214
  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                         8
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 11(4P16.3) MUTATED                                           0   105
  DEL PEAK 11(4P16.3) WILD-TYPE                                         1   169
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                                                             105
                                           clus
vv                                          DEL PEAK 11(4P16.3) WILD-TYPE
  ASIAN                                                                50
  BLACK OR AFRICAN AMERICAN                                             8
  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"
D47V13, binary
                               cls
clus                              0   1
  DEL PEAK 11(4P16.3) MUTATED     1 121
  DEL PEAK 11(4P16.3) WILD-TYPE   3 192
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P16.3) MUTATED      1  121
  DEL PEAK 11(4P16.3) WILD-TYPE    3  192
                        clus
vv                       DEL PEAK 11(4P16.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         121
                        clus
vv                       DEL PEAK 11(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           192
[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   108  69
  DEL PEAK 12(4Q22.1) WILD-TYPE 146  81
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                          177                           227 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                           69                            81 
$`DEL PEAK 12(4Q22.1) MUTATED`
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6458 
       11.01         9.44         6.61        18.35        17.29        19.33 
TCGA-BR-6565 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7957 
        9.17        21.11        31.20        28.01        18.15         9.07 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 
       18.71        17.49        14.43         0.69         9.60        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8361 TCGA-BR-8364 
        2.66        16.31         2.20        15.58        19.50        22.19 
TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       17.52        14.04        14.79         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8690 
        9.21        20.22        15.81        11.54         9.86        10.68 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 
        7.53        22.26         1.48         0.72         0.66        13.51 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
        1.15        13.64         5.13         3.25        13.15         0.30 
TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 
        0.07         0.07         0.07         0.07         0.10         0.16 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         0.13         0.13        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4437 
        6.58        12.20        20.02         3.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 
       54.08         4.01        47.05        19.07        12.03        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5720 TCGA-CG-5724 TCGA-CG-5727 
        7.07        22.98        30.97         0.99        12.03        79.07 
TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
        4.01        69.04        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 
       20.55        17.19        10.26        15.22        15.98        10.55 
TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A74A 
       11.31        19.50        18.21        16.44        11.31         7.40 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        0.62         7.99        72.23        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HU-8238 
       14.07        17.06        13.58         5.52         0.23         1.51 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G3 
        5.92        12.59        14.17        12.10         0.76         5.59 
TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
       22.75         8.98         6.25         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
       23.84        12.30         9.67        27.42        21.21        18.81 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT 
        3.39         5.36         1.41         6.44         6.74         5.56 
TCGA-IP-7968 TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-R5-A805 
        2.53         9.86        45.67        18.21         6.08         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 
       11.05         8.61        16.67        37.91       115.69         8.94 
TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
       35.61        48.79        13.25        13.02        18.48        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PO 
       21.73         7.73        46.26        12.79         2.70         9.27 
TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91Q 
       13.35        14.33        65.16        36.69        18.74        20.81 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A94O 
        9.50         9.73        52.24         4.54         5.72        21.04 
TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       42.54        22.09        40.08        32.94        29.98        54.12 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       16.14        21.11        12.43 

$`DEL PEAK 12(4Q22.1) WILD-TYPE`
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-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        7.43        30.90         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 
       32.94        12.82         9.21        24.76        35.24        23.93 
TCGA-BR-7715 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7958 
       15.42        15.32        28.73        12.43         3.45        12.76 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8297 
       11.44        12.26        20.55         8.05         0.56         7.40 
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-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8487 
        3.32        11.80        19.17         0.26        15.85         1.12 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U 
       15.81        16.44        15.68         8.22        12.56        13.87 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        6.08        13.41        13.51        12.89         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53        12.82        19.36         0.46        20.65        20.42 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8529 TCGA-CD-8531 
       11.57         2.83        13.18         0.07         0.13         0.10 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 
        0.10         3.42         9.34         0.10        12.62        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4460 TCGA-CG-4462 
       15.95         1.02        14.01        29.98        21.99         0.00 
TCGA-CG-4465 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5721 
        9.01        12.00         6.97        36.00         1.02         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 
        0.99       105.07        15.02        28.96        65.10        21.07 
TCGA-CG-5734 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
        7.99        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 
       12.79        12.33        24.72        16.80        17.19        14.66 
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        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        13.71        11.24        11.44         9.76         2.96 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 
       15.65         8.38         4.34         7.13        16.24        14.47 
TCGA-F1-A448 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HF-A5NB 
       21.27        22.29        59.54         5.03         0.56        18.08 
TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G6 
       26.47        14.27        11.41        10.62        24.30        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       11.84        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        10.19        19.36         8.88 
TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS 
        8.81         3.45        18.38         5.19        13.08        12.59 
TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 
        6.51         1.81         7.82        13.51         5.56        60.56 
TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI 
       20.15        37.64         3.72        19.73         8.52        61.25 
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 
       34.45        27.88        32.48        28.96        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-A8PU TCGA-VQ-A8PX TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       26.24        27.35        64.57        11.70        11.93        61.22 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A922 TCGA-VQ-A923 
       22.68         1.71        36.16         7.36         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 
       55.43         6.58        64.18         2.66        11.24        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       28.41        17.13        26.04        10.62         0.79 

  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                         0.07                          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 
                        12.36                         13.35 
[1] "0.1 - 115.7 (12.4)" "0.0 - 122.3 (13.3)"
[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        4       13       17        18
  DEL PEAK 12(4Q22.1) WILD-TYPE       3       10       28       14        20
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 12(4Q22.1) MUTATED          25         2         42         24
  DEL PEAK 12(4Q22.1) WILD-TYPE        30         2         43         38
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 12(4Q22.1) MUTATED           19       20
  DEL PEAK 12(4Q22.1) WILD-TYPE         22       26
D48V3, multiclass
            clus
vv           DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  STAGE I                              0                             3
  STAGE IA                             4                            10
  STAGE IB                            13                            28
  STAGE II                            17                            14
  STAGE IIA                           18                            20
  STAGE IIB                           25                            30
  STAGE III                            2                             2
  STAGE IIIA                          42                            43
  STAGE IIIB                          24                            38
  STAGE IIIC                          19                            22
  STAGE IV                            20                            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 12(4Q22.1) MUTATED     5  37  95  48
  DEL PEAK 12(4Q22.1) WILD-TYPE  17  53 100  71
D48V4, multiclass
    clus
vv   DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  T1                           5                            17
  T2                          37                            53
  T3                          95                           100
  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   49 52 42 40
  DEL PEAK 12(4Q22.1) WILD-TYPE 80 66 42 49
D48V5, multiclass
    clus
vv   DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  N0                          49                            80
  N1                          52                            66
  N2                          42                            42
  N3                          40                            49
[1] 4 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   172  10
  DEL PEAK 12(4Q22.1) WILD-TYPE 215  20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED    172   10
  DEL PEAK 12(4Q22.1) WILD-TYPE  215   20
   clus
vv  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  0                         172                           215
  1                          10                            20
[1] 2 2
[1] FALSE
D48V7, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q22.1) MUTATED    66 124
  DEL PEAK 12(4Q22.1) WILD-TYPE  92 154
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED     66  124
  DEL PEAK 12(4Q22.1) WILD-TYPE   92  154
        clus
vv       DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  FEMALE                          66                            92
  MALE                           124                           154
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 12(4Q22.1) MUTATED                                      23
  DEL PEAK 12(4Q22.1) WILD-TYPE                                    48
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 12(4Q22.1) MUTATED                                                       66
  DEL PEAK 12(4Q22.1) WILD-TYPE                                                     96
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 12(4Q22.1) MUTATED                                                                  41
  DEL PEAK 12(4Q22.1) WILD-TYPE                                                                40
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 12(4Q22.1) MUTATED                                                 37
  DEL PEAK 12(4Q22.1) WILD-TYPE                                               41
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 12(4Q22.1) MUTATED                                                          9
  DEL PEAK 12(4Q22.1) WILD-TYPE                                                       12
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 12(4Q22.1) MUTATED                                                           5
  DEL PEAK 12(4Q22.1) WILD-TYPE                                                         3
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 12(4Q22.1) MUTATED                                          8
  DEL PEAK 12(4Q22.1) WILD-TYPE                                        5
D48V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 12(4Q22.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      23
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     66
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          41
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    8
                                                                   clus
vv                                                                  DEL PEAK 12(4Q22.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       96
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             41
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      5
[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"
D48V9, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q22.1) MUTATED     4 186
  DEL PEAK 12(4Q22.1) WILD-TYPE   2 244
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED      4  186
  DEL PEAK 12(4Q22.1) WILD-TYPE    2  244
     clus
vv    DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  NO                            4                             2
  YES                         186                           244
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 12(4Q22.1) MUTATED   146  10  10   8
  DEL PEAK 12(4Q22.1) WILD-TYPE 201   8   9  17
D48V10, multiclass
    clus
vv   DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  R0                         146                           201
  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                         4
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 12(4Q22.1) MUTATED                                           1   113
  DEL PEAK 12(4Q22.1) WILD-TYPE                                         0   161
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                                                             113
                                           clus
vv                                          DEL PEAK 12(4Q22.1) WILD-TYPE
  ASIAN                                                                45
  BLACK OR AFRICAN AMERICAN                                             4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               161
[1] 4 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     1 135
  DEL PEAK 12(4Q22.1) WILD-TYPE   3 178
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED      1  135
  DEL PEAK 12(4Q22.1) WILD-TYPE    3  178
                        clus
vv                       DEL PEAK 12(4Q22.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         135
                        clus
vv                       DEL PEAK 12(4Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           178
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 13(4Q34.3) MUTATION ANALYSIS
D49V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(4Q34.3) MUTATED   116  70
  DEL PEAK 13(4Q34.3) WILD-TYPE 138  80
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                          186                           218 
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                           70                            80 
$`DEL PEAK 13(4Q34.3) MUTATED`
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6458 
       19.56        11.01         9.44        18.35        17.29        19.33 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6709 TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7704 
        9.17        25.61        12.16        31.20         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7959 
       15.42        18.15        28.73        12.43         9.07        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8291 
       17.49        14.43         0.69         9.60         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
        2.20        15.58         7.40        19.50        22.19        17.52 
TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.04        14.79         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-A452 TCGA-BR-A4CQ 
       20.22         0.49        11.54         9.86         7.53        22.26 
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-5802 TCGA-CD-5803 TCGA-CD-8524 
       13.64         3.25        13.15         0.30         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8532 
        0.07         0.07         0.07         0.10         0.16         0.10 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        0.13         0.13        11.31        12.43        11.61        12.20 
TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       20.02        27.02         7.99         8.05        54.08         4.01 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4475 
       47.05        19.07        12.03         9.01        18.97        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5725 TCGA-CG-5727 TCGA-D7-5578 
       30.97         6.97         1.02        15.02        79.07        12.66 
TCGA-D7-6518 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       19.13        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-A4YT 
       12.79        11.31        12.33        19.50        18.21        14.27 
TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A74A 
       16.44        11.24        11.31        11.44         2.96         7.40 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 
        0.62         7.99        16.24        11.38        19.53        14.07 
TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HU-8238 TCGA-HU-8243 
       17.06        13.58         5.52         0.23         1.51         5.92 
TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4GU 
       12.59        12.10         0.76        22.75         8.98         6.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        12.30         9.67 
TCGA-HU-A4HD TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
       27.42         5.36         5.19        13.08         1.41         6.44 
TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F7 TCGA-MX-A663 
        6.74         5.56         1.81         2.53        60.56         9.86 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BS 
       45.67        18.21         8.52         6.08         9.24        11.05 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DL 
       16.67       122.30        37.91         8.94        35.61         0.92 
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        35.24        21.73 
TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PS TCGA-VQ-A8PU 
        7.73        46.26        22.19        12.79        13.35        27.35 
TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U 
       64.57        65.16        36.69        18.74        22.68         1.71 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R 
        9.50         9.73        52.24         4.54        21.04        42.54 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       22.09        18.41        40.08        32.94        29.98        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        21.11        12.43         0.79 

$`DEL PEAK 13(4Q34.3) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       26.70        11.70         9.47         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        7.43        30.90         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-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 
       18.05        19.89         8.98        21.11        30.90        32.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7901 
       12.82        24.76        23.93        28.01        15.32         3.45 
TCGA-BR-7958 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       12.76        11.44        12.26        20.55         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 
       12.95         6.18        13.08         0.26         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        19.17         0.26        15.85 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
        7.53        15.81        16.44        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       12.56        13.87         6.08        13.41        13.51        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        12.82        19.36         0.46 
TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-8529 
       20.42        11.57         5.13         2.83        13.18         0.13 
TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MI 
        0.10         0.10         3.42         9.34         6.58         0.10 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 
       12.62         3.02        15.95         1.02        14.01        29.98 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5720 
       21.99         0.00         7.07        12.00        36.00         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-CG-5734 TCGA-D7-5577 TCGA-D7-5579 
        4.01        69.04        21.07         7.99        12.36        11.93 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6818 
       20.55        18.84        18.54        18.61        17.85        10.55 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       24.72        16.80        17.19        14.66        21.14        20.91 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EZ 
        5.92        15.16        13.78        14.76        13.71         9.76 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-6875 
       15.65         8.38         4.34         7.13        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 
       21.27         3.48        22.29        59.54         5.03         0.56 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 
       18.08        26.47        14.27        14.17        11.41        10.62 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        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 
       10.19        19.36         8.88         8.81        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V 
       18.81         3.39        18.38        12.59         6.51         7.82 
TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
       13.51         5.56        20.15        37.64         3.72        19.73 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8N0 TCGA-RD-A8N1 
       61.25         4.60         8.61         5.13        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-A8DU TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
        5.46        34.45        27.88        32.48        28.96        34.29 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
       16.31         2.50         2.70        17.85         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A91D TCGA-VQ-A91E 
       23.41        15.65        26.24        14.33        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A922 TCGA-VQ-A923 
       61.22        20.81        36.16         7.36         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T 
       55.43         6.58         5.72        64.18         2.66        11.24 
TCGA-VQ-AA69 TCGA-ZA-A8F6 
       28.41        10.62 

  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                         0.07                          0.00 
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                       122.30                        116.38 
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                       12.725                        12.920 
[1] "0.1 - 122.3 (12.7)" "0.0 - 116.4 (12.9)"
[1] "hr=" "1.1"
D49V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 13(4Q34.3) MUTATED         0        4       15       20        19
  DEL PEAK 13(4Q34.3) WILD-TYPE       3       10       26       11        19
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 13(4Q34.3) MUTATED          22         2         42         29
  DEL PEAK 13(4Q34.3) WILD-TYPE        33         2         43         33
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 13(4Q34.3) MUTATED           24       14
  DEL PEAK 13(4Q34.3) WILD-TYPE         17       32
D49V3, multiclass
            clus
vv           DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  STAGE I                              0                             3
  STAGE IA                             4                            10
  STAGE IB                            15                            26
  STAGE II                            20                            11
  STAGE IIA                           19                            19
  STAGE IIB                           22                            33
  STAGE III                            2                             2
  STAGE IIIA                          42                            43
  STAGE IIIB                          29                            33
  STAGE IIIC                          24                            17
  STAGE IV                            14                            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 13(4Q34.3) MUTATED     8  35  93  56
  DEL PEAK 13(4Q34.3) WILD-TYPE  14  55 102  63
D49V4, multiclass
    clus
vv   DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  T1                           8                            14
  T2                          35                            55
  T3                          93                           102
  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
  DEL PEAK 13(4Q34.3) MUTATED   55 52 38 45
  DEL PEAK 13(4Q34.3) WILD-TYPE 74 66 46 44
D49V5, multiclass
    clus
vv   DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  N0                          55                            74
  N1                          52                            66
  N2                          38                            46
  N3                          45                            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"
D49V6, binary
                               cls
clus                              0   1
  DEL PEAK 13(4Q34.3) MUTATED   179   9
  DEL PEAK 13(4Q34.3) WILD-TYPE 208  21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q34.3) MUTATED    179    9
  DEL PEAK 13(4Q34.3) WILD-TYPE  208   21
   clus
vv  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  0                         179                           208
  1                           9                            21
[1] 2 2
[1] FALSE
D49V7, binary
                               cls
clus                              0   1
  DEL PEAK 13(4Q34.3) MUTATED    74 123
  DEL PEAK 13(4Q34.3) WILD-TYPE  84 155
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q34.3) MUTATED     74  123
  DEL PEAK 13(4Q34.3) WILD-TYPE   84  155
        clus
vv       DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  FEMALE                          74                            84
  MALE                           123                           155
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 13(4Q34.3) MUTATED                                      21
  DEL PEAK 13(4Q34.3) WILD-TYPE                                    50
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 13(4Q34.3) MUTATED                                                       66
  DEL PEAK 13(4Q34.3) WILD-TYPE                                                     96
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 13(4Q34.3) MUTATED                                                                  48
  DEL PEAK 13(4Q34.3) WILD-TYPE                                                                33
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 13(4Q34.3) MUTATED                                                 42
  DEL PEAK 13(4Q34.3) WILD-TYPE                                               36
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 13(4Q34.3) MUTATED                                                          8
  DEL PEAK 13(4Q34.3) WILD-TYPE                                                       13
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 13(4Q34.3) MUTATED                                                           4
  DEL PEAK 13(4Q34.3) WILD-TYPE                                                         4
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 13(4Q34.3) MUTATED                                          7
  DEL PEAK 13(4Q34.3) WILD-TYPE                                        6
D49V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 13(4Q34.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      21
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     66
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          48
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           42
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    7
                                                                   clus
vv                                                                  DEL PEAK 13(4Q34.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       96
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            33
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      6
[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"
D49V9, binary
                               cls
clus                              0   1
  DEL PEAK 13(4Q34.3) MUTATED     4 193
  DEL PEAK 13(4Q34.3) WILD-TYPE   2 237
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q34.3) MUTATED      4  193
  DEL PEAK 13(4Q34.3) WILD-TYPE    2  237
     clus
vv    DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  NO                            4                             2
  YES                         193                           237
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 13(4Q34.3) MUTATED   160   8   6   6
  DEL PEAK 13(4Q34.3) WILD-TYPE 187  10  13  19
D49V10, multiclass
    clus
vv   DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  R0                         160                           187
  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(4Q34.3) MUTATED      42                         7
  DEL PEAK 13(4Q34.3) WILD-TYPE    46                         4
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 13(4Q34.3) MUTATED                                           0   122
  DEL PEAK 13(4Q34.3) WILD-TYPE                                         1   152
D49V12, multiclass
                                           clus
vv                                          DEL PEAK 13(4Q34.3) MUTATED
  ASIAN                                                              42
  BLACK OR AFRICAN AMERICAN                                           7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             122
                                           clus
vv                                          DEL PEAK 13(4Q34.3) WILD-TYPE
  ASIAN                                                                46
  BLACK OR AFRICAN AMERICAN                                             4
  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(4Q34.3) MUTATED     1 138
  DEL PEAK 13(4Q34.3) WILD-TYPE   3 175
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q34.3) MUTATED      1  138
  DEL PEAK 13(4Q34.3) WILD-TYPE    3  175
                        clus
vv                       DEL PEAK 13(4Q34.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         138
                        clus
vv                       DEL PEAK 13(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           175
[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    98  59
  DEL PEAK 14(5Q12.1) WILD-TYPE 156  91
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                          157                           247 
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                           59                            91 
$`DEL PEAK 14(5Q12.1) MUTATED`
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-6458 TCGA-BR-6565 
       19.56        11.01         9.44         6.61        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        15.42        28.01         3.45        12.76 
TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 
       18.71        11.44         0.69        12.95         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        11.54 
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        22.26 
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        13.64        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.18         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.13         3.42         9.34        11.31 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 
       11.61        12.20        27.02         7.99         4.01        14.01 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 
       47.05        19.07        12.03        18.97        22.98        30.97 
TCGA-CG-5718 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6525 
       36.00        15.02        69.04        11.93        18.84        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-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 
       12.33        24.72        11.24        11.31         2.96        15.65 
TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-8099 
        7.40         0.62         7.99        72.23        19.53        17.06 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56         5.52         1.51         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       14.17         0.76         5.59         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 
       11.77         6.25         2.10        12.95        23.84         9.67 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL 
       27.42        21.21        18.81         3.39        18.38         5.19 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V 
       13.08         6.44         6.74         6.51         5.56         7.82 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
        2.53        60.56        37.64         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DU 
        8.52        37.91       115.69         8.94         5.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PC 
       13.25        13.02        35.24        34.45         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-A8PU TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91Y 
       27.35        14.33        36.69        18.74         1.71         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94R 
       52.24         9.04         4.54         5.72        21.04        42.54 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6J 
       18.41        40.08        32.94        17.13        54.12        21.11 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK 14(5Q12.1) WILD-TYPE`
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-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         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-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 
       23.93        18.15        15.32        28.73        12.43         9.07 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        0.56        16.31        15.58         7.40         6.18        19.50 
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-8381 TCGA-BR-8382 
        4.31         3.32        11.80        19.17         0.26        15.85 
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        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        15.81        16.44 
TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       15.68        12.56         6.08        13.41        13.51        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        12.82         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       13.51         0.46        20.65        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5803 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        3.25         0.07         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
        0.10        12.43         6.58         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4443 
        3.02        15.95         1.02         8.05        54.08        29.98 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 
       21.99         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-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07        65.10         4.01        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 
       12.36        12.66        19.13        20.55        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6818 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       17.85        10.55        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-A6EY TCGA-D7-A6EZ 
       15.16        13.78        14.76        13.71        11.44         9.76 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 
        8.38         4.34         7.13        16.24        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-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 
        0.23        18.08        26.47        14.27        11.41        12.10 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ 
       10.62        24.30        12.30        11.84        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        10.19         0.26 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-A6RJ 
       19.36        12.30         8.88         8.81         3.45         5.36 
TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NU TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A93G 
        1.41        12.59         1.81        13.51         5.56        20.15 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
        3.72        19.73        61.25         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-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-A8DT TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        0.92        48.79        18.48        21.73        27.88        32.48 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PP 
       28.96        34.29        16.31         2.50         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E 
       15.65        26.24        64.57        65.16        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       61.22        20.81        22.68        36.16         7.36         9.50 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T 
        2.01        55.43         6.58        64.18         2.66        11.24 
TCGA-VQ-A94U TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K 
       22.09        28.41        29.98        26.04        16.14        12.43 
TCGA-ZA-A8F6 
       10.62 

  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                         0.07                          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 
                        12.33                         13.45 
[1] "0.1 - 115.7 (12.3)" "0.0 - 122.3 (13.4)"
[1] "hr=" "1.1"
D50V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 14(5Q12.1) MUTATED         1        5       13       11        11
  DEL PEAK 14(5Q12.1) WILD-TYPE       2        9       28       20        27
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 14(5Q12.1) MUTATED          26         0         42         22
  DEL PEAK 14(5Q12.1) WILD-TYPE        29         4         43         40
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 14(5Q12.1) MUTATED           14       17
  DEL PEAK 14(5Q12.1) WILD-TYPE         27       29
D50V3, multiclass
            clus
vv           DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  STAGE I                              1                             2
  STAGE IA                             5                             9
  STAGE IB                            13                            28
  STAGE II                            11                            20
  STAGE IIA                           11                            27
  STAGE IIB                           26                            29
  STAGE III                            0                             4
  STAGE IIIA                          42                            43
  STAGE IIIB                          22                            40
  STAGE IIIC                          14                            27
  STAGE IV                            17                            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 14(5Q12.1) MUTATED     9  35  79  40
  DEL PEAK 14(5Q12.1) WILD-TYPE  13  55 116  79
D50V4, multiclass
    clus
vv   DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  T1                           9                            13
  T2                          35                            55
  T3                          79                           116
  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   40 48 39 34
  DEL PEAK 14(5Q12.1) WILD-TYPE 89 70 45 55
D50V5, multiclass
    clus
vv   DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  N0                          40                            89
  N1                          48                            70
  N2                          39                            45
  N3                          34                            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   150  10
  DEL PEAK 14(5Q12.1) WILD-TYPE 237  20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q12.1) MUTATED    150   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                         150                           237
  1                          10                            20
[1] 2 2
[1] FALSE
D50V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q12.1) MUTATED    59 107
  DEL PEAK 14(5Q12.1) WILD-TYPE  99 171
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q12.1) MUTATED     59  107
  DEL PEAK 14(5Q12.1) WILD-TYPE   99  171
        clus
vv       DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  FEMALE                          59                            99
  MALE                           107                           171
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 14(5Q12.1) MUTATED                                      11
  DEL PEAK 14(5Q12.1) WILD-TYPE                                    60
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 14(5Q12.1) MUTATED                                                       59
  DEL PEAK 14(5Q12.1) WILD-TYPE                                                    103
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 14(5Q12.1) MUTATED                                                                  33
  DEL PEAK 14(5Q12.1) WILD-TYPE                                                                48
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 14(5Q12.1) MUTATED                                                 44
  DEL PEAK 14(5Q12.1) WILD-TYPE                                               34
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 14(5Q12.1) MUTATED                                                         10
  DEL PEAK 14(5Q12.1) WILD-TYPE                                                       11
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 14(5Q12.1) MUTATED                                                           4
  DEL PEAK 14(5Q12.1) WILD-TYPE                                                         4
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 14(5Q12.1) MUTATED                                          4
  DEL PEAK 14(5Q12.1) WILD-TYPE                                        9
D50V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 14(5Q12.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      11
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     59
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          33
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           44
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    4
                                                                   clus
vv                                                                  DEL PEAK 14(5Q12.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        60
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      103
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            48
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      9
[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"
D50V9, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q12.1) MUTATED     3 163
  DEL PEAK 14(5Q12.1) WILD-TYPE   3 267
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q12.1) MUTATED      3  163
  DEL PEAK 14(5Q12.1) WILD-TYPE    3  267
     clus
vv    DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  NO                            3                             3
  YES                         163                           267
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 14(5Q12.1) MUTATED   134   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                         134                           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                         6
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 14(5Q12.1) MUTATED                                           0   103
  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                                                             103
                                           clus
vv                                          DEL PEAK 14(5Q12.1) WILD-TYPE
  ASIAN                                                                50
  BLACK OR AFRICAN AMERICAN                                             6
  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     1 117
  DEL PEAK 14(5Q12.1) WILD-TYPE   3 196
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q12.1) MUTATED      1  117
  DEL PEAK 14(5Q12.1) WILD-TYPE    3  196
                        clus
vv                       DEL PEAK 14(5Q12.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         117
                        clus
vv                       DEL PEAK 14(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           196
[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  56
  DEL PEAK 15(5Q23.2) WILD-TYPE 159  94
  DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE 
                          151                           253 
  DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE 
                           56                            94 
$`DEL PEAK 15(5Q23.2) MUTATED`
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4267 TCGA-BR-6458 
       19.56        11.01         9.44         6.61         6.18        19.33 
TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7901 
        9.17         9.21        35.24        15.42        28.01         3.45 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 
       12.76        18.71        11.44        12.95         2.66         2.20 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 
        4.31        14.04        14.79         5.39         9.21        20.22 
TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ 
       11.54         9.86         8.22        10.68         7.53        22.26 
TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-5800 
        1.48         0.72        20.65        20.42        13.64        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 
       13.18         0.30         0.07         0.07         0.07         0.10 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A4MH TCGA-CG-4304 TCGA-CG-4436 
        0.13         0.13        11.31        12.20        27.02         7.99 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        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        11.93        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         2.96        15.65 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-8211 TCGA-FP-8631 
        7.99        16.24        72.23        19.53        13.58         0.56 
TCGA-FP-A4BF TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8610 TCGA-HU-A4GC 
        5.52         1.51         5.92        12.59         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         6.25         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
       12.95        23.84         9.67        27.42        21.21        18.81 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38         5.19        13.08         1.41         6.44         6.74 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H 
        6.51         5.56         7.82         2.53        60.56        37.64 
TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-RD-A7BT 
        9.86        45.67        18.21         8.52         6.08         8.61 
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-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PC 
       13.25        13.02        35.24        34.45         7.73        46.26 
TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A8PU 
       22.19        12.79         2.70        17.85        13.35        27.35 
TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91Y 
       36.69        18.74        20.81         1.71        36.16         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R 
       52.24         9.04         2.01         4.54        21.04        42.54 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6F 
       22.09        18.41        40.08        32.94        17.13        54.12 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK 15(5Q23.2) WILD-TYPE`
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-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         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        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        32.94        12.82        24.76        23.93 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-8058 
       18.15        15.32        28.73        12.43         9.07        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        0.56        16.31        15.58         7.40         6.18        19.50 
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-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        19.17         0.26        15.85         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        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 
        6.28         7.53         0.49        15.81        16.44        15.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       12.56        13.87         6.08        13.41        13.51        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        12.82         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       13.51         0.46         1.15        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5803 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        3.25         0.07         0.07         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         0.10         3.42         9.34        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 
        6.58         0.10        12.62        20.02         3.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
        1.02         8.05        12.03        21.99         0.00         9.01 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 
        7.07        12.00        22.98         6.97         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
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        12.36 
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        10.55        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 
       15.16        13.78        14.76        13.71        11.44         9.76 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 
        8.38         4.34         7.40         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-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 
       59.54         5.03         0.23        18.08        26.47        14.27 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.17        11.41        12.10        10.62        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
       12.30        11.84        24.20        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        10.19         0.26        19.36        12.30         8.88 
TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RS TCGA-IN-A7NU 
        8.81         3.45         3.39         5.36        12.59         1.81 
TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZI 
       13.51         5.56        20.15         3.72        19.73        61.25 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        4.60         9.24        11.05         5.13        16.67       122.30 
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-A8DT TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       19.04        48.79        18.48        21.73        27.88        32.48 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO 
       28.96        34.29        16.31         2.50         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        26.24        64.57        14.33        65.16 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91X 
       11.70        11.93        61.22        22.68         7.36         9.50 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T 
       55.43         6.58         5.72        64.18         2.66        11.24 
TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       28.41        29.98        26.04        16.14        21.11        12.43 
TCGA-ZA-A8F6 
       10.62 

  DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE 
                         0.07                          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 
                        12.79                         12.89 
[1] "0.1 - 115.7 (12.8)" "0.0 - 122.3 (12.9)"
[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       14       10        12
  DEL PEAK 15(5Q23.2) WILD-TYPE       2        7       27       21        26
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 15(5Q23.2) MUTATED          22         1         42         17
  DEL PEAK 15(5Q23.2) WILD-TYPE        33         3         43         45
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 15(5Q23.2) MUTATED           14       14
  DEL PEAK 15(5Q23.2) WILD-TYPE         27       32
D51V3, multiclass
            clus
vv           DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE
  STAGE I                              1                             2
  STAGE IA                             7                             7
  STAGE IB                            14                            27
  STAGE II                            10                            21
  STAGE IIA                           12                            26
  STAGE IIB                           22                            33
  STAGE III                            1                             3
  STAGE IIIA                          42                            43
  STAGE IIIB                          17                            45
  STAGE IIIC                          14                            27
  STAGE IV                            14                            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 15(5Q23.2) MUTATED    10  30  76  38
  DEL PEAK 15(5Q23.2) WILD-TYPE  12  60 119  81
D51V4, multiclass
    clus
vv   DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE
  T1                          10                            12
  T2                          30                            60
  T3                          76                           119
  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   45 44 33 30
  DEL PEAK 15(5Q23.2) WILD-TYPE 84 74 51 59
D51V5, multiclass
    clus
vv   DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE
  N0                          45                            84
  N1                          44                            74
  N2                          33                            51
  N3                          30                            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   142   8
  DEL PEAK 15(5Q23.2) WILD-TYPE 245  22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q23.2) MUTATED    142    8
  DEL PEAK 15(5Q23.2) WILD-TYPE  245   22
   clus
vv  DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE
  0                         142                           245
  1                           8                            22
[1] 2 2
[1] FALSE
D51V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q23.2) MUTATED    54 102
  DEL PEAK 15(5Q23.2) WILD-TYPE 104 176
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q23.2) MUTATED     54  102
  DEL PEAK 15(5Q23.2) WILD-TYPE  104  176
        clus
vv       DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE
  FEMALE                          54                           104
  MALE                           102                           176
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 15(5Q23.2) MUTATED                                       9
  DEL PEAK 15(5Q23.2) WILD-TYPE                                    62
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 15(5Q23.2) MUTATED                                                       56
  DEL PEAK 15(5Q23.2) WILD-TYPE                                                    106
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 15(5Q23.2) MUTATED                                                                  32
  DEL PEAK 15(5Q23.2) WILD-TYPE                                                                49
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 15(5Q23.2) MUTATED                                                 45
  DEL PEAK 15(5Q23.2) WILD-TYPE                                               33
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 15(5Q23.2) MUTATED                                                          7
  DEL PEAK 15(5Q23.2) WILD-TYPE                                                       14
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 15(5Q23.2) MUTATED                                                           3
  DEL PEAK 15(5Q23.2) WILD-TYPE                                                         5
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 15(5Q23.2) MUTATED                                          4
  DEL PEAK 15(5Q23.2) WILD-TYPE                                        9
D51V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 15(5Q23.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     56
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          32
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           45
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    4
                                                                   clus
vv                                                                  DEL PEAK 15(5Q23.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      106
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            49
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             33
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      9
[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"
D51V9, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q23.2) MUTATED     2 154
  DEL PEAK 15(5Q23.2) WILD-TYPE   4 276
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q23.2) MUTATED      2  154
  DEL PEAK 15(5Q23.2) WILD-TYPE    4  276
     clus
vv    DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE
  NO                            2                             4
  YES                         154                           276
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 15(5Q23.2) MUTATED   128   7   6   4
  DEL PEAK 15(5Q23.2) WILD-TYPE 219  11  13  21
D51V10, multiclass
    clus
vv   DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE
  R0                         128                           219
  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                         6
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 15(5Q23.2) MUTATED                                           1    97
  DEL PEAK 15(5Q23.2) WILD-TYPE                                         0   177
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                                                              97
                                           clus
vv                                          DEL PEAK 15(5Q23.2) WILD-TYPE
  ASIAN                                                                55
  BLACK OR AFRICAN AMERICAN                                             6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               177
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V13, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q23.2) MUTATED     1 108
  DEL PEAK 15(5Q23.2) WILD-TYPE   3 205
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q23.2) MUTATED      1  108
  DEL PEAK 15(5Q23.2) WILD-TYPE    3  205
                        clus
vv                       DEL PEAK 15(5Q23.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         108
                        clus
vv                       DEL PEAK 15(5Q23.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           205
[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  43
  DEL PEAK 16(6P25.3) WILD-TYPE 190 107
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                          107                           297 
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                           43                           107 
$`DEL PEAK 16(6P25.3) MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6709 TCGA-BR-6803 
       26.70         6.97        17.29        19.33        12.16        31.20 
TCGA-BR-7716 TCGA-BR-7901 TCGA-BR-8077 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8485 
       28.01         3.45         0.69         6.18        19.50         9.21 
TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A4CQ TCGA-BR-A4CS 
       20.22        11.54         9.86         8.22        22.26         1.48 
TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5800 
       12.89         0.72        13.51        20.65         1.15        13.15 
TCGA-CD-5802 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A487 
        0.30         0.07         0.07         0.10         0.13         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CG-4437 TCGA-CG-4466 TCGA-CG-5719 TCGA-CG-5724 
       11.31        12.43         8.05        18.97         1.02        12.03 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 
       79.07        65.10        69.04        12.66        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6822 
       18.84        18.54        13.35        15.22        15.98        12.33 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-A4SO TCGA-F1-6875 
       11.31        11.44        15.65         7.40        16.24        72.23 
TCGA-F1-A72C TCGA-FP-8099 TCGA-FP-8211 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 
       11.38        17.06        13.58        18.08        26.47         5.92 
TCGA-HU-8604 TCGA-HU-A4G3 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU 
       12.10         5.59        22.75        11.77         8.98         6.25 
TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO 
       12.95         9.67        27.42         5.36         5.19         1.41 
TCGA-IN-A6RR TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR 
        6.74         1.81         5.56        45.67        18.21         6.08 
TCGA-R5-A805 TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 
        9.24        16.67       122.30       115.69        57.44         8.94 
TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PJ 
        0.92         5.46        32.48         7.73        22.19         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A91N 
       17.85         1.87        13.35        27.35        14.33        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A928 TCGA-VQ-A94R TCGA-VQ-AA68 
       20.81        52.24         9.04         5.72        42.54        40.08 
TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-ZQ-A9CR 
       32.94        54.12        26.04        16.14         0.79 

$`DEL PEAK 16(6P25.3) WILD-TYPE`
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-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        4.64         7.43        18.35        30.90         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        21.11        30.90        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 
       24.76        35.24        23.93        15.42        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73        12.43         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.56        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        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        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         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        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8690 
        7.53         0.49        15.81        16.44        15.68        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
       12.56        13.87         7.53         6.08        13.41        13.51 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98        14.17         0.53        12.82         0.66        19.36 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.42        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8528 
        3.25        13.18         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 
        0.13         0.16         0.10         0.13         0.10         3.42 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 
        3.02        27.02        15.95         1.02         7.99        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
       21.99         0.00         9.01         7.07        12.00        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       30.97         6.97        36.00         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 
      105.07        15.02        28.96         4.01        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 
       12.36        11.93        18.61        17.85        17.19        10.26 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.79        10.55        11.31        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-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       11.24         9.76         2.96         8.38         4.34         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        0.62         7.99        14.47        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BF 
       14.07        22.29        59.54         5.03         0.56         5.52 
TCGA-FP-A8CX TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        0.23         1.51        14.27        12.59        14.17        11.41 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       10.62         0.76        24.30        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT 
        3.25        25.81        21.37        29.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
       10.19         0.26         2.10        19.36        23.84        12.30 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88         8.81        21.21         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       18.38        13.08         6.44        12.59         6.51         5.56 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H 
        7.82        13.51         2.53        60.56        20.15        37.64 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
        3.72        19.73         9.86         8.52        61.25         4.60 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 
       11.05         8.61         5.13        37.91        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT 
       71.38        35.61        16.87        19.04         5.79        48.79 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       13.25        13.02        18.48        35.24        21.73        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
       27.88        28.96        34.29        46.26        16.31         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX 
       12.79         9.27        23.41        15.65        26.24        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S 
       65.16        36.69        11.70        11.93        61.22        22.68 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A923 
        1.71        36.16         7.36         9.50         9.73         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P 
       55.43         4.54         6.58        64.18        21.04         2.66 
TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D 
       11.24        22.09        18.41        28.41        29.98        17.13 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       21.11        12.43        10.62 

  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                         0.07                          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 
                        12.89                         12.82 
[1] "0.1 - 122.3 (12.9)" "0.0 - 116.4 (12.8)"
[1] "hr=" "1"  
D52V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 16(6P25.3) MUTATED         0        4        9        6        11
  DEL PEAK 16(6P25.3) WILD-TYPE       3       10       32       25        27
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 16(6P25.3) MUTATED          14         1         25         16
  DEL PEAK 16(6P25.3) WILD-TYPE        41         3         60         46
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 16(6P25.3) MUTATED           10       12
  DEL PEAK 16(6P25.3) WILD-TYPE         31       34
D52V3, multiclass
            clus
vv           DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  STAGE I                              0                             3
  STAGE IA                             4                            10
  STAGE IB                             9                            32
  STAGE II                             6                            25
  STAGE IIA                           11                            27
  STAGE IIB                           14                            41
  STAGE III                            1                             3
  STAGE IIIA                          25                            60
  STAGE IIIB                          16                            46
  STAGE IIIC                          10                            31
  STAGE IV                            12                            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 16(6P25.3) MUTATED     4  24  57  26
  DEL PEAK 16(6P25.3) WILD-TYPE  18  66 138  93
D52V4, multiclass
    clus
vv   DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  T1                           4                            18
  T2                          24                            66
  T3                          57                           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
  DEL PEAK 16(6P25.3) MUTATED   31 29 24 23
  DEL PEAK 16(6P25.3) WILD-TYPE 98 89 60 66
D52V5, multiclass
    clus
vv   DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  N0                          31                            98
  N1                          29                            89
  N2                          24                            60
  N3                          23                            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"
D52V6, binary
                               cls
clus                              0   1
  DEL PEAK 16(6P25.3) MUTATED   101   4
  DEL PEAK 16(6P25.3) WILD-TYPE 286  26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6P25.3) MUTATED    101    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                         101                           286
  1                           4                            26
[1] 2 2
[1] FALSE
D52V7, binary
                               cls
clus                              0   1
  DEL PEAK 16(6P25.3) MUTATED    43  70
  DEL PEAK 16(6P25.3) WILD-TYPE 115 208
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6P25.3) MUTATED     43   70
  DEL PEAK 16(6P25.3) WILD-TYPE  115  208
        clus
vv       DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  FEMALE                          43                           115
  MALE                            70                           208
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 16(6P25.3) MUTATED                                      13
  DEL PEAK 16(6P25.3) WILD-TYPE                                    58
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 16(6P25.3) MUTATED                                                       36
  DEL PEAK 16(6P25.3) WILD-TYPE                                                    126
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 16(6P25.3) MUTATED                                                                  22
  DEL PEAK 16(6P25.3) WILD-TYPE                                                                59
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 16(6P25.3) MUTATED                                                 34
  DEL PEAK 16(6P25.3) WILD-TYPE                                               44
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 16(6P25.3) MUTATED                                                          4
  DEL PEAK 16(6P25.3) WILD-TYPE                                                       17
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 16(6P25.3) MUTATED                                                           2
  DEL PEAK 16(6P25.3) WILD-TYPE                                                         6
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 16(6P25.3) MUTATED                                          2
  DEL PEAK 16(6P25.3) WILD-TYPE                                       11
D52V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 16(6P25.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      13
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     36
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          22
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    2
                                                                   clus
vv                                                                  DEL PEAK 16(6P25.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        58
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            59
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             44
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     11
[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"
D52V9, binary
                               cls
clus                              0   1
  DEL PEAK 16(6P25.3) MUTATED     1 112
  DEL PEAK 16(6P25.3) WILD-TYPE   5 318
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6P25.3) MUTATED      1  112
  DEL PEAK 16(6P25.3) WILD-TYPE    5  318
     clus
vv    DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  NO                            1                             5
  YES                         112                           318
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 16(6P25.3) MUTATED    91   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                          91                           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                         9
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 16(6P25.3) MUTATED                                           0    73
  DEL PEAK 16(6P25.3) WILD-TYPE                                         1   201
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                                                              73
                                           clus
vv                                          DEL PEAK 16(6P25.3) WILD-TYPE
  ASIAN                                                                64
  BLACK OR AFRICAN AMERICAN                                             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  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"
D52V13, binary
                               cls
clus                              0   1
  DEL PEAK 16(6P25.3) MUTATED     1  80
  DEL PEAK 16(6P25.3) WILD-TYPE   3 233
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6P25.3) MUTATED      1   80
  DEL PEAK 16(6P25.3) WILD-TYPE    3  233
                        clus
vv                       DEL PEAK 16(6P25.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          80
                        clus
vv                       DEL PEAK 16(6P25.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           233
[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    52  30
  DEL PEAK 17(6Q14.1) WILD-TYPE 202 120
  DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE 
                           82                           322 
  DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE 
                           30                           120 
$`DEL PEAK 17(6Q14.1) MUTATED`
TCGA-B7-A5TI TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-7716 
       19.56        18.35         6.18        17.29         9.17        28.01 
TCGA-BR-7722 TCGA-BR-8080 TCGA-BR-8486 TCGA-BR-A4CQ TCGA-BR-A4J4 TCGA-BR-A4J8 
       15.32         9.60        20.22        22.26         0.53        13.51 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5803 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8535 
       20.65         1.15         0.07         0.16         0.10         0.13 
TCGA-CD-A486 TCGA-CD-A48A TCGA-CG-4301 TCGA-CG-4437 TCGA-CG-4443 TCGA-CG-4444 
        3.42        12.43         3.02         8.05        29.98        47.05 
TCGA-CG-4455 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 TCGA-D7-5578 
       12.03        36.00         1.02        12.03        15.02        12.66 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-8570 TCGA-D7-8576 
       18.84        18.54        13.35        10.26        24.72        14.66 
TCGA-D7-A4YY TCGA-D7-A6EX TCGA-D7-A74A TCGA-EQ-A4SO TCGA-F1-A72C TCGA-FP-8099 
       13.78        11.31         7.40        16.24        11.38        17.06 
TCGA-FP-8211 TCGA-FP-8631 TCGA-HJ-7597 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GP 
       13.58         0.56        26.47        22.75        11.77         8.98 
TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO 
       12.30        27.42        21.21         5.19        13.08         1.41 
TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-R5-A7O7 TCGA-R5-A7ZE 
        6.44        12.59         5.56         1.81        45.67        18.21 
TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N5 TCGA-SW-A7EA TCGA-VQ-A8E0 
        6.08        16.67       122.30        57.44        19.04        18.48 
TCGA-VQ-A8P5 TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91N 
        7.73        13.35        27.35        14.33        36.69        18.74 
TCGA-VQ-A91Q TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-AA68 TCGA-VQ-AA6F 
       20.81         2.01         4.54        21.04        40.08        54.12 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        21.11        10.62         0.79 

$`DEL PEAK 17(6Q14.1) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 
        6.97         4.64         7.43        30.90         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        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 
        9.21        24.76        35.24        23.93        15.42        18.15 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 
       17.49        14.43        11.44         0.69        12.26        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        12.95         2.66        16.31         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        19.50        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        19.17        14.79         0.26        15.85 
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 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS 
       10.68        12.56        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 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI 
       12.82         0.66        19.36         0.46        20.42        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.30         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 
        0.13         0.10         0.13         0.10         9.34        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         0.10        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-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       14.01        19.07        21.99         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5720 
        7.07        12.00        22.98        30.97         6.97         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        6.02         0.99       105.07        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 
        4.01        69.04        21.07         7.99        12.36        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6528 
       19.13        20.55        18.61        17.85        17.19        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 
       15.98        12.79        10.55        11.31        12.33        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-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44         5.92        15.16        14.76        13.71        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44         9.76         2.96        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-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
        3.48        19.53        14.07        22.29        59.54         5.03 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        5.52         0.23        18.08         1.51         5.92        14.27 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        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         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        9.67         8.88         8.81         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         5.36         6.74         6.51         7.82        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG 
        2.53         5.56        60.56        20.15        37.64         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 
       19.73         9.86         8.52        61.25         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-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB 
      116.38        71.38         8.94        35.61        16.87         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        34.45        27.88        32.48        28.96        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-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       17.85         1.87         9.27        23.41        15.65        26.24 
TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S 
       64.57        65.16        11.70        11.93        61.22        22.68 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
        1.71        36.16         7.36         9.50         9.73        52.24 
TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P 
        9.04        55.43         6.58         5.72        64.18         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       42.54        11.24        22.09        18.41        28.41        32.94 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6K 
       29.98        17.13        26.04        12.43 

  DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE 
                         0.07                          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 
                       13.545                        12.775 
[1] "0.1 - 122.3 (13.5)" "0.0 - 116.4 (12.8)"
[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        7         6
  DEL PEAK 17(6Q14.1) WILD-TYPE       3        9       33       24        32
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 17(6Q14.1) MUTATED           9         1         21         12
  DEL PEAK 17(6Q14.1) WILD-TYPE        46         3         64         50
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 17(6Q14.1) MUTATED            9        6
  DEL PEAK 17(6Q14.1) WILD-TYPE         32       40
D53V3, multiclass
            clus
vv           DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE
  STAGE I                              0                             3
  STAGE IA                             5                             9
  STAGE IB                             8                            33
  STAGE II                             7                            24
  STAGE IIA                            6                            32
  STAGE IIB                            9                            46
  STAGE III                            1                             3
  STAGE IIIA                          21                            64
  STAGE IIIB                          12                            50
  STAGE IIIC                           9                            32
  STAGE IV                             6                            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 17(6Q14.1) MUTATED     7  19  43  17
  DEL PEAK 17(6Q14.1) WILD-TYPE  15  71 152 102
D53V4, multiclass
    clus
vv   DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE
  T1                           7                            15
  T2                          19                            71
  T3                          43                           152
  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  26  17  18
  DEL PEAK 17(6Q14.1) WILD-TYPE 105  92  67  71
D53V5, multiclass
    clus
vv   DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE
  N0                          24                           105
  N1                          26                            92
  N2                          17                            67
  N3                          18                            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    75   4
  DEL PEAK 17(6Q14.1) WILD-TYPE 312  26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(6Q14.1) MUTATED     75    4
  DEL PEAK 17(6Q14.1) WILD-TYPE  312   26
   clus
vv  DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE
  0                          75                           312
  1                           4                            26
[1] 2 2
[1] FALSE
D53V7, binary
                               cls
clus                              0   1
  DEL PEAK 17(6Q14.1) MUTATED    26  62
  DEL PEAK 17(6Q14.1) WILD-TYPE 132 216
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(6Q14.1) MUTATED     26   62
  DEL PEAK 17(6Q14.1) WILD-TYPE  132  216
        clus
vv       DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE
  FEMALE                          26                           132
  MALE                            62                           216
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 17(6Q14.1) MUTATED                                      11
  DEL PEAK 17(6Q14.1) WILD-TYPE                                    60
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 17(6Q14.1) MUTATED                                                       35
  DEL PEAK 17(6Q14.1) WILD-TYPE                                                    127
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 17(6Q14.1) MUTATED                                                                  15
  DEL PEAK 17(6Q14.1) WILD-TYPE                                                                66
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 17(6Q14.1) MUTATED                                                 20
  DEL PEAK 17(6Q14.1) WILD-TYPE                                               58
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 17(6Q14.1) MUTATED                                                          4
  DEL PEAK 17(6Q14.1) WILD-TYPE                                                       17
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 17(6Q14.1) MUTATED                                                           2
  DEL PEAK 17(6Q14.1) WILD-TYPE                                                         6
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 17(6Q14.1) MUTATED                                          1
  DEL PEAK 17(6Q14.1) WILD-TYPE                                       12
D53V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 17(6Q14.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      11
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     35
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          15
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    1
                                                                   clus
vv                                                                  DEL PEAK 17(6Q14.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        60
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            66
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             58
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     12
[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"
D53V9, binary
                               cls
clus                              0   1
  DEL PEAK 17(6Q14.1) MUTATED     1  87
  DEL PEAK 17(6Q14.1) WILD-TYPE   5 343
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(6Q14.1) MUTATED      1   87
  DEL PEAK 17(6Q14.1) WILD-TYPE    5  343
     clus
vv    DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE
  NO                            1                             5
  YES                          87                           343
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 17(6Q14.1) MUTATED    72   1   3   5
  DEL PEAK 17(6Q14.1) WILD-TYPE 275  17  16  20
D53V10, multiclass
    clus
vv   DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE
  R0                          72                           275
  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                         7
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 17(6Q14.1) MUTATED                                           0    56
  DEL PEAK 17(6Q14.1) WILD-TYPE                                         1   218
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                                                              56
                                           clus
vv                                          DEL PEAK 17(6Q14.1) WILD-TYPE
  ASIAN                                                                73
  BLACK OR AFRICAN AMERICAN                                             7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V13, binary
                               cls
clus                              0   1
  DEL PEAK 17(6Q14.1) MUTATED     1  61
  DEL PEAK 17(6Q14.1) WILD-TYPE   3 252
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(6Q14.1) MUTATED      1   61
  DEL PEAK 17(6Q14.1) WILD-TYPE    3  252
                        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                                 3
  NOT HISPANIC OR LATINO                           252
[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    41  30
  DEL PEAK 18(6Q24.3) WILD-TYPE 213 120
  DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE 
                           71                           333 
  DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE 
                           30                           120 
$`DEL PEAK 18(6Q24.3) MUTATED`
TCGA-B7-A5TI TCGA-BR-4267 TCGA-BR-6565 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-8077 
       19.56         6.18         9.17        28.01        15.32         0.69 
TCGA-BR-8080 TCGA-BR-8360 TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QI 
        9.60         6.18         0.72        13.51         1.15        13.64 
TCGA-CD-5803 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 
        0.07         0.16         0.10         0.13         0.13         3.42 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4472 TCGA-CG-4475 
        4.01        14.01        29.98        12.03        12.00        22.98 
TCGA-CG-5725 TCGA-D7-5578 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6817 TCGA-D7-8570 
       15.02        12.66        18.54        13.35        12.79        24.72 
TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A 
       19.50        18.21        14.66        11.31        15.65         7.40 
TCGA-F1-A72C TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 TCGA-HJ-7597 TCGA-HU-A4GU 
       11.38        17.06        13.58         0.56        26.47         6.25 
TCGA-HU-A4H4 TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NT TCGA-KB-A93H TCGA-MX-A663 
       23.84         5.19         6.44         5.56        37.64         9.86 
TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N5 
       18.21         6.08         8.61        16.67       122.30        57.44 
TCGA-RD-A8N6 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PC TCGA-VQ-A8PS TCGA-VQ-A8PY 
        8.94        35.24        21.73        46.26        13.35        14.33 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A94O 
       18.74        20.81        22.68         2.01         4.54        21.04 
TCGA-VQ-AA68 TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       40.08        54.12        16.14        21.11         0.79 

$`DEL PEAK 18(6Q24.3) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4279 
        6.97         4.64         7.43        18.35        30.90         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-6566 TCGA-BR-6705 TCGA-BR-6706 
       19.33        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        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       32.94        12.82         9.21        24.76        35.24        23.93 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       15.42        18.15        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 
       12.76        18.71        17.49        14.43        11.44        12.26 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       20.55         8.05         0.56        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
        2.20        15.58         7.40        19.50        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        19.17        14.79         0.26        15.85 
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        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        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        12.82         0.66        19.36         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.65        20.42        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.15        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A487 
        0.07         0.10         0.13         0.10         0.10         9.34 
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         0.10 
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-4444 TCGA-CG-4449 TCGA-CG-4460 
        7.99         8.05        54.08        47.05        19.07        21.99 
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-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        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        12.36        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.84        18.61        17.85        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8574 
       15.98        10.55        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        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        13.71        11.24        11.44         9.76 
TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        2.96         8.38         4.34         7.13         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF TCGA-FP-A8CX 
       14.07        22.29        59.54         5.03         5.52         0.23 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
       18.08         1.51         5.92        14.27        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        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 
       10.19         0.26         2.10        12.95        19.36        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
        9.67         8.88         8.81        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO 
       18.81         3.39        18.38         5.36        13.08         1.41 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
        6.74        12.59         6.51         1.81         7.82        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        60.56        20.15         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        61.25         4.60         9.24        11.05 
TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
        5.13        37.91        40.64       115.69       116.38        71.38 
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-A8E0 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        18.48        34.45        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE 
       32.48         7.73        28.96        34.29        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-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ 
       23.41        15.65        26.24        27.35        64.57        65.16 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91V 
       36.69        11.70        11.93        61.22         1.71        36.16 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 
        7.36         9.50         9.73        52.24         9.04        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
        6.58         5.72        64.18         2.66        42.54        11.24 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       22.09        18.41        28.41        32.94        29.98        17.13 
TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        12.43        10.62 

  DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE 
                         0.07                          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 
                        13.51                         12.79 
[1] "0.1 - 122.3 (13.5)" "0.0 - 116.4 (12.8)"
[1] "hr=" "1.2"
D54V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 18(6Q24.3) MUTATED         0        1        5        5         8
  DEL PEAK 18(6Q24.3) WILD-TYPE       3       13       36       26        30
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 18(6Q24.3) MUTATED           9         1         22         11
  DEL PEAK 18(6Q24.3) WILD-TYPE        46         3         63         51
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 18(6Q24.3) MUTATED            7        5
  DEL PEAK 18(6Q24.3) WILD-TYPE         34       41
D54V3, multiclass
            clus
vv           DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE
  STAGE I                              0                             3
  STAGE IA                             1                            13
  STAGE IB                             5                            36
  STAGE II                             5                            26
  STAGE IIA                            8                            30
  STAGE IIB                            9                            46
  STAGE III                            1                             3
  STAGE IIIA                          22                            63
  STAGE IIIB                          11                            51
  STAGE IIIC                           7                            34
  STAGE IV                             5                            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 18(6Q24.3) MUTATED     2  14  45  14
  DEL PEAK 18(6Q24.3) WILD-TYPE  20  76 150 105
D54V4, multiclass
    clus
vv   DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE
  T1                           2                            20
  T2                          14                            76
  T3                          45                           150
  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  22  17  16
  DEL PEAK 18(6Q24.3) WILD-TYPE 110  96  67  73
D54V5, multiclass
    clus
vv   DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE
  N0                          19                           110
  N1                          22                            96
  N2                          17                            67
  N3                          16                            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"
D54V6, binary
                               cls
clus                              0   1
  DEL PEAK 18(6Q24.3) MUTATED    71   1
  DEL PEAK 18(6Q24.3) WILD-TYPE 316  29
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(6Q24.3) MUTATED     71    1
  DEL PEAK 18(6Q24.3) WILD-TYPE  316   29
   clus
vv  DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE
  0                          71                           316
  1                           1                            29
[1] 2 2
[1] FALSE
D54V7, binary
                               cls
clus                              0   1
  DEL PEAK 18(6Q24.3) MUTATED    21  56
  DEL PEAK 18(6Q24.3) WILD-TYPE 137 222
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(6Q24.3) MUTATED     21   56
  DEL PEAK 18(6Q24.3) WILD-TYPE  137  222
        clus
vv       DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE
  FEMALE                          21                           137
  MALE                            56                           222
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 18(6Q24.3) MUTATED                                       7
  DEL PEAK 18(6Q24.3) WILD-TYPE                                    64
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 18(6Q24.3) MUTATED                                                       25
  DEL PEAK 18(6Q24.3) WILD-TYPE                                                    137
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 18(6Q24.3) MUTATED                                                                  16
  DEL PEAK 18(6Q24.3) WILD-TYPE                                                                65
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 18(6Q24.3) MUTATED                                                 22
  DEL PEAK 18(6Q24.3) WILD-TYPE                                               56
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 18(6Q24.3) MUTATED                                                          3
  DEL PEAK 18(6Q24.3) WILD-TYPE                                                       18
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 18(6Q24.3) MUTATED                                                           0
  DEL PEAK 18(6Q24.3) WILD-TYPE                                                         8
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 18(6Q24.3) MUTATED                                          2
  DEL PEAK 18(6Q24.3) WILD-TYPE                                       11
D54V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 18(6Q24.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     25
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          16
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           22
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    2
                                                                   clus
vv                                                                  DEL PEAK 18(6Q24.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        64
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      137
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            65
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             56
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     11
[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"
D54V9, binary
                               cls
clus                              0   1
  DEL PEAK 18(6Q24.3) MUTATED     2  75
  DEL PEAK 18(6Q24.3) WILD-TYPE   4 355
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(6Q24.3) MUTATED      2   75
  DEL PEAK 18(6Q24.3) WILD-TYPE    4  355
     clus
vv    DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE
  NO                            2                             4
  YES                          75                           355
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 18(6Q24.3) MUTATED    63   2   3   4
  DEL PEAK 18(6Q24.3) WILD-TYPE 284  16  16  21
D54V10, multiclass
    clus
vv   DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE
  R0                          63                           284
  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                         7
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 18(6Q24.3) MUTATED                                           1    48
  DEL PEAK 18(6Q24.3) WILD-TYPE                                         0   226
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                                                              48
                                           clus
vv                                          DEL PEAK 18(6Q24.3) WILD-TYPE
  ASIAN                                                                75
  BLACK OR AFRICAN AMERICAN                                             7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  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"
D54V13, binary
                               cls
clus                              0   1
  DEL PEAK 18(6Q24.3) MUTATED     0  52
  DEL PEAK 18(6Q24.3) WILD-TYPE   4 261
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(6Q24.3) MUTATED      0   52
  DEL PEAK 18(6Q24.3) WILD-TYPE    4  261
                        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                                 4
  NOT HISPANIC OR LATINO                           261
[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    55  40
  DEL PEAK 19(6Q26) WILD-TYPE 199 110
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                         95                         309 
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                         40                         110 
$`DEL PEAK 19(6Q26) MUTATED`
TCGA-B7-A5TI TCGA-BR-4183 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7716 
       19.56         6.61        19.33         9.17        12.16        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7958 TCGA-BR-8077 TCGA-BR-8080 
       18.15        15.32        28.73        12.76         0.69         9.60 
TCGA-BR-8680 TCGA-BR-A4IY TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-CD-5800 
       15.81        12.89        13.51        20.42         1.15        13.15 
TCGA-CD-5803 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
        0.07         0.13         0.16         0.10         0.13         0.13 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4437 TCGA-CG-4440 
        3.42         9.34         3.02        15.95         8.05         4.01 
TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5719 
       29.98        12.03         7.07        12.00         6.97         1.02 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6521 
       12.03        15.02        69.04        12.66        20.55        18.54 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 
       13.35        17.19        24.72        19.50        18.21        14.66 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F2 TCGA-D7-A74A TCGA-F1-A72C TCGA-FP-8099 
       11.31        11.44        15.65         7.40        11.38        17.06 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-A4G3 
       13.58         0.56         5.52         0.23        26.47         5.59 
TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-HU-A4HD TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NT 
        6.25        23.84        27.42         5.19         6.44         5.56 
TCGA-IN-A7NU TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7C1 
        1.81         9.86        45.67        18.21         6.08        16.67 
TCGA-RD-A8MV TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-VQ-A8DL TCGA-VQ-A8DZ TCGA-VQ-A8E2 
      122.30        57.44         8.94         0.92        13.02        35.24 
TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PF TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A91Q 
        7.73        46.26         2.50        13.35        14.33        20.81 
TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA68 
       52.24         2.01         4.54        21.04        42.54        40.08 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       17.13        54.12        16.14        21.11         0.79 

$`DEL PEAK 19(6Q26) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 
       26.70        11.70        11.01         9.47         9.44         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        4.64         7.43        18.35        30.90         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-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10        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        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7851 
        9.21        24.76        35.24        23.93        15.42        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        3.45         9.07        18.71        17.49        14.43        11.44 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       12.26        20.55         8.05         0.56        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
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        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         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        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        11.54        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
        6.08        22.26         1.48        13.41        13.51         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        12.82         0.66        19.36 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.65        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        3.25        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A48A 
        0.07         0.10         0.10         0.10        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4444 
       27.02         1.02         7.99        54.08        14.01        47.05 
TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4475 
       19.07        21.99         0.00         9.01        18.97        22.98 
TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       30.97        36.00         0.99         6.02         0.99       105.07 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07        65.10         4.01        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
       12.36        11.93        19.13        18.84        18.61        17.85 
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        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       12.33        16.80        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        15.16        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       11.24         9.76         2.96         8.38         4.34         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
        3.48        19.53        14.07        22.29        59.54         5.03 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
       18.08         1.51         5.92        14.27        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 
       11.41        12.10        10.62         0.76        24.30        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        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-A4GX 
       21.37        29.98         8.98         0.10         6.51        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        19.36        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88         8.81        21.21         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38         5.36        13.08         1.41         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        6.51         7.82        13.51         2.53         5.56        60.56 
TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI 
       20.15        37.64         3.72        19.73         8.52        61.25 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MW 
        4.60         9.24        11.05         8.61         5.13        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 TCGA-RD-A8NB 
       40.64       115.69       116.38        71.38        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E0 
       19.04         5.79        48.79         5.46        13.25        18.48 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        34.45        27.88        32.48        28.96        34.29 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       16.31        22.19        12.79         2.70        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX 
        9.27        23.41        15.65        26.24        27.35        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       65.16        36.69        11.70        11.93        61.22        18.74 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       22.68         1.71        36.16         7.36         9.50         9.73 
TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P 
        9.04        55.43         6.58         5.72        64.18         2.66 
TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        22.09        18.41        28.41        32.94        29.98 
TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        12.43        10.62 

  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                       0.07                        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 
                      12.89                       12.82 
[1] "0.1 - 122.3 (12.9)" "0.0 - 116.4 (12.8)"
[1] "hr=" "1.3"
D55V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 19(6Q26) MUTATED         0        1        5        9         7
  DEL PEAK 19(6Q26) WILD-TYPE       3       13       36       22        31
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 19(6Q26) MUTATED          11         1         25         16
  DEL PEAK 19(6Q26) WILD-TYPE        44         3         60         46
                             vv
clus                          STAGE IIIC STAGE IV
  DEL PEAK 19(6Q26) MUTATED            9       15
  DEL PEAK 19(6Q26) WILD-TYPE         32       31
D55V3, multiclass
            clus
vv           DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  STAGE I                            0                           3
  STAGE IA                           1                          13
  STAGE IB                           5                          36
  STAGE II                           9                          22
  STAGE IIA                          7                          31
  STAGE IIB                         11                          44
  STAGE III                          1                           3
  STAGE IIIA                        25                          60
  STAGE IIIB                        16                          46
  STAGE IIIC                         9                          32
  STAGE IV                          15                          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 19(6Q26) MUTATED     2  19  57  22
  DEL PEAK 19(6Q26) WILD-TYPE  20  71 138  97
D55V4, multiclass
    clus
vv   DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  T1                         2                          20
  T2                        19                          71
  T3                        57                         138
  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  30  22  24
  DEL PEAK 19(6Q26) WILD-TYPE 106  88  62  65
D55V5, multiclass
    clus
vv   DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  N0                        23                         106
  N1                        30                          88
  N2                        22                          62
  N3                        24                          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"
D55V6, binary
                             cls
clus                            0   1
  DEL PEAK 19(6Q26) MUTATED    87   8
  DEL PEAK 19(6Q26) WILD-TYPE 300  22
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(6Q26) MUTATED     87    8
  DEL PEAK 19(6Q26) WILD-TYPE  300   22
   clus
vv  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  0                        87                         300
  1                         8                          22
[1] 2 2
[1] FALSE
D55V7, binary
                             cls
clus                            0   1
  DEL PEAK 19(6Q26) MUTATED    32  69
  DEL PEAK 19(6Q26) WILD-TYPE 126 209
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(6Q26) MUTATED     32   69
  DEL PEAK 19(6Q26) WILD-TYPE  126  209
        clus
vv       DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  FEMALE                        32                         126
  MALE                          69                         209
[1] 2 2
[1] FALSE
                             vv
clus                          STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 19(6Q26) MUTATED                                      10
  DEL PEAK 19(6Q26) WILD-TYPE                                    61
                             vv
clus                          STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 19(6Q26) MUTATED                                                       33
  DEL PEAK 19(6Q26) WILD-TYPE                                                    129
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 19(6Q26) MUTATED                                                                  18
  DEL PEAK 19(6Q26) WILD-TYPE                                                                63
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 19(6Q26) MUTATED                                                 28
  DEL PEAK 19(6Q26) WILD-TYPE                                               50
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 19(6Q26) MUTATED                                                          5
  DEL PEAK 19(6Q26) WILD-TYPE                                                       16
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 19(6Q26) MUTATED                                                           1
  DEL PEAK 19(6Q26) WILD-TYPE                                                         7
                             vv
clus                          STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 19(6Q26) MUTATED                                          5
  DEL PEAK 19(6Q26) WILD-TYPE                                        8
D55V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 19(6Q26) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                    10
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                   33
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        18
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                         28
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                  5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                 1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                  5
                                                                   clus
vv                                                                  DEL PEAK 19(6Q26) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      61
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          63
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           50
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    8
[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"
D55V9, binary
                             cls
clus                            0   1
  DEL PEAK 19(6Q26) MUTATED     2  99
  DEL PEAK 19(6Q26) WILD-TYPE   4 331
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(6Q26) MUTATED      2   99
  DEL PEAK 19(6Q26) WILD-TYPE    4  331
     clus
vv    DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  NO                          2                           4
  YES                        99                         331
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 19(6Q26) MUTATED    81   6   5   3
  DEL PEAK 19(6Q26) WILD-TYPE 266  12  14  22
D55V10, multiclass
    clus
vv   DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  R0                        81                         266
  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                         7
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 19(6Q26) MUTATED                                           0    60
  DEL PEAK 19(6Q26) WILD-TYPE                                         1   214
D55V12, multiclass
                                           clus
vv                                          DEL PEAK 19(6Q26) MUTATED
  ASIAN                                                            18
  BLACK OR AFRICAN AMERICAN                                         4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         0
  WHITE                                                            60
                                           clus
vv                                          DEL PEAK 19(6Q26) WILD-TYPE
  ASIAN                                                              70
  BLACK OR AFRICAN AMERICAN                                           7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  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"
D55V13, binary
                             cls
clus                            0   1
  DEL PEAK 19(6Q26) MUTATED     1  65
  DEL PEAK 19(6Q26) WILD-TYPE   3 248
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(6Q26) MUTATED      1   65
  DEL PEAK 19(6Q26) WILD-TYPE    3  248
                        clus
vv                       DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             1                           3
  NOT HISPANIC OR LATINO                        65                         248
[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    43  22
  DEL PEAK 20(7Q31.1) WILD-TYPE 211 128
  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                           65                           339 
  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                           22                           128 
$`DEL PEAK 20(7Q31.1) MUTATED`
TCGA-BR-6564 TCGA-BR-6706 TCGA-BR-7723 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8369 
       26.10        18.05        28.73         6.18        19.50        14.04 
TCGA-BR-8678 TCGA-BR-A452 TCGA-BR-A4CS TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-8524 
       11.54         7.53         1.48         1.15        13.64         0.07 
TCGA-CD-8527 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CG-4301 TCGA-CG-4437 
        0.07         3.42         9.34        11.31         3.02         8.05 
TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4472 TCGA-CG-4475 TCGA-D7-6815 
       54.08        19.07        12.03        12.00        22.98        15.98 
TCGA-D7-6820 TCGA-D7-8575 TCGA-D7-A4YX TCGA-D7-A6EX TCGA-F1-6875 TCGA-FP-7829 
       11.31        18.21        15.16        11.31        72.23        19.53 
TCGA-FP-8631 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-HU-A4H4 
        0.56        22.75        11.77         6.25        12.95        23.84 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
        9.67         8.88        27.42        18.81         3.39        18.38 
TCGA-IN-A6RN TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A93H TCGA-RD-A7BT TCGA-RD-A8MW 
       13.08         7.82         2.53        37.64         8.61        37.91 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8P3 
        8.94        35.61         5.46        13.02        18.48        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8PS TCGA-VQ-A91Q TCGA-VQ-A923 TCGA-VQ-A928 TCGA-VQ-A94U 
        7.73        13.35        20.81         2.01         5.72        22.09 
TCGA-VQ-AA68 TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       40.08        17.13        54.12        26.04        16.14 

$`DEL PEAK 20(7Q31.1) WILD-TYPE`
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-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
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        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        32.94        12.82         9.21        24.76        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 
       23.93        15.42        28.01        18.15        15.32        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.56        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        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        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         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        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 
       15.68         8.22        10.68        12.56        13.87         6.08 
TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
       22.26        13.41        13.51        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        12.82         0.66        19.36        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.65        20.42        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 
        3.25        13.15        13.18         0.30         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        0.13         0.13         0.10        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         0.10        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-4444 
        1.02         7.99         4.01        14.01        29.98        47.05 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       21.99         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-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-5727 TCGA-CG-5728 
      105.07        12.03        15.02        28.96        79.07        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        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        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-D7-6817 
       17.85        13.35        17.19        10.26        15.22        12.79 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       10.55        12.33        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-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        13.71        11.24        11.44         9.76 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
        2.96        15.65         8.38         4.34         7.40         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        16.24        14.47        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-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       13.58         5.52         0.23        18.08        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        5.92        14.27        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       24.20         3.25        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-A4H3 
        0.10         6.51        10.19         0.26         2.10        19.36 
TCGA-HU-A4H5 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RJ TCGA-IN-A6RL 
       12.30         8.81        21.21         3.45         5.36         5.19 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
        1.41         6.44         6.74        12.59         6.51         5.56 
TCGA-IN-A7NU TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG 
        1.81        13.51         5.56        60.56        20.15         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73         9.86        45.67        18.21         8.52        61.25 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
        6.08         4.60         9.24        11.05         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-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-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       35.24        21.73        34.45        27.88        28.96        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-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       17.85         1.87         9.27        23.41        15.65        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       27.35        64.57        14.33        65.16        36.69        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       11.93        61.22        18.74        22.68         1.71        36.16 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 
        7.36         9.50         9.73        52.24         9.04        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
        4.54         6.58        64.18        21.04         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6J 
       11.24        18.41        28.41        32.94        29.98        21.11 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        10.62         0.79 

  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                         0.07                          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 
                        13.08                         12.79 
[1] "0.1 - 72.2 (13.1)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.2"
D56V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 20(7Q31.1) MUTATED         1        3        2        7         7
  DEL PEAK 20(7Q31.1) WILD-TYPE       2       11       39       24        31
                               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        41         4         68         55
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 20(7Q31.1) MUTATED            4        7
  DEL PEAK 20(7Q31.1) WILD-TYPE         37       39
D56V3, multiclass
            clus
vv           DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  STAGE I                              1                             2
  STAGE IA                             3                            11
  STAGE IB                             2                            39
  STAGE II                             7                            24
  STAGE IIA                            7                            31
  STAGE IIB                           14                            41
  STAGE III                            0                             4
  STAGE IIIA                          17                            68
  STAGE IIIB                           7                            55
  STAGE IIIC                           4                            37
  STAGE IV                             7                            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 20(7Q31.1) MUTATED     5  13  39  12
  DEL PEAK 20(7Q31.1) WILD-TYPE  17  77 156 107
D56V4, multiclass
    clus
vv   DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  T1                           5                            17
  T2                          13                            77
  T3                          39                           156
  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  26  17  11
  DEL PEAK 20(7Q31.1) WILD-TYPE 114  92  67  78
D56V5, multiclass
    clus
vv   DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  N0                          15                           114
  N1                          26                            92
  N2                          17                            67
  N3                          11                            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    66   2
  DEL PEAK 20(7Q31.1) WILD-TYPE 321  28
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(7Q31.1) MUTATED     66    2
  DEL PEAK 20(7Q31.1) WILD-TYPE  321   28
   clus
vv  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  0                          66                           321
  1                           2                            28
[1] 2 2
[1] FALSE
D56V7, binary
                               cls
clus                              0   1
  DEL PEAK 20(7Q31.1) MUTATED    19  51
  DEL PEAK 20(7Q31.1) WILD-TYPE 139 227
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(7Q31.1) MUTATED     19   51
  DEL PEAK 20(7Q31.1) WILD-TYPE  139  227
        clus
vv       DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  FEMALE                          19                           139
  MALE                            51                           227
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 20(7Q31.1) MUTATED                                       6
  DEL PEAK 20(7Q31.1) WILD-TYPE                                    65
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 20(7Q31.1) MUTATED                                                       23
  DEL PEAK 20(7Q31.1) WILD-TYPE                                                    139
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 20(7Q31.1) MUTATED                                                                  15
  DEL PEAK 20(7Q31.1) WILD-TYPE                                                                66
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 20(7Q31.1) MUTATED                                                 18
  DEL PEAK 20(7Q31.1) WILD-TYPE                                               60
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 20(7Q31.1) MUTATED                                                          3
  DEL PEAK 20(7Q31.1) WILD-TYPE                                                       18
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 20(7Q31.1) MUTATED                                                           1
  DEL PEAK 20(7Q31.1) WILD-TYPE                                                         7
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 20(7Q31.1) MUTATED                                          2
  DEL PEAK 20(7Q31.1) WILD-TYPE                                       11
D56V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 20(7Q31.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     23
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          15
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    2
                                                                   clus
vv                                                                  DEL PEAK 20(7Q31.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        65
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      139
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            66
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             60
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     11
[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"
D56V9, binary
                               cls
clus                              0   1
  DEL PEAK 20(7Q31.1) MUTATED     1  69
  DEL PEAK 20(7Q31.1) WILD-TYPE   5 361
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(7Q31.1) MUTATED      1   69
  DEL PEAK 20(7Q31.1) WILD-TYPE    5  361
     clus
vv    DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  NO                            1                             5
  YES                          69                           361
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 20(7Q31.1) MUTATED    62   1   3   2
  DEL PEAK 20(7Q31.1) WILD-TYPE 285  17  16  23
D56V10, multiclass
    clus
vv   DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  R0                          62                           285
  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                         8
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 20(7Q31.1) MUTATED                                           1    39
  DEL PEAK 20(7Q31.1) WILD-TYPE                                         0   235
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                                                              39
                                           clus
vv                                          DEL PEAK 20(7Q31.1) WILD-TYPE
  ASIAN                                                                71
  BLACK OR AFRICAN AMERICAN                                             8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               235
[1] 4 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   4 267
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(7Q31.1) MUTATED      0   46
  DEL PEAK 20(7Q31.1) WILD-TYPE    4  267
                        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                                 4
  NOT HISPANIC OR LATINO                           267
[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  33
  DEL PEAK 21(7Q36.3) WILD-TYPE 196 117
  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                           91                           313 
  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                           33                           117 
$`DEL PEAK 21(7Q36.3) MUTATED`
TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-7704 
       19.56         9.44        17.29        19.33        26.10        35.24 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8296 TCGA-BR-8369 
       28.73         3.45        11.44         0.69        15.58        14.04 
TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-A4CS TCGA-BR-A4PF TCGA-CD-5802 TCGA-CD-8524 
        9.21        11.54         1.48         1.15         0.30         0.07 
TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
        0.07         0.10         0.13         0.13         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48C TCGA-CG-4301 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4449 
       11.31        11.61         3.02         8.05        54.08        19.07 
TCGA-CG-4455 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5724 TCGA-D7-6519 TCGA-D7-6525 
       12.03        12.00        22.98        12.03        20.55        13.35 
TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8575 
       17.19        15.98        12.79        10.55        11.31        18.21 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-A4SO TCGA-FP-7829 
       11.24        11.31         2.96         7.40        16.24        19.53 
TCGA-FP-8631 TCGA-HU-8243 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H2 
        0.56         5.92        22.75        11.77         6.25        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       23.84         9.67        27.42         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT 
       18.38         5.36        13.08         6.44         6.74         5.56 
TCGA-IN-AB1V TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-RD-A8MW TCGA-RD-A8N9 
        7.82        37.64        45.67        18.21        37.91        35.61 
TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PJ 
        5.46        13.02        18.48        32.48         7.73         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A928 TCGA-VQ-A92D 
       17.85        13.35        18.74        20.81         5.72        64.18 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       22.09        18.41        40.08        54.12        26.04        16.14 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK 21(7Q36.3) WILD-TYPE`
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-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        4.64         7.43        18.35        30.90         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-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        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       15.32        12.43         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       14.43        12.26         9.60        20.55         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       12.95         2.66        16.31         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       19.50        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        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 
        0.26        15.85         3.72         5.39        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        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
       22.26        13.41        13.51        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        12.82         0.66        19.36        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
        0.46        20.65        20.42        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8526 
        2.83         3.25        13.15        13.18         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 
        0.07         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 
       27.02        15.95         1.02         7.99         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        47.05        21.99         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        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-5727 
        6.02         0.99       105.07        15.02        28.96        79.07 
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        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.66        11.93        19.13        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       17.85        10.26        15.22        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-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       11.44         9.76        15.65         8.38         4.34         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        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-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       13.58         5.52         0.23        18.08        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       14.27        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        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        10.19         0.26         2.10        19.36        12.30 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RS 
        8.88         8.81        21.21         5.19         1.41        12.59 
TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        6.51         1.81        13.51         2.53         5.56        60.56 
TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZF TCGA-R5-A7ZI 
       20.15         3.72        19.73         9.86         8.52        61.25 
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-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       48.79        13.25        35.24        21.73        34.45        27.88 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       28.96        34.29        46.26        16.31        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       12.79         1.87         9.27        23.41        15.65        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       27.35        64.57        14.33        65.16        36.69        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       11.93        61.22        22.68         1.71        36.16         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
        9.50         9.73        52.24         9.04         2.01        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
        4.54         6.58        21.04         2.66        42.54        11.24 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6J TCGA-VQ-AA6K 
       28.41        32.94        29.98        17.13        21.11        12.43 
TCGA-ZA-A8F6 
       10.62 

  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                         0.07                          0.00 
  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                        64.18                        122.30 
  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                        12.03                         12.89 
[1] "0.1 - 64.2 (12.0)"  "0.0 - 122.3 (12.9)"
[1] "hr=" "1.1"
D57V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 21(7Q36.3) MUTATED         1        2        4        8         5
  DEL PEAK 21(7Q36.3) WILD-TYPE       2       12       37       23        33
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 21(7Q36.3) MUTATED          20         1         23         11
  DEL PEAK 21(7Q36.3) WILD-TYPE        35         3         62         51
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 21(7Q36.3) MUTATED            9       11
  DEL PEAK 21(7Q36.3) WILD-TYPE         32       35
D57V3, multiclass
            clus
vv           DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  STAGE I                              1                             2
  STAGE IA                             2                            12
  STAGE IB                             4                            37
  STAGE II                             8                            23
  STAGE IIA                            5                            33
  STAGE IIB                           20                            35
  STAGE III                            1                             3
  STAGE IIIA                          23                            62
  STAGE IIIB                          11                            51
  STAGE IIIC                           9                            32
  STAGE IV                            11                            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 21(7Q36.3) MUTATED     6  18  50  21
  DEL PEAK 21(7Q36.3) WILD-TYPE  16  72 145  98
D57V4, multiclass
    clus
vv   DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  T1                           6                            16
  T2                          18                            72
  T3                          50                           145
  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  23  21
  DEL PEAK 21(7Q36.3) WILD-TYPE 110  87  61  68
D57V5, multiclass
    clus
vv   DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  N0                          19                           110
  N1                          31                            87
  N2                          23                            61
  N3                          21                            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 300  23
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q36.3) MUTATED     87    7
  DEL PEAK 21(7Q36.3) WILD-TYPE  300   23
   clus
vv  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  0                          87                           300
  1                           7                            23
[1] 2 2
[1] FALSE
D57V7, binary
                               cls
clus                              0   1
  DEL PEAK 21(7Q36.3) MUTATED    33  64
  DEL PEAK 21(7Q36.3) WILD-TYPE 125 214
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q36.3) MUTATED     33   64
  DEL PEAK 21(7Q36.3) WILD-TYPE  125  214
        clus
vv       DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  FEMALE                          33                           125
  MALE                            64                           214
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 21(7Q36.3) MUTATED                                      12
  DEL PEAK 21(7Q36.3) WILD-TYPE                                    59
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 21(7Q36.3) MUTATED                                                       34
  DEL PEAK 21(7Q36.3) WILD-TYPE                                                    128
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 21(7Q36.3) MUTATED                                                                  17
  DEL PEAK 21(7Q36.3) WILD-TYPE                                                                64
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 21(7Q36.3) MUTATED                                                 24
  DEL PEAK 21(7Q36.3) WILD-TYPE                                               54
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 21(7Q36.3) MUTATED                                                          5
  DEL PEAK 21(7Q36.3) WILD-TYPE                                                       16
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 21(7Q36.3) MUTATED                                                           1
  DEL PEAK 21(7Q36.3) WILD-TYPE                                                         7
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 21(7Q36.3) MUTATED                                          2
  DEL PEAK 21(7Q36.3) WILD-TYPE                                       11
D57V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 21(7Q36.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     34
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           24
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    2
                                                                   clus
vv                                                                  DEL PEAK 21(7Q36.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            64
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             54
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     11
[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"
D57V9, binary
                               cls
clus                              0   1
  DEL PEAK 21(7Q36.3) MUTATED     3  94
  DEL PEAK 21(7Q36.3) WILD-TYPE   3 336
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q36.3) MUTATED      3   94
  DEL PEAK 21(7Q36.3) WILD-TYPE    3  336
     clus
vv    DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  NO                            3                             3
  YES                          94                           336
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 21(7Q36.3) MUTATED    80   1   4   3
  DEL PEAK 21(7Q36.3) WILD-TYPE 267  17  15  22
D57V10, multiclass
    clus
vv   DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  R0                          80                           267
  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                         9
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 21(7Q36.3) MUTATED                                           0    62
  DEL PEAK 21(7Q36.3) WILD-TYPE                                         1   212
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                                                              62
                                           clus
vv                                          DEL PEAK 21(7Q36.3) WILD-TYPE
  ASIAN                                                                67
  BLACK OR AFRICAN AMERICAN                                             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V13, binary
                               cls
clus                              0   1
  DEL PEAK 21(7Q36.3) MUTATED     1  68
  DEL PEAK 21(7Q36.3) WILD-TYPE   3 245
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q36.3) MUTATED      1   68
  DEL PEAK 21(7Q36.3) WILD-TYPE    3  245
                        clus
vv                       DEL PEAK 21(7Q36.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          68
                        clus
vv                       DEL PEAK 21(7Q36.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           245
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 22(8P23.3) MUTATION ANALYSIS
D58V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 22(8P23.3) MUTATED    69  46
  DEL PEAK 22(8P23.3) WILD-TYPE 185 104
  DEL PEAK 22(8P23.3) MUTATED DEL PEAK 22(8P23.3) WILD-TYPE 
                          115                           289 
  DEL PEAK 22(8P23.3) MUTATED DEL PEAK 22(8P23.3) WILD-TYPE 
                           46                           104 
$`DEL PEAK 22(8P23.3) MUTATED`
TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6565 
       19.56         9.44        18.35        17.29        13.68         9.17 
TCGA-BR-6705 TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 
       25.61        12.16         9.21        15.42        28.01        28.73 
TCGA-BR-7958 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 
       12.76         0.69         9.60        12.95         2.66        15.58 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8485 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
       19.50        13.08         9.21        15.81        16.44         9.86 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CS TCGA-BR-A4IY 
        8.22        10.68        13.87         7.53         1.48        12.89 
TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5800 
        0.72        13.51        20.65         1.15        13.64        13.15 
TCGA-CD-5802 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A48A 
        0.30         0.07         0.07         0.13         3.42        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4438 
       11.61        12.20         3.02        27.02         7.99        54.08 
TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4475 TCGA-CG-5718 
        4.01        29.98        47.05        19.07        22.98        36.00 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6518 
       12.03        15.02         4.01        69.04        12.66        19.13 
TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-A4YU 
       18.54        17.19        15.22        11.31        24.72        16.44 
TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-F1-6875 TCGA-FP-8099 TCGA-HU-8243 
       15.65         7.40         0.62        72.23        17.06         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4GU TCGA-HU-A4HD 
       12.59        14.17         0.76        22.75         6.25        27.42 
TCGA-IN-8663 TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-AB1V 
        3.39         1.41         6.44         6.74         6.51         7.82 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A805 TCGA-RD-A7BT 
        2.53         5.56        45.67         8.52         9.24         8.61 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8E0 TCGA-VQ-A8E2 
      122.30        37.91         8.94         5.79        18.48        35.24 
TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM 
       34.45         7.73        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        36.69         1.71        52.24         4.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J 
       18.41        40.08        29.98        54.12        16.14        21.11 
TCGA-VQ-AA6K 
       12.43 

$`DEL PEAK 22(8P23.3) WILD-TYPE`
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-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.64         7.43        30.90         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        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        32.94        12.82        24.76        35.24        23.93 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 
       18.15        15.32        12.43         3.45         9.07        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43        11.44        12.26        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
        0.56        16.31         2.20         7.40         6.18         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        19.17        14.79         0.26        15.85 
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 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU 
       11.54        15.68        12.56         6.08        22.26        13.41 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       13.51         8.98        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       19.36         0.46        20.42        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8528 
        3.25        13.18         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
        9.34        11.31         6.58         0.10        12.62        20.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4460 
       15.95         1.02         8.05        14.01        12.03        21.99 
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-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-5727 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        79.07        65.10        21.07         7.99        12.36 
TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       11.93        20.55        18.84        18.61        17.85        13.35 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8572 
       10.26        15.98        12.79        10.55        12.33        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-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 
       11.24        11.31        11.44         9.76         2.96         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 
        4.34         7.13         7.99        16.24        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-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB 
        5.03        13.58         0.56         5.52         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       26.47         1.51        14.27        11.41        12.10        10.62 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        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        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       23.84        12.30         9.67         8.88         8.81        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45        18.81        18.38         5.36         5.19        13.08 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-KB-A93G 
       12.59         5.56         1.81        13.51        60.56        20.15 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZI 
       37.64         3.72        19.73         9.86        18.21        61.25 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N0 
        6.08         4.60        11.05         5.13        16.67        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-A8DV TCGA-VQ-A8DZ 
       19.04         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       21.73        27.88        32.48        28.96        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       16.31         2.50         2.70         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D 
       26.24        27.35        64.57        14.33        65.16        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V 
       11.93        61.22        18.74        20.81        22.68        36.16 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
        7.36         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        64.18        21.04         2.66        42.54 
TCGA-VQ-A94U TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-ZA-A8F6 
       22.09        28.41        32.94        17.13        26.04        10.62 
TCGA-ZQ-A9CR 
        0.79 

  DEL PEAK 22(8P23.3) MUTATED DEL PEAK 22(8P23.3) WILD-TYPE 
                         0.07                          0.00 
  DEL PEAK 22(8P23.3) MUTATED DEL PEAK 22(8P23.3) WILD-TYPE 
                       122.30                        116.38 
  DEL PEAK 22(8P23.3) MUTATED DEL PEAK 22(8P23.3) WILD-TYPE 
                        12.89                         12.82 
[1] "0.1 - 122.3 (12.9)" "0.0 - 116.4 (12.8)"
[1] "hr=" "1.1"
D58V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 22(8P23.3) MUTATED         1        5        5        8         9
  DEL PEAK 22(8P23.3) WILD-TYPE       2        9       36       23        29
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 22(8P23.3) MUTATED          14         0         23         25
  DEL PEAK 22(8P23.3) WILD-TYPE        41         4         62         37
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 22(8P23.3) MUTATED           14       16
  DEL PEAK 22(8P23.3) WILD-TYPE         27       30
D58V3, multiclass
            clus
vv           DEL PEAK 22(8P23.3) MUTATED DEL PEAK 22(8P23.3) WILD-TYPE
  STAGE I                              1                             2
  STAGE IA                             5                             9
  STAGE IB                             5                            36
  STAGE II                             8                            23
  STAGE IIA                            9                            29
  STAGE IIB                           14                            41
  STAGE III                            0                             4
  STAGE IIIA                          23                            62
  STAGE IIIB                          25                            37
  STAGE IIIC                          14                            27
  STAGE IV                            16                            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 22(8P23.3) MUTATED     6  19  64  32
  DEL PEAK 22(8P23.3) WILD-TYPE  16  71 131  87
D58V4, multiclass
    clus
vv   DEL PEAK 22(8P23.3) MUTATED DEL PEAK 22(8P23.3) WILD-TYPE
  T1                           6                            16
  T2                          19                            71
  T3                          64                           131
  T4                          32                            87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 22(8P23.3) MUTATED    29  28  29  34
  DEL PEAK 22(8P23.3) WILD-TYPE 100  90  55  55
D58V5, multiclass
    clus
vv   DEL PEAK 22(8P23.3) MUTATED DEL PEAK 22(8P23.3) WILD-TYPE
  N0                          29                           100
  N1                          28                            90
  N2                          29                            55
  N3                          34                            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(8P23.3) MUTATED   109  11
  DEL PEAK 22(8P23.3) WILD-TYPE 278  19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(8P23.3) MUTATED    109   11
  DEL PEAK 22(8P23.3) WILD-TYPE  278   19
   clus
vv  DEL PEAK 22(8P23.3) MUTATED DEL PEAK 22(8P23.3) WILD-TYPE
  0                         109                           278
  1                          11                            19
[1] 2 2
[1] FALSE
D58V7, binary
                               cls
clus                              0   1
  DEL PEAK 22(8P23.3) MUTATED    34  89
  DEL PEAK 22(8P23.3) WILD-TYPE 124 189
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(8P23.3) MUTATED     34   89
  DEL PEAK 22(8P23.3) WILD-TYPE  124  189
        clus
vv       DEL PEAK 22(8P23.3) MUTATED DEL PEAK 22(8P23.3) WILD-TYPE
  FEMALE                          34                           124
  MALE                            89                           189
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 22(8P23.3) MUTATED                                       8
  DEL PEAK 22(8P23.3) WILD-TYPE                                    63
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 22(8P23.3) MUTATED                                                       50
  DEL PEAK 22(8P23.3) WILD-TYPE                                                    112
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 22(8P23.3) MUTATED                                                                  28
  DEL PEAK 22(8P23.3) WILD-TYPE                                                                53
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 22(8P23.3) MUTATED                                                 26
  DEL PEAK 22(8P23.3) WILD-TYPE                                               52
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 22(8P23.3) MUTATED                                                          6
  DEL PEAK 22(8P23.3) WILD-TYPE                                                       15
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 22(8P23.3) MUTATED                                                           2
  DEL PEAK 22(8P23.3) WILD-TYPE                                                         6
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 22(8P23.3) MUTATED                                          2
  DEL PEAK 22(8P23.3) WILD-TYPE                                       11
D58V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 22(8P23.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     50
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          28
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           26
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    2
                                                                   clus
vv                                                                  DEL PEAK 22(8P23.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      112
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            53
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             52
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     11
[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"
D58V9, binary
                               cls
clus                              0   1
  DEL PEAK 22(8P23.3) MUTATED     2 121
  DEL PEAK 22(8P23.3) WILD-TYPE   4 309
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(8P23.3) MUTATED      2  121
  DEL PEAK 22(8P23.3) WILD-TYPE    4  309
     clus
vv    DEL PEAK 22(8P23.3) MUTATED DEL PEAK 22(8P23.3) WILD-TYPE
  NO                            2                             4
  YES                         121                           309
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 22(8P23.3) MUTATED    96   7   7   3
  DEL PEAK 22(8P23.3) WILD-TYPE 251  11  12  22
D58V10, multiclass
    clus
vv   DEL PEAK 22(8P23.3) MUTATED DEL PEAK 22(8P23.3) WILD-TYPE
  R0                          96                           251
  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(8P23.3) MUTATED      26                         5
  DEL PEAK 22(8P23.3) WILD-TYPE    62                         6
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 22(8P23.3) MUTATED                                           1    72
  DEL PEAK 22(8P23.3) WILD-TYPE                                         0   202
D58V12, multiclass
                                           clus
vv                                          DEL PEAK 22(8P23.3) MUTATED
  ASIAN                                                              26
  BLACK OR AFRICAN AMERICAN                                           5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              72
                                           clus
vv                                          DEL PEAK 22(8P23.3) WILD-TYPE
  ASIAN                                                                62
  BLACK OR AFRICAN AMERICAN                                             6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  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"
D58V13, binary
                               cls
clus                              0   1
  DEL PEAK 22(8P23.3) MUTATED     1  83
  DEL PEAK 22(8P23.3) WILD-TYPE   3 230
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(8P23.3) MUTATED      1   83
  DEL PEAK 22(8P23.3) WILD-TYPE    3  230
                        clus
vv                       DEL PEAK 22(8P23.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          83
                        clus
vv                       DEL PEAK 22(8P23.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           230
[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   110  67
  DEL PEAK 23(9P23) WILD-TYPE 144  83
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                        177                         227 
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                         67                          83 
$`DEL PEAK 23(9P23) MUTATED`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4191 
       26.70        19.56        11.01         9.44         6.61        18.35 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6803 
       17.29        13.68        19.33        19.89        12.16        31.20 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        35.24        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 
       28.73         3.45        18.71        17.49        11.44         0.69 
TCGA-BR-8284 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 
        8.05         2.66        16.31        22.19        17.52        14.04 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8676 TCGA-BR-8682 
        5.39        25.18         9.21        20.22         7.53        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS 
        9.86        15.68         8.22        13.87        22.26         1.48 
TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI 
        0.72         0.66        13.51        20.65         1.15        13.64 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        3.25        13.15         0.07         0.07         0.07         0.07 
TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C 
        0.16         0.10         0.13         3.42        12.43        11.61 
TCGA-CG-4301 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4444 
        3.02         8.05        54.08         4.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5719 
       19.07        12.03        18.97        12.00        36.00         1.02 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-5578 
      105.07        12.03         4.01        69.04        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 
       11.93        19.13        20.55        18.84        18.54        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8573 
       17.19        10.26        15.98        12.79        11.31        19.50 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6EX 
       18.21        14.66        21.14        16.44        11.24        11.31 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-A72C TCGA-FP-7829 
        2.96        15.65         7.40         7.99        11.38        19.53 
TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8238 TCGA-HU-8243 
       14.07        17.06         0.56         5.52         1.51         5.92 
TCGA-HU-8245 TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H6 
       12.59        25.81        11.77         6.25        19.36         9.67 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       27.42        21.21        18.81        18.38         5.36         5.19 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
        1.41         6.44         6.74        12.59         6.51         5.56 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZF 
        7.82        13.51         5.56        37.64        45.67         8.52 
TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        6.08         9.24         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DV 
       37.91       115.69         8.94         5.79        48.79        13.25 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PF 
       18.48        35.24        34.45         7.73        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A8PX 
       12.79         2.70        17.85         1.87        27.35        64.57 
TCGA-VQ-A8PY TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X 
       14.33        18.74        20.81         1.71        36.16         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A94O TCGA-VQ-A94R 
        9.73        52.24         9.04         2.01        21.04        42.54 
TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6F 
       11.24        22.09        18.41        40.08        32.94        54.12 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       21.11        12.43         0.79 

$`DEL PEAK 23(9P23) WILD-TYPE`
TCGA-B7-5818 TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
       11.70         9.47         6.97         4.64         7.43        30.90 
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-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-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
        8.98        21.11        30.90        32.94        12.82        24.76 
TCGA-BR-7707 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8078 
       23.93        12.43         9.07        12.76        14.43        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8296 
        9.60        20.55         0.56        12.95         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        19.50        13.08         0.26         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        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        0.26        15.85         3.72         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        9.34        13.45         6.28         0.49        11.54        15.81 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
       10.68        12.56         7.53         6.08        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 
       12.89         8.98        14.17         0.53        12.82        19.36 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 
        0.46        20.42        11.57         5.13         2.83        13.18 
TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8535 
        0.30         0.07         0.10         0.13         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        0.10         9.34        11.31         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02        27.02        15.95         1.02         7.99 
TCGA-CG-4441 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4475 
       14.01        21.99         0.00         9.01         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5725 
       30.97         6.97         0.99         6.02         0.99        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-6522 
       28.96        79.07        65.10        21.07         7.99        18.61 
TCGA-D7-6524 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       17.85        15.22        10.55        12.33        24.72        16.80 
TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       17.19        20.91        14.27         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 
       14.76        13.71        11.44         9.76         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A8CX 
        3.48        22.29        59.54         5.03        13.58         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       18.08        26.47        14.27        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
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-A4H0 TCGA-HU-A4H2 
        0.10         6.51        10.19         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8663 
       23.84        12.30         8.88         8.81         3.45         3.39 
TCGA-IN-A6RN TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG 
       13.08         1.81         2.53        60.56        20.15         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS 
       19.73         9.86        18.21        61.25         4.60        11.05 
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-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8P2 
       19.04         0.92         5.46        13.02        21.73        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PO 
       32.48        28.96        34.29        46.26        16.31         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91A 
       23.41        15.65        13.35        26.24        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A924 
       11.70        11.93        61.22        22.68         7.36        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-AA69 
        4.54         6.58         5.72        64.18         2.66        28.41 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-ZA-A8F6 
       29.98        17.13        26.04        16.14        10.62 

  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                       0.07                        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 
                      13.15                       12.82 
[1] "0.1 - 122.3 (13.2)" "0.0 - 116.4 (12.8)"
[1] "hr=" "1"  
D59V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 23(9P23) MUTATED         1        7       10       16        17
  DEL PEAK 23(9P23) WILD-TYPE       2        7       31       15        21
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 23(9P23) MUTATED          24         1         41         29
  DEL PEAK 23(9P23) WILD-TYPE        31         3         44         33
                             vv
clus                          STAGE IIIC STAGE IV
  DEL PEAK 23(9P23) MUTATED           17       22
  DEL PEAK 23(9P23) WILD-TYPE         24       24
D59V3, multiclass
            clus
vv           DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  STAGE I                            1                           2
  STAGE IA                           7                           7
  STAGE IB                          10                          31
  STAGE II                          16                          15
  STAGE IIA                         17                          21
  STAGE IIB                         24                          31
  STAGE III                          1                           3
  STAGE IIIA                        41                          44
  STAGE IIIB                        29                          33
  STAGE IIIC                        17                          24
  STAGE IV                          22                          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
  DEL PEAK 23(9P23) MUTATED    10  36  95  45
  DEL PEAK 23(9P23) WILD-TYPE  12  54 100  74
D59V4, multiclass
    clus
vv   DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  T1                        10                          12
  T2                        36                          54
  T3                        95                         100
  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   48 53 42 41
  DEL PEAK 23(9P23) WILD-TYPE 81 65 42 48
D59V5, multiclass
    clus
vv   DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  N0                        48                          81
  N1                        53                          65
  N2                        42                          42
  N3                        41                          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"
D59V6, binary
                             cls
clus                            0   1
  DEL PEAK 23(9P23) MUTATED   174  11
  DEL PEAK 23(9P23) WILD-TYPE 213  19
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 23(9P23) MUTATED    174   11
  DEL PEAK 23(9P23) WILD-TYPE  213   19
   clus
vv  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  0                       174                         213
  1                        11                          19
[1] 2 2
[1] FALSE
D59V7, binary
                             cls
clus                            0   1
  DEL PEAK 23(9P23) MUTATED    67 124
  DEL PEAK 23(9P23) WILD-TYPE  91 154
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 23(9P23) MUTATED     67  124
  DEL PEAK 23(9P23) WILD-TYPE   91  154
        clus
vv       DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  FEMALE                        67                          91
  MALE                         124                         154
[1] 2 2
[1] FALSE
                             vv
clus                          STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 23(9P23) MUTATED                                      22
  DEL PEAK 23(9P23) WILD-TYPE                                    49
                             vv
clus                          STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 23(9P23) MUTATED                                                       67
  DEL PEAK 23(9P23) WILD-TYPE                                                     95
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 23(9P23) MUTATED                                                                  43
  DEL PEAK 23(9P23) WILD-TYPE                                                                38
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 23(9P23) MUTATED                                                 42
  DEL PEAK 23(9P23) WILD-TYPE                                               36
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 23(9P23) MUTATED                                                          9
  DEL PEAK 23(9P23) WILD-TYPE                                                       12
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 23(9P23) MUTATED                                                           3
  DEL PEAK 23(9P23) WILD-TYPE                                                         5
                             vv
clus                          STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 23(9P23) MUTATED                                          4
  DEL PEAK 23(9P23) WILD-TYPE                                        9
D59V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 23(9P23) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                    22
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                   67
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        43
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                         42
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                  9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                 3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                  4
                                                                   clus
vv                                                                  DEL PEAK 23(9P23) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     95
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    9
[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"
D59V9, binary
                             cls
clus                            0   1
  DEL PEAK 23(9P23) MUTATED     3 188
  DEL PEAK 23(9P23) WILD-TYPE   3 242
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 23(9P23) MUTATED      3  188
  DEL PEAK 23(9P23) WILD-TYPE    3  242
     clus
vv    DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  NO                          3                           3
  YES                       188                         242
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 23(9P23) MUTATED   152   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                       152                         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                         6
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 23(9P23) MUTATED                                           1   123
  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                                                           123
                                           clus
vv                                          DEL PEAK 23(9P23) WILD-TYPE
  ASIAN                                                              55
  BLACK OR AFRICAN AMERICAN                                           6
  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     1 135
  DEL PEAK 23(9P23) WILD-TYPE   3 178
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 23(9P23) MUTATED      1  135
  DEL PEAK 23(9P23) WILD-TYPE    3  178
                        clus
vv                       DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  HISPANIC OR LATINO                             1                           3
  NOT HISPANIC OR LATINO                       135                         178
[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   111  68
  DEL PEAK 24(9P21.3) WILD-TYPE 143  82
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                          179                           225 
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                           68                            82 
$`DEL PEAK 24(9P21.3) MUTATED`
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-6456 
       19.56        11.01         9.44         6.61        18.35        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 
       15.42        28.01        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 
       18.71        17.49        14.43        11.44         0.69        16.31 
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         0.49        16.44         9.86        15.68         8.22 
TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 
       13.87        22.26         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        13.64         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.15         0.07         0.07         0.07         0.07         0.07 
TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C 
        0.16         0.10         0.13         3.42        12.43        11.61 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        3.02        27.02        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4477 
       47.05        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        11.93        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         2.96         7.40         7.99        72.23        11.38 
TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       17.06        13.58         0.56         1.51         5.92        14.27 
TCGA-HU-8245 TCGA-HU-A4G3 TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H5 TCGA-HU-A4H6 
       12.59         5.59        11.77         6.25        12.30         9.67 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO 
       27.42        21.21        18.81         5.36         5.19         1.41 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X 
        6.74        12.59         6.51         5.56         7.82        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZF 
        2.53         5.56        60.56        37.64        45.67         8.52 
TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW 
        6.08         9.24         8.61         5.13        16.67        37.91 
TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ 
      115.69         8.94         5.79        48.79        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       18.48        35.24        21.73        34.45        32.48         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-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U 
       27.35        64.57        14.33        18.74        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94O 
       36.16         9.50         9.73        52.24         9.04        21.04 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A 
       42.54        11.24        22.09        18.41        40.08        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       54.12        21.11        12.43        10.62         0.79 

$`DEL PEAK 24(9P21.3) WILD-TYPE`
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-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.87        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 
       18.05        19.89         8.98        21.11        30.90        32.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 
       12.82        24.76        23.93        12.43         9.07        12.76 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       12.26         9.60        20.55         8.05         0.56        12.95 
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        19.50 
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-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 
        7.53        11.54        15.81        10.68        12.56         7.53 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        6.08        13.41        13.51        12.89         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-BR-A4QM 
        0.53        12.82        19.36         0.46        11.57         5.13 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8535 
       13.18         0.30         0.10         0.13         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        0.10         9.34        11.31         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       12.62        20.02        15.95         1.02         7.99         8.05 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-5717 
       21.99         0.00         9.01         7.07        22.98         6.97 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        6.02         0.99       105.07        28.96        79.07        65.10 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 
       21.07         7.99        12.36        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        10.55        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        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       13.71        11.44         9.76        15.65         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 
        7.13         0.62        16.24        14.47        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF 
       19.53        14.07        22.29        59.54         5.03         5.52 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        0.23        18.08        26.47        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       10.62         0.76        24.30        12.30        11.84        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        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8663 
       19.36        23.84         8.88         8.81         3.45         3.39 
TCGA-IN-A6RI TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NU TCGA-KB-A93G TCGA-MX-A5UG 
       18.38        13.08         6.44         1.81        20.15         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS 
       19.73         9.86        18.21        61.25         4.60        11.05 
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-A8DL TCGA-VQ-A8DU TCGA-VQ-A8P2 TCGA-VQ-A8P8 
       16.87        19.04         0.92         5.46        27.88        28.96 
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-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       13.35        26.24        65.16        36.69        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
       61.22        22.68         7.36         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-AA69 TCGA-VQ-AA6B 
        6.58         5.72        64.18         2.66        28.41        29.98 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I 
       17.13        26.04        16.14 

  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                         0.07                          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 
                        13.25                         12.76 
[1] "0.1 - 115.7 (13.2)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1"  
D60V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 24(9P21.3) MUTATED         0        9       17       16        15
  DEL PEAK 24(9P21.3) WILD-TYPE       3        5       24       15        23
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 24(9P21.3) MUTATED          24         2         39         28
  DEL PEAK 24(9P21.3) WILD-TYPE        31         2         46         34
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 24(9P21.3) MUTATED           13       22
  DEL PEAK 24(9P21.3) WILD-TYPE         28       24
D60V3, multiclass
            clus
vv           DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  STAGE I                              0                             3
  STAGE IA                             9                             5
  STAGE IB                            17                            24
  STAGE II                            16                            15
  STAGE IIA                           15                            23
  STAGE IIB                           24                            31
  STAGE III                            2                             2
  STAGE IIIA                          39                            46
  STAGE IIIB                          28                            34
  STAGE IIIC                          13                            28
  STAGE IV                            22                            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
  DEL PEAK 24(9P21.3) MUTATED    10  41  91  43
  DEL PEAK 24(9P21.3) WILD-TYPE  12  49 104  76
D60V4, multiclass
    clus
vv   DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  T1                          10                            12
  T2                          41                            49
  T3                          91                           104
  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   54 52 43 35
  DEL PEAK 24(9P21.3) WILD-TYPE 75 66 41 54
D60V5, multiclass
    clus
vv   DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  N0                          54                            75
  N1                          52                            66
  N2                          43                            41
  N3                          35                            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"
D60V6, binary
                               cls
clus                              0   1
  DEL PEAK 24(9P21.3) MUTATED   170  11
  DEL PEAK 24(9P21.3) WILD-TYPE 217  19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 24(9P21.3) MUTATED    170   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                         170                           217
  1                          11                            19
[1] 2 2
[1] FALSE
D60V7, binary
                               cls
clus                              0   1
  DEL PEAK 24(9P21.3) MUTATED    67 122
  DEL PEAK 24(9P21.3) WILD-TYPE  91 156
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 24(9P21.3) MUTATED     67  122
  DEL PEAK 24(9P21.3) WILD-TYPE   91  156
        clus
vv       DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  FEMALE                          67                            91
  MALE                           122                           156
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 24(9P21.3) MUTATED                                      18
  DEL PEAK 24(9P21.3) WILD-TYPE                                    53
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 24(9P21.3) MUTATED                                                       67
  DEL PEAK 24(9P21.3) WILD-TYPE                                                     95
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 24(9P21.3) MUTATED                                                                  45
  DEL PEAK 24(9P21.3) WILD-TYPE                                                                36
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 24(9P21.3) MUTATED                                                 40
  DEL PEAK 24(9P21.3) WILD-TYPE                                               38
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 24(9P21.3) MUTATED                                                          9
  DEL PEAK 24(9P21.3) WILD-TYPE                                                       12
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 24(9P21.3) MUTATED                                                           4
  DEL PEAK 24(9P21.3) WILD-TYPE                                                         4
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 24(9P21.3) MUTATED                                          5
  DEL PEAK 24(9P21.3) WILD-TYPE                                        8
D60V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 24(9P21.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      18
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     67
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          45
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           40
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    5
                                                                   clus
vv                                                                  DEL PEAK 24(9P21.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        53
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       95
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      8
[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"
D60V9, binary
                               cls
clus                              0   1
  DEL PEAK 24(9P21.3) MUTATED     3 186
  DEL PEAK 24(9P21.3) WILD-TYPE   3 244
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 24(9P21.3) MUTATED      3  186
  DEL PEAK 24(9P21.3) WILD-TYPE    3  244
     clus
vv    DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  NO                            3                             3
  YES                         186                           244
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 24(9P21.3) MUTATED   153   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                         153                           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                         4
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 24(9P21.3) MUTATED                                           1   115
  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                                                             115
                                           clus
vv                                          DEL PEAK 24(9P21.3) WILD-TYPE
  ASIAN                                                                54
  BLACK OR AFRICAN AMERICAN                                             4
  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     1 127
  DEL PEAK 24(9P21.3) WILD-TYPE   3 186
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 24(9P21.3) MUTATED      1  127
  DEL PEAK 24(9P21.3) WILD-TYPE    3  186
                        clus
vv                       DEL PEAK 24(9P21.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         127
                        clus
vv                       DEL PEAK 24(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           186
[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    64  41
  DEL PEAK 25(9Q21.11) WILD-TYPE 190 109
  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                           105                            299 
  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                            41                            109 
$`DEL PEAK 25(9Q21.11) MUTATED`
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       11.01         9.44         6.61        17.29        13.68        19.33 
TCGA-BR-6803 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 
       31.20        15.42        28.01        18.15        28.73         3.45 
TCGA-BR-8058 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8483 
       17.49        12.95        16.31        22.19        17.52         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A4CQ 
       25.18         9.21        16.44        15.68         8.22        22.26 
TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 
        1.48         0.72        13.51         1.15        13.64         3.25 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8532 
       13.15         0.30         0.07         0.07         0.07         0.10 
TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4304 
        0.13         3.42        11.31        11.61        12.20        27.02 
TCGA-CG-4438 TCGA-CG-4455 TCGA-CG-5724 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       54.08        12.03        12.03        20.55        18.84        18.54 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       13.35        10.26        15.98        18.21        14.66        21.14 
TCGA-D7-A4YU TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C 
       16.44         2.96         7.40         7.99        72.23        11.38 
TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       17.06        13.58         0.56         5.92        12.59        14.17 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H6 TCGA-IN-A6RI 
       25.81        11.77         6.25         2.10         9.67        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-AB1V TCGA-KB-A93H 
        5.36         6.44         6.74         6.51         7.82        37.64 
TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N6 
       45.67         8.52         6.08        16.67        37.91         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PH 
        5.79        13.25        18.48        35.24        22.19        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91Y 
        2.70        17.85        13.35        20.81        36.16         9.73 
TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA68 
        9.04        21.04        42.54        11.24        22.09        40.08 
TCGA-VQ-AA6A TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       32.94        21.11         0.79 

$`DEL PEAK 25(9Q21.11) WILD-TYPE`
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-4267 TCGA-BR-4279 TCGA-BR-4280 
        7.43        18.35        30.90         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 
       21.11        30.90        32.94        12.82         9.21        24.76 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 
       35.24        23.93        15.32        12.43         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        14.43        11.44         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 
       20.55         8.05         0.56         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        19.50        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        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8486 TCGA-BR-8487 
       14.79         0.26        15.85         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        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44T 
        0.49        11.54        15.81         9.86        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       13.87         7.53         6.08        13.41        13.51        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        12.82         0.66        19.36 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.65        20.42        11.57         5.13         2.83 
TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       13.18         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A4MG 
        0.10         0.13         0.10         9.34        12.43         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 
        0.10        12.62        20.02         3.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        7.99         8.05         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        21.99         0.00         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       12.00        22.98        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-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 
       12.36        12.66        11.93        19.13        18.61        17.85 
TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       17.19        15.22        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YT 
       24.72        16.80        19.50        17.19        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        11.44         9.76        15.65         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 
        7.13         0.62        16.24        14.47        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF 
       19.53        14.07        22.29        59.54         5.03         5.52 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8602 
        0.23        18.08        26.47         1.51        14.27        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GJ TCGA-HU-A4GN 
       11.84        24.20         3.25        22.75        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 
        8.98         0.10         6.51        10.19         0.26        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       19.36        23.84        12.30         8.88         8.81        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RN 
       21.21         3.45        18.81         3.39         5.19        13.08 
TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 
        1.41        12.59         5.56         1.81        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        5.56        60.56        20.15         3.72        19.73         9.86 
TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       18.21        61.25         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-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        5.46        13.02        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
        7.73        28.96        34.29        46.26        16.31         2.50 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU 
        1.87         9.27        23.41        15.65        26.24        27.35 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        65.16        36.69        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X 
       61.22        18.74        22.68         1.71         7.36         9.50 
TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
       52.24         2.01        55.43         4.54         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D 
       64.18         2.66        18.41        28.41        29.98        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        12.43        10.62 

  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                          0.07                           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 
                         13.25                          12.79 
[1] "0.1 - 72.2 (13.2)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D61V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 25(9Q21.11) MUTATED         1        3        7       10        13
  DEL PEAK 25(9Q21.11) WILD-TYPE       2       11       34       21        25
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 25(9Q21.11) MUTATED          15         1         21         15
  DEL PEAK 25(9Q21.11) WILD-TYPE        40         3         64         47
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 25(9Q21.11) MUTATED           13       11
  DEL PEAK 25(9Q21.11) WILD-TYPE         28       35
D61V3, multiclass
            clus
vv           DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  STAGE I                               1                              2
  STAGE IA                              3                             11
  STAGE IB                              7                             34
  STAGE II                             10                             21
  STAGE IIA                            13                             25
  STAGE IIB                            15                             40
  STAGE III                             1                              3
  STAGE IIIA                           21                             64
  STAGE IIIB                           15                             47
  STAGE IIIC                           13                             28
  STAGE IV                             11                             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 25(9Q21.11) MUTATED     5  18  58  29
  DEL PEAK 25(9Q21.11) WILD-TYPE  17  72 137  90
D61V4, multiclass
    clus
vv   DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  T1                            5                             17
  T2                           18                             72
  T3                           58                            137
  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   32 29 25 22
  DEL PEAK 25(9Q21.11) WILD-TYPE 97 89 59 67
D61V5, multiclass
    clus
vv   DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  N0                           32                             97
  N1                           29                             89
  N2                           25                             59
  N3                           22                             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"
D61V6, binary
                                cls
clus                               0   1
  DEL PEAK 25(9Q21.11) MUTATED   103   5
  DEL PEAK 25(9Q21.11) WILD-TYPE 284  25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(9Q21.11) MUTATED    103    5
  DEL PEAK 25(9Q21.11) WILD-TYPE  284   25
   clus
vv  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  0                          103                            284
  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 122 201
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(9Q21.11) MUTATED     36   77
  DEL PEAK 25(9Q21.11) WILD-TYPE  122  201
        clus
vv       DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  FEMALE                           36                            122
  MALE                             77                            201
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 25(9Q21.11) MUTATED                                      13
  DEL PEAK 25(9Q21.11) WILD-TYPE                                    58
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 25(9Q21.11) MUTATED                                                       46
  DEL PEAK 25(9Q21.11) WILD-TYPE                                                    116
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 25(9Q21.11) MUTATED                                                                  19
  DEL PEAK 25(9Q21.11) WILD-TYPE                                                                62
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 25(9Q21.11) MUTATED                                                 26
  DEL PEAK 25(9Q21.11) WILD-TYPE                                               52
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 25(9Q21.11) MUTATED                                                          5
  DEL PEAK 25(9Q21.11) WILD-TYPE                                                       16
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 25(9Q21.11) MUTATED                                                           3
  DEL PEAK 25(9Q21.11) WILD-TYPE                                                         5
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 25(9Q21.11) MUTATED                                          1
  DEL PEAK 25(9Q21.11) WILD-TYPE                                       12
D61V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 25(9Q21.11) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       13
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      46
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           19
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            26
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     1
                                                                   clus
vv                                                                  DEL PEAK 25(9Q21.11) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         58
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       116
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             62
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              52
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      12
[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"
D61V9, binary
                                cls
clus                               0   1
  DEL PEAK 25(9Q21.11) MUTATED     1 112
  DEL PEAK 25(9Q21.11) WILD-TYPE   5 318
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(9Q21.11) MUTATED      1  112
  DEL PEAK 25(9Q21.11) WILD-TYPE    5  318
     clus
vv    DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  NO                             1                              5
  YES                          112                            318
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 25(9Q21.11) MUTATED    88   4   3   5
  DEL PEAK 25(9Q21.11) WILD-TYPE 259  14  16  20
D61V10, multiclass
    clus
vv   DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  R0                           88                            259
  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                         5
                                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   204
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                                              5
  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"
D61V13, binary
                                cls
clus                               0   1
  DEL PEAK 25(9Q21.11) MUTATED     1  86
  DEL PEAK 25(9Q21.11) WILD-TYPE   3 227
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(9Q21.11) MUTATED      1   86
  DEL PEAK 25(9Q21.11) WILD-TYPE    3  227
                        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                                  3
  NOT HISPANIC OR LATINO                            227
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 26(10P12.31) MUTATION ANALYSIS
D62V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 26(10P12.31) MUTATED    33  27
  DEL PEAK 26(10P12.31) WILD-TYPE 221 123
  DEL PEAK 26(10P12.31) MUTATED DEL PEAK 26(10P12.31) WILD-TYPE 
                             60                             344 
  DEL PEAK 26(10P12.31) MUTATED DEL PEAK 26(10P12.31) WILD-TYPE 
                             27                             123 
$`DEL PEAK 26(10P12.31) MUTATED`
TCGA-B7-A5TI TCGA-BR-4267 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-7901 TCGA-BR-8059 
       19.56         6.18        19.33        26.10         3.45        14.43 
TCGA-BR-8060 TCGA-BR-8291 TCGA-BR-8365 TCGA-BR-8372 TCGA-BR-8486 TCGA-BR-A452 
       11.44        16.31        17.52        19.17        20.22         7.53 
TCGA-BR-A4IY TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8533 TCGA-CG-4301 
       12.89         0.07         0.07         0.10         0.13         3.02 
TCGA-CG-4455 TCGA-CG-4475 TCGA-CG-5732 TCGA-D7-6521 TCGA-D7-6528 TCGA-D7-6815 
       12.03        22.98        69.04        18.54        15.22        15.98 
TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8575 TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-EQ-A4SO 
       11.31        24.72        18.21        11.24         2.96        16.24 
TCGA-FP-7829 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HU-8249 TCGA-HU-A4H5 
       19.53         0.56         5.52         0.23        14.17        12.30 
TCGA-IN-8462 TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-R5-A7O7 TCGA-R5-A7ZF 
       18.81         1.41         6.44         6.74        45.67         8.52 
TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DZ TCGA-VQ-A8E0 
      115.69         8.94         5.79        48.79        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8PS TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A922 TCGA-VQ-A925 
       35.24        13.35        18.74        20.81         9.04         4.54 
TCGA-VQ-A928 TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6I TCGA-ZQ-A9CR 
        5.72        11.24        18.41        40.08        16.14         0.79 

$`DEL PEAK 26(10P12.31) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4279 
        6.97         4.64         7.43        18.35        30.90         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-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12         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        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       12.82         9.21        24.76        35.24        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 
       28.01        18.15        15.32        28.73        12.43         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       12.76        18.71        17.49         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 
       20.55         8.05         0.56        12.95         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        19.50        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-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       13.87         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       19.36        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 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8529 
       13.18         0.30         0.07         0.07         0.07         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        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 
        0.10        12.62        20.02        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-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        21.99         0.00         9.01        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-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07        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 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6817 
       18.61        17.85        13.35        17.19        10.26        12.79 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 
       10.55        12.33        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        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        13.71        11.31        11.44         9.76 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34         7.40         7.13         0.62 
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-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       18.08        26.47         1.51         5.92        14.27        12.59 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        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 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84         9.67         8.88         8.81        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45         3.39        18.38         5.36         5.19        13.08 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51         5.56         1.81         7.82        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG 
        2.53         5.56        60.56        20.15        37.64         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       19.73         9.86        18.21        61.25         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-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
       37.91        40.64       116.38        71.38        57.44        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E3 
       16.87        19.04         0.92         5.46        13.25        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       34.45        27.88        32.48         7.73        28.96        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-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       17.85         1.87         9.27        23.41        15.65        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       27.35        64.57        14.33        65.16        36.69        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       11.93        61.22        22.68         1.71        36.16         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
        9.50         9.73        52.24         2.01        55.43         6.58 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA69 
       64.18        21.04         2.66        42.54        22.09        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J 
       32.94        29.98        17.13        54.12        26.04        21.11 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        10.62 

  DEL PEAK 26(10P12.31) MUTATED DEL PEAK 26(10P12.31) WILD-TYPE 
                           0.07                            0.00 
  DEL PEAK 26(10P12.31) MUTATED DEL PEAK 26(10P12.31) WILD-TYPE 
                         115.69                          122.30 
  DEL PEAK 26(10P12.31) MUTATED DEL PEAK 26(10P12.31) WILD-TYPE 
                         13.185                          12.790 
[1] "0.1 - 115.7 (13.2)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.3"
D62V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 26(10P12.31) MUTATED         0        2        4        3         1
  DEL PEAK 26(10P12.31) WILD-TYPE       3       12       37       28        37
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 26(10P12.31) MUTATED          11         1         16          8
  DEL PEAK 26(10P12.31) WILD-TYPE        44         3         69         54
                                 vv
clus                              STAGE IIIC STAGE IV
  DEL PEAK 26(10P12.31) MUTATED            7       10
  DEL PEAK 26(10P12.31) WILD-TYPE         34       36
D62V3, multiclass
            clus
vv           DEL PEAK 26(10P12.31) MUTATED DEL PEAK 26(10P12.31) WILD-TYPE
  STAGE I                                0                               3
  STAGE IA                               2                              12
  STAGE IB                               4                              37
  STAGE II                               3                              28
  STAGE IIA                              1                              37
  STAGE IIB                             11                              44
  STAGE III                              1                               3
  STAGE IIIA                            16                              69
  STAGE IIIB                             8                              54
  STAGE IIIC                             7                              34
  STAGE IV                              10                              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 26(10P12.31) MUTATED     3  15  29  16
  DEL PEAK 26(10P12.31) WILD-TYPE  19  75 166 103
D62V4, multiclass
    clus
vv   DEL PEAK 26(10P12.31) MUTATED DEL PEAK 26(10P12.31) WILD-TYPE
  T1                             3                              19
  T2                            15                              75
  T3                            29                             166
  T4                            16                             103
[1] 4 2
[1] TRUE
[1] "dimension of 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(10P12.31) MUTATED    10  20  17  16
  DEL PEAK 26(10P12.31) WILD-TYPE 119  98  67  73
D62V5, multiclass
    clus
vv   DEL PEAK 26(10P12.31) MUTATED DEL PEAK 26(10P12.31) WILD-TYPE
  N0                            10                             119
  N1                            20                              98
  N2                            17                              67
  N3                            16                              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"
D62V6, binary
                                 cls
clus                                0   1
  DEL PEAK 26(10P12.31) MUTATED    58   4
  DEL PEAK 26(10P12.31) WILD-TYPE 329  26
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(10P12.31) MUTATED     58    4
  DEL PEAK 26(10P12.31) WILD-TYPE  329   26
   clus
vv  DEL PEAK 26(10P12.31) MUTATED DEL PEAK 26(10P12.31) WILD-TYPE
  0                            58                             329
  1                             4                              26
[1] 2 2
[1] FALSE
D62V7, binary
                                 cls
clus                                0   1
  DEL PEAK 26(10P12.31) MUTATED    22  44
  DEL PEAK 26(10P12.31) WILD-TYPE 136 234
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(10P12.31) MUTATED     22   44
  DEL PEAK 26(10P12.31) WILD-TYPE  136  234
        clus
vv       DEL PEAK 26(10P12.31) MUTATED DEL PEAK 26(10P12.31) WILD-TYPE
  FEMALE                            22                             136
  MALE                              44                             234
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 26(10P12.31) MUTATED                                       6
  DEL PEAK 26(10P12.31) WILD-TYPE                                    65
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 26(10P12.31) MUTATED                                                       22
  DEL PEAK 26(10P12.31) WILD-TYPE                                                    140
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 26(10P12.31) MUTATED                                                                  11
  DEL PEAK 26(10P12.31) WILD-TYPE                                                                70
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 26(10P12.31) MUTATED                                                 16
  DEL PEAK 26(10P12.31) WILD-TYPE                                               62
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 26(10P12.31) MUTATED                                                          5
  DEL PEAK 26(10P12.31) WILD-TYPE                                                       16
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 26(10P12.31) MUTATED                                                           2
  DEL PEAK 26(10P12.31) WILD-TYPE                                                         6
                                 vv
clus                              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 26(10P12.31) MUTATED                                          3
  DEL PEAK 26(10P12.31) WILD-TYPE                                       10
D62V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 26(10P12.31) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       22
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      3
                                                                   clus
vv                                                                  DEL PEAK 26(10P12.31) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          65
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        140
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              70
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               62
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       10
[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"
D62V9, binary
                                 cls
clus                                0   1
  DEL PEAK 26(10P12.31) MUTATED     1  65
  DEL PEAK 26(10P12.31) WILD-TYPE   5 365
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(10P12.31) MUTATED      1   65
  DEL PEAK 26(10P12.31) WILD-TYPE    5  365
     clus
vv    DEL PEAK 26(10P12.31) MUTATED DEL PEAK 26(10P12.31) WILD-TYPE
  NO                              1                               5
  YES                            65                             365
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 26(10P12.31) MUTATED    52   3   3   5
  DEL PEAK 26(10P12.31) WILD-TYPE 295  15  16  20
D62V10, multiclass
    clus
vv   DEL PEAK 26(10P12.31) MUTATED DEL PEAK 26(10P12.31) WILD-TYPE
  R0                            52                             295
  R1                             3                              15
  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"
D62V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 26(10P12.31) MUTATED      10                         3
  DEL PEAK 26(10P12.31) WILD-TYPE    78                         8
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 26(10P12.31) MUTATED                                           0
  DEL PEAK 26(10P12.31) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 26(10P12.31) MUTATED      43
  DEL PEAK 26(10P12.31) WILD-TYPE   231
D62V12, multiclass
                                           clus
vv                                          DEL PEAK 26(10P12.31) MUTATED
  ASIAN                                                                10
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                43
                                           clus
vv                                          DEL PEAK 26(10P12.31) WILD-TYPE
  ASIAN                                                                  78
  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"
D62V13, binary
                                 cls
clus                                0   1
  DEL PEAK 26(10P12.31) MUTATED     1  46
  DEL PEAK 26(10P12.31) WILD-TYPE   3 267
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(10P12.31) MUTATED      1   46
  DEL PEAK 26(10P12.31) WILD-TYPE    3  267
                        clus
vv                       DEL PEAK 26(10P12.31) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            46
                        clus
vv                       DEL PEAK 26(10P12.31) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             267
[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    41  32
  DEL PEAK 27(10Q22.3) WILD-TYPE 213 118
  DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE 
                            73                            331 
  DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE 
                            32                            118 
$`DEL PEAK 27(10Q22.3) MUTATED`
TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8291 TCGA-BR-8365 
       28.01        28.73         3.45        11.44        16.31        17.52 
TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4QI TCGA-CD-5799 
        5.39        20.22        13.87        22.26        13.64         3.25 
TCGA-CD-5802 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A4MG 
        0.30         0.07         0.10         3.42        12.43         6.58 
TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4466 
       12.20         7.99         4.01        14.01        12.03        18.97 
TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5730 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6527 
       22.98        36.00         4.01        19.13        18.54        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YX 
       15.22        15.98        12.79        21.14        14.27        15.16 
TCGA-EQ-8122 TCGA-FP-7829 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HU-8243 TCGA-HU-8249 
        7.99        19.53         5.52         0.23         5.92        14.17 
TCGA-HU-8604 TCGA-HU-A4G6 TCGA-HU-A4GH TCGA-IN-8462 TCGA-IN-A6RO TCGA-IN-A6RR 
       12.10        12.30        11.77        18.81         1.41         6.74 
TCGA-IN-A7NR TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A805 
        6.51        37.64        45.67         8.52         6.08         9.24 
TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        8.94         5.79        48.79         5.46        13.02        18.48 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91X 
       22.19        17.85         1.87        18.74         1.71         9.50 
TCGA-VQ-A91Y TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6A 
        9.73        64.18        21.04        11.24        40.08        32.94 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK 27(10Q22.3) WILD-TYPE`
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-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
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-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 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 
       24.76        35.24        23.93        15.42        18.15        15.32 
TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       12.43         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        12.26         9.60        20.55         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       12.95         2.66         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 
       19.50        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-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 
        0.26        15.85         3.72        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        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS 
        8.22        10.68        12.56         7.53         6.08         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        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        12.82         0.66        19.36        13.51         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        11.57         5.13         2.83 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 
       13.15        13.18         0.07         0.07         0.07         0.07 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
        0.13         0.16         0.10         0.10         0.13         0.13 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.10         9.34        11.31        11.61         0.10        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-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 
       54.08        29.98        47.05        19.07        21.99         0.00 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 
        9.01         7.07        12.00        30.97         6.97         1.02 
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-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07        65.10        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
       12.36        12.66        11.93        20.55        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       17.85        13.35        17.19        10.55        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-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       20.91        16.44         5.92        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44         9.76         2.96        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO 
        8.38         4.34         7.40         7.13         0.62        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 
       14.47        72.23        21.27        11.38         3.48        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-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       18.08        26.47         1.51        14.27        12.59        11.41 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 
       10.62         0.76        24.30         5.59        11.84        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         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI 
        8.81        27.42        21.21         3.45         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NT 
        5.36         5.19        13.08         6.44        12.59         5.56 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        1.81         7.82        13.51         2.53         5.56        60.56 
TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZI 
       20.15         3.72        19.73         9.86        18.21        61.25 
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        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        34.45        27.88        32.48         7.73        28.96 
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-A8PU 
        9.27        23.41        15.65        13.35        26.24        27.35 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        65.16        36.69        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Z 
       61.22        20.81        22.68        36.16         7.36        52.24 
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-A94P TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B 
        2.66        42.54        22.09        18.41        28.41        29.98 
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        21.11        12.43 
TCGA-ZA-A8F6 
       10.62 

  DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE 
                         64.18                         122.30 
  DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE 
                         12.30                          12.95 
[1] "0.1 - 64.2 (12.3)"  "0.0 - 122.3 (12.9)"
[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        5        5         7
  DEL PEAK 27(10Q22.3) WILD-TYPE       3       10       36       26        31
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 27(10Q22.3) MUTATED          11         1         17          8
  DEL PEAK 27(10Q22.3) WILD-TYPE        44         3         68         54
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 27(10Q22.3) MUTATED            8        8
  DEL PEAK 27(10Q22.3) WILD-TYPE         33       38
D63V3, multiclass
            clus
vv           DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE
  STAGE I                               0                              3
  STAGE IA                              4                             10
  STAGE IB                              5                             36
  STAGE II                              5                             26
  STAGE IIA                             7                             31
  STAGE IIB                            11                             44
  STAGE III                             1                              3
  STAGE IIIA                           17                             68
  STAGE IIIB                            8                             54
  STAGE IIIC                            8                             33
  STAGE IV                              8                             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 27(10Q22.3) MUTATED     4  19  37  14
  DEL PEAK 27(10Q22.3) WILD-TYPE  18  71 158 105
D63V4, multiclass
    clus
vv   DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE
  T1                            4                             18
  T2                           19                             71
  T3                           37                            158
  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    18  21  14  21
  DEL PEAK 27(10Q22.3) WILD-TYPE 111  97  70  68
D63V5, multiclass
    clus
vv   DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE
  N0                           18                            111
  N1                           21                             97
  N2                           14                             70
  N3                           21                             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"
D63V6, binary
                                cls
clus                               0   1
  DEL PEAK 27(10Q22.3) MUTATED    69   6
  DEL PEAK 27(10Q22.3) WILD-TYPE 318  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10Q22.3) MUTATED     69    6
  DEL PEAK 27(10Q22.3) WILD-TYPE  318   24
   clus
vv  DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE
  0                           69                            318
  1                            6                             24
[1] 2 2
[1] FALSE
D63V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(10Q22.3) MUTATED    26  52
  DEL PEAK 27(10Q22.3) WILD-TYPE 132 226
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10Q22.3) MUTATED     26   52
  DEL PEAK 27(10Q22.3) WILD-TYPE  132  226
        clus
vv       DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE
  FEMALE                           26                            132
  MALE                             52                            226
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 27(10Q22.3) MUTATED                                       5
  DEL PEAK 27(10Q22.3) WILD-TYPE                                    66
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 27(10Q22.3) MUTATED                                                       25
  DEL PEAK 27(10Q22.3) WILD-TYPE                                                    137
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 27(10Q22.3) MUTATED                                                                  19
  DEL PEAK 27(10Q22.3) WILD-TYPE                                                                62
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 27(10Q22.3) MUTATED                                                 19
  DEL PEAK 27(10Q22.3) WILD-TYPE                                               59
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 27(10Q22.3) MUTATED                                                          3
  DEL PEAK 27(10Q22.3) WILD-TYPE                                                       18
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 27(10Q22.3) MUTATED                                                           2
  DEL PEAK 27(10Q22.3) WILD-TYPE                                                         6
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 27(10Q22.3) MUTATED                                          4
  DEL PEAK 27(10Q22.3) WILD-TYPE                                        9
D63V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 27(10Q22.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      25
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           19
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     4
                                                                   clus
vv                                                                  DEL PEAK 27(10Q22.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         66
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       137
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             62
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              59
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       9
[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"
D63V9, binary
                                cls
clus                               0   1
  DEL PEAK 27(10Q22.3) MUTATED     1  77
  DEL PEAK 27(10Q22.3) WILD-TYPE   5 353
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10Q22.3) MUTATED      1   77
  DEL PEAK 27(10Q22.3) WILD-TYPE    5  353
     clus
vv    DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE
  NO                             1                              5
  YES                           77                            353
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 27(10Q22.3) MUTATED    57   2   4   4
  DEL PEAK 27(10Q22.3) WILD-TYPE 290  16  15  21
D63V10, multiclass
    clus
vv   DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE
  R0                           57                            290
  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                         6
                                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      46
  DEL PEAK 27(10Q22.3) WILD-TYPE   228
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                                                               46
                                           clus
vv                                          DEL PEAK 27(10Q22.3) WILD-TYPE
  ASIAN                                                                 72
  BLACK OR AFRICAN AMERICAN                                              6
  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"
D63V13, binary
                                cls
clus                               0   1
  DEL PEAK 27(10Q22.3) MUTATED     1  52
  DEL PEAK 27(10Q22.3) WILD-TYPE   3 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10Q22.3) MUTATED      1   52
  DEL PEAK 27(10Q22.3) WILD-TYPE    3  261
                        clus
vv                       DEL PEAK 27(10Q22.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           52
                        clus
vv                       DEL PEAK 27(10Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            261
[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    61  48
  DEL PEAK 28(10Q23.31) WILD-TYPE 193 102
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                            109                             295 
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                             48                             102 
$`DEL PEAK 28(10Q23.31) MUTATED`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-6455 TCGA-BR-7704 TCGA-BR-7716 
       11.70         6.61        18.35        13.87        35.24        28.01 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8291 TCGA-BR-8295 
       28.73         3.45        17.49        11.44        16.31         2.20 
TCGA-BR-8365 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       17.52         4.31        14.04         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8683 TCGA-BR-A4CQ TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5802 
       20.22         9.86        22.26        13.64         3.25         0.30 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-A486 TCGA-CD-A48A 
        0.07         0.07         0.07         0.10         3.42        12.43 
TCGA-CD-A4MH TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       12.20        27.02         7.99         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-5718 TCGA-CG-5725 
       47.05        12.03        21.99        18.97        36.00        15.02 
TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6527 
        4.01        69.04        12.36        19.13        18.54        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A6F0 
       15.22        15.98        12.79        21.14        14.27         2.96 
TCGA-EQ-8122 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
        7.99         3.48        19.53        13.58         0.56         5.52 
TCGA-FP-A8CX TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GH TCGA-HU-A4GT 
        0.23         5.92        14.17        12.10        11.77         6.51 
TCGA-HU-A4GU TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RO 
        6.25        12.30        27.42        18.81        18.38         1.41 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NU TCGA-KB-A93H TCGA-R5-A7O7 
        6.44         6.74         6.51         1.81        37.64        45.67 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DL 
        8.52         6.08         9.24         8.94         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       48.79         5.46        13.02        18.48        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91X 
        1.87        13.35        36.69        18.74         1.71         9.50 
TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R 
        9.73         9.04         5.72        64.18        21.04        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6G TCGA-VQ-AA6I 
       11.24        18.41        40.08        32.94        26.04        16.14 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK 28(10Q23.31) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 
       26.70        19.56        11.01         9.47         9.44         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.64         7.43        30.90         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       34.68        15.95        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        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 
       12.82         9.21        24.76        23.93        15.42        18.15 
TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 
       15.32        12.43         9.07        12.76        18.71        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        12.26         9.60        20.55         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       12.95         2.66        15.58         7.40         6.18        19.50 
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-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 
        7.53         0.49        11.54        15.81        16.44        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        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        12.82         0.66        19.36        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        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8527 TCGA-CD-8529 
        2.83        13.15        13.18         0.07         0.07         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.16         0.10         0.10         0.13         0.13         0.10 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        9.34        11.31        11.61         6.58         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 
       20.02         3.02        15.95         1.02         8.05        54.08 
TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
       19.07         0.00         9.01         7.07        12.00        22.98 
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-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5733 
      105.07        12.03        28.96        79.07        65.10        21.07 
TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
        7.99        12.66        11.93        20.55        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       17.85        13.35        17.19        10.55        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        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 
       13.71        11.24        11.31        11.44         9.76        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO 
        8.38         4.34         7.40         7.13         0.62        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 
       14.47        72.23        21.27        11.38        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       17.06        59.54         5.03        18.08        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.27        12.59        11.41        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        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        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
        0.26         2.10        12.95        19.36        23.84         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ 
        8.88         8.81        21.21         3.45         3.39         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X 
        5.19        13.08        12.59         5.56         7.82        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        60.56        20.15         3.72        19.73 
TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT 
        9.86        18.21        61.25         4.60        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-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44        35.61        16.87        19.04 
TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        35.24        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
        7.73        28.96        34.29        46.26        16.31         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       12.79         2.70         9.27        23.41        15.65        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E 
       27.35        64.57        14.33        65.16        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Z 
       61.22        20.81        22.68        36.16         7.36        52.24 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A94P TCGA-VQ-A94U 
        2.01        55.43         4.54         6.58         2.66        22.09 
TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6J TCGA-VQ-AA6K 
       28.41        29.98        17.13        54.12        21.11        12.43 
TCGA-ZA-A8F6 
       10.62 

  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                           0.07                            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 
                          12.36                           12.95 
[1] "0.1 - 69.0 (12.4)"  "0.0 - 122.3 (12.9)"
[1] "hr=" "1.4"
D64V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 28(10Q23.31) MUTATED         1        4       12        7         9
  DEL PEAK 28(10Q23.31) WILD-TYPE       2       10       29       24        29
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 28(10Q23.31) MUTATED          13         1         25         13
  DEL PEAK 28(10Q23.31) WILD-TYPE        42         3         60         49
                                 vv
clus                              STAGE IIIC STAGE IV
  DEL PEAK 28(10Q23.31) MUTATED           11       13
  DEL PEAK 28(10Q23.31) WILD-TYPE         30       33
D64V3, multiclass
            clus
vv           DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  STAGE I                                1                               2
  STAGE IA                               4                              10
  STAGE IB                              12                              29
  STAGE II                               7                              24
  STAGE IIA                              9                              29
  STAGE IIB                             13                              42
  STAGE III                              1                               3
  STAGE IIIA                            25                              60
  STAGE IIIB                            13                              49
  STAGE IIIC                            11                              30
  STAGE IV                              13                              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 28(10Q23.31) MUTATED     6  29  52  22
  DEL PEAK 28(10Q23.31) WILD-TYPE  16  61 143  97
D64V4, multiclass
    clus
vv   DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  T1                             6                              16
  T2                            29                              61
  T3                            52                             143
  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   31 29 21 29
  DEL PEAK 28(10Q23.31) WILD-TYPE 98 89 63 60
D64V5, multiclass
    clus
vv   DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  N0                            31                              98
  N1                            29                              89
  N2                            21                              63
  N3                            29                              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"
D64V6, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10Q23.31) MUTATED   101   7
  DEL PEAK 28(10Q23.31) WILD-TYPE 286  23
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10Q23.31) MUTATED    101    7
  DEL PEAK 28(10Q23.31) WILD-TYPE  286   23
   clus
vv  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  0                           101                             286
  1                             7                              23
[1] 2 2
[1] FALSE
D64V7, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10Q23.31) MUTATED    40  74
  DEL PEAK 28(10Q23.31) WILD-TYPE 118 204
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10Q23.31) MUTATED     40   74
  DEL PEAK 28(10Q23.31) WILD-TYPE  118  204
        clus
vv       DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  FEMALE                            40                             118
  MALE                              74                             204
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 28(10Q23.31) MUTATED                                       7
  DEL PEAK 28(10Q23.31) WILD-TYPE                                    64
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 28(10Q23.31) MUTATED                                                       39
  DEL PEAK 28(10Q23.31) WILD-TYPE                                                    123
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 28(10Q23.31) MUTATED                                                                  31
  DEL PEAK 28(10Q23.31) WILD-TYPE                                                                50
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 28(10Q23.31) MUTATED                                                 25
  DEL PEAK 28(10Q23.31) WILD-TYPE                                               53
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 28(10Q23.31) MUTATED                                                          5
  DEL PEAK 28(10Q23.31) WILD-TYPE                                                       16
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 28(10Q23.31) MUTATED                                                           3
  DEL PEAK 28(10Q23.31) WILD-TYPE                                                         5
                                 vv
clus                              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 28(10Q23.31) MUTATED                                          4
  DEL PEAK 28(10Q23.31) WILD-TYPE                                        9
D64V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 28(10Q23.31) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       39
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            31
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             25
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      4
                                                                   clus
vv                                                                  DEL PEAK 28(10Q23.31) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          64
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        123
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              50
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               53
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                        9
[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"
D64V9, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10Q23.31) MUTATED     1 113
  DEL PEAK 28(10Q23.31) WILD-TYPE   5 317
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10Q23.31) MUTATED      1  113
  DEL PEAK 28(10Q23.31) WILD-TYPE    5  317
     clus
vv    DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  NO                              1                               5
  YES                           113                             317
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 28(10Q23.31) MUTATED    90   3   5   6
  DEL PEAK 28(10Q23.31) WILD-TYPE 257  15  14  19
D64V10, multiclass
    clus
vv   DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  R0                            90                             257
  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                         5
                                 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      70
  DEL PEAK 28(10Q23.31) WILD-TYPE   204
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                                                                70
                                           clus
vv                                          DEL PEAK 28(10Q23.31) WILD-TYPE
  ASIAN                                                                  67
  BLACK OR AFRICAN AMERICAN                                               5
  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"
D64V13, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10Q23.31) MUTATED     1  74
  DEL PEAK 28(10Q23.31) WILD-TYPE   3 239
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10Q23.31) MUTATED      1   74
  DEL PEAK 28(10Q23.31) WILD-TYPE    3  239
                        clus
vv                       DEL PEAK 28(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            74
                        clus
vv                       DEL PEAK 28(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             239
[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    52  40
  DEL PEAK 29(11P15.5) WILD-TYPE 202 110
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                            92                            312 
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                            40                            110 
$`DEL PEAK 29(11P15.5) MUTATED`
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4279 TCGA-BR-6564 TCGA-BR-7703 
        6.61         6.97        18.35         9.57        26.10        24.76 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-8080 TCGA-BR-8297 
       35.24        15.42        28.01        28.73         9.60         7.40 
TCGA-BR-8369 TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-CD-5799 TCGA-CD-5800 
       14.04         1.48         0.72         0.53         3.25        13.15 
TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-A48A TCGA-CG-4304 
        0.30         0.07         0.07         0.07        12.43        27.02 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-5717 
       29.98        47.05        19.07        21.99        18.97         6.97 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-5579 
       12.03        15.02         4.01        69.04        12.66        11.93 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       20.55        18.84        18.54        10.26        15.22        15.98 
TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A74A TCGA-EQ-5647 TCGA-F1-6875 TCGA-F1-A72C 
       21.14        14.27         7.40         0.62        72.23        11.38 
TCGA-FP-8211 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-A4GD TCGA-HU-A4H0 
       13.58        26.47         5.92        12.59        22.75         2.10 
TCGA-HU-A4H5 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN 
       12.30        18.81         3.39        18.38         5.19        13.08 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IP-7968 TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE 
        6.44         6.74         2.53        37.64        45.67        18.21 
TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DU 
       16.67        37.91         8.94        35.61        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       13.25        13.02        18.48        34.45        32.48         7.73 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A91E 
       22.19        17.85        13.35        27.35        14.33        11.93 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94U 
        9.73        52.24         4.54        21.04        42.54        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA68 
       18.41        40.08 

$`DEL PEAK 29(11P15.5) WILD-TYPE`
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-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 
        4.64         7.43        30.90         6.18         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-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        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 
        9.21        23.93        18.15        15.32        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        12.76        18.71        17.49        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69        12.26        20.55         8.05         0.56        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 
        2.66        16.31         2.20        15.58         6.18        19.50 
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        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         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        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08        22.26        13.41        13.51        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
       14.17        12.82         0.66        19.36        13.51         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 
        2.83        13.18         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.16         0.10         0.10         0.13         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        3.42         9.34        11.31        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 
        0.10        12.62        20.02         3.02        15.95         1.02 
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-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01         7.07        12.00        22.98        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-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        79.07        65.10        21.07         7.99        12.36 
TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6817 
       19.13        18.61        17.85        13.35        17.19        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        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 
       15.16        13.78        14.76        13.71        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44         9.76         2.96        15.65         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 
        7.13         7.99        16.24        14.47        21.27         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-A8CX TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 
        0.56         5.52         0.23        18.08         1.51        14.27 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
        5.59        12.30        11.84        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-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.25        10.19         0.26        12.95        19.36        23.84 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
        9.67         8.88         8.81        27.42        21.21         3.45 
TCGA-IN-A6RJ TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        5.36         1.41        12.59         6.51         5.56         1.81 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG 
        7.82        13.51         5.56        60.56        20.15         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       19.73         9.86         8.52        61.25         6.08         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-A8NB TCGA-SW-A7EA 
      115.69       116.38        71.38        57.44        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P8 
        5.79         0.92        35.24        21.73        27.88        28.96 
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-A8PT TCGA-VQ-A8PX 
        1.87         9.27        23.41        15.65        26.24        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       65.16        36.69        11.70        61.22        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A922 
       22.68         1.71        36.16         7.36         9.50         9.04 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P 
        2.01        55.43         6.58         5.72        64.18         2.66 
TCGA-VQ-A94T TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       11.24        28.41        32.94        29.98        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        21.11        12.43        10.62         0.79 

  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                          0.07                           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 
                        14.300                         12.495 
[1] "0.1 - 72.2 (14.3)"  "0.0 - 122.3 (12.5)"
[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         5
  DEL PEAK 29(11P15.5) WILD-TYPE       2       11       32       20        33
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 29(11P15.5) MUTATED           8         0         24         12
  DEL PEAK 29(11P15.5) WILD-TYPE        47         4         61         50
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 29(11P15.5) MUTATED           10       10
  DEL PEAK 29(11P15.5) WILD-TYPE         31       36
D65V3, multiclass
            clus
vv           DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  STAGE I                               1                              2
  STAGE IA                              3                             11
  STAGE IB                              9                             32
  STAGE II                             11                             20
  STAGE IIA                             5                             33
  STAGE IIB                             8                             47
  STAGE III                             0                              4
  STAGE IIIA                           24                             61
  STAGE IIIB                           12                             50
  STAGE IIIC                           10                             31
  STAGE IV                             10                             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 29(11P15.5) MUTATED     5  31  40  18
  DEL PEAK 29(11P15.5) WILD-TYPE  17  59 155 101
D65V4, multiclass
    clus
vv   DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  T1                            5                             17
  T2                           31                             59
  T3                           40                            155
  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  20  21
  DEL PEAK 29(11P15.5) WILD-TYPE 105  88  64  68
D65V5, multiclass
    clus
vv   DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  N0                           24                            105
  N1                           30                             88
  N2                           20                             64
  N3                           21                             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 301  23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(11P15.5) MUTATED     86    7
  DEL PEAK 29(11P15.5) WILD-TYPE  301   23
   clus
vv  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  0                           86                            301
  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 127 212
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(11P15.5) MUTATED     31   66
  DEL PEAK 29(11P15.5) WILD-TYPE  127  212
        clus
vv       DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  FEMALE                           31                            127
  MALE                             66                            212
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 29(11P15.5) MUTATED                                       9
  DEL PEAK 29(11P15.5) WILD-TYPE                                    62
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 29(11P15.5) MUTATED                                                       31
  DEL PEAK 29(11P15.5) WILD-TYPE                                                    131
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 29(11P15.5) MUTATED                                                                  21
  DEL PEAK 29(11P15.5) WILD-TYPE                                                                60
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 29(11P15.5) MUTATED                                                 23
  DEL PEAK 29(11P15.5) WILD-TYPE                                               55
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 29(11P15.5) MUTATED                                                          5
  DEL PEAK 29(11P15.5) WILD-TYPE                                                       16
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 29(11P15.5) MUTATED                                                           5
  DEL PEAK 29(11P15.5) WILD-TYPE                                                         3
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 29(11P15.5) MUTATED                                          3
  DEL PEAK 29(11P15.5) WILD-TYPE                                       10
D65V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 29(11P15.5) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      31
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           21
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            23
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     3
                                                                   clus
vv                                                                  DEL PEAK 29(11P15.5) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             60
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              55
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      10
[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"
D65V9, binary
                                cls
clus                               0   1
  DEL PEAK 29(11P15.5) MUTATED     1  96
  DEL PEAK 29(11P15.5) WILD-TYPE   5 334
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(11P15.5) MUTATED      1   96
  DEL PEAK 29(11P15.5) WILD-TYPE    5  334
     clus
vv    DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  NO                             1                              5
  YES                           96                            334
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 29(11P15.5) MUTATED    74   3   7   8
  DEL PEAK 29(11P15.5) WILD-TYPE 273  15  12  17
D65V10, multiclass
    clus
vv   DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  R0                           74                            273
  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                         7
                                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   211
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                                              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  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"
D65V13, binary
                                cls
clus                               0   1
  DEL PEAK 29(11P15.5) MUTATED     1  61
  DEL PEAK 29(11P15.5) WILD-TYPE   3 252
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(11P15.5) MUTATED      1   61
  DEL PEAK 29(11P15.5) WILD-TYPE    3  252
                        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                                  3
  NOT HISPANIC OR LATINO                            252
[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    50  41
  DEL PEAK 30(11Q23.2) WILD-TYPE 204 109
  DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE 
                            91                            313 
  DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE 
                            41                            109 
$`DEL PEAK 30(11Q23.2) MUTATED`
TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6564 
        6.97        18.35         6.18         9.57        17.29        26.10 
TCGA-BR-6709 TCGA-BR-7722 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8289 
       12.16        15.32        17.49        11.44         9.60         2.66 
TCGA-BR-8297 TCGA-BR-8365 TCGA-BR-8486 TCGA-BR-8687 TCGA-BR-A4CQ TCGA-BR-A4CS 
        7.40        17.52        20.22         8.22        22.26         1.48 
TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 
        0.72        13.51         1.15        13.64         3.25        13.15 
TCGA-CD-5802 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-A48A TCGA-CG-4301 
        0.30         0.07         0.13         0.10        12.43         3.02 
TCGA-CG-4304 TCGA-CG-4437 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-5718 TCGA-CG-5719 
       27.02         8.05        29.98        12.03        36.00         1.02 
TCGA-CG-5724 TCGA-CG-5725 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6521 TCGA-D7-6527 
       12.03        15.02        12.66        11.93        18.54        10.26 
TCGA-D7-6815 TCGA-D7-8575 TCGA-D7-A4YT TCGA-D7-A6EZ TCGA-D7-A74A TCGA-EQ-5647 
       15.98        18.21        14.27         9.76         7.40         0.62 
TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HJ-7597 
       14.07        17.06        13.58         0.56         0.23        26.47 
TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4H0 
       14.17         0.76         3.25        22.75        11.77         2.10 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-AB1X 
       23.84         9.67         1.41         6.44         5.56        13.51 
TCGA-IP-7968 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A8N1 
        2.53        45.67        18.21         6.08         9.24       115.69 
TCGA-RD-A8N6 TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8P5 TCGA-VQ-A8PJ 
        8.94         0.92        48.79        13.25         7.73         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A91A TCGA-VQ-A91Q TCGA-VQ-A91Z 
       17.85        13.35        27.35        36.69        20.81        52.24 
TCGA-VQ-A922 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA6F 
        9.04        64.18        21.04        42.54        11.24        54.12 
TCGA-VQ-AA6K 
       12.43 

$`DEL PEAK 30(11Q23.2) WILD-TYPE`
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-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6452 
        6.61         4.64         7.43        30.90         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        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 
       35.24        23.93        15.42        28.01        18.15        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 
       12.43         3.45         9.07        12.76        18.71        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69        12.26        20.55         8.05         0.56        12.95 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       16.31         2.20        15.58         6.18        19.50        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        19.17        14.79         0.26        15.85 
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 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 
       11.54        15.81        16.44         9.86        15.68        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
       12.56        13.87         7.53         6.08        13.41        13.51 
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        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM 
       19.36         0.46        20.65        20.42        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        2.83        13.18         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.10         0.16         0.10         0.13         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        3.42         9.34        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 
        0.10        12.62        20.02        15.95         1.02         7.99 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 
       54.08         4.01        14.01        47.05        19.07        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
        0.00         9.01        18.97         7.07        12.00        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       30.97         6.97         0.99         6.02         0.99       105.07 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
        7.99        12.36        19.13        20.55        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 
       17.85        13.35        17.19        15.22        12.79        10.55 
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-D7-8576 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        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        13.71        11.24        11.31        11.44 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 
        2.96        15.65         8.38         4.34         7.13         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
       16.24        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF TCGA-HF-A5NB 
       19.53        22.29        59.54         5.03         5.52        18.08 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        14.27        12.59        11.41        12.10 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       10.62        24.30         5.59        12.30        11.84        24.20 
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-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
        6.25        10.19         0.26        12.95        19.36        12.30 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        8.88         8.81        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR 
        3.39        18.38         5.36         5.19        13.08         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-KB-A6F5 TCGA-KB-A6F7 
       12.59         6.51         1.81         7.82         5.56        60.56 
TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZF 
       20.15        37.64         3.72        19.73         9.86         8.52 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
       61.25         4.60        11.05         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-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DZ 
       35.61        16.87        19.04         5.79         5.46        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       18.48        35.24        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       28.96        34.29        46.26        16.31        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       12.79         1.87         9.27        23.41        15.65        26.24 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       64.57        14.33        65.16        11.70        11.93        61.22 
TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       18.74        22.68         1.71        36.16         7.36         9.50 
TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        9.73         2.01        55.43         4.54         6.58         5.72 
TCGA-VQ-A94P TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
        2.66        22.09        18.41        40.08        28.41        32.94 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       29.98        17.13        26.04        16.14        21.11        10.62 
TCGA-ZQ-A9CR 
        0.79 

  DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE 
                          0.07                           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 
                         12.16                          12.95 
[1] "0.1 - 115.7 (12.2)" "0.0 - 122.3 (12.9)"
[1] "hr=" "1.5"
D66V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 30(11Q23.2) MUTATED         1        5        6       10         8
  DEL PEAK 30(11Q23.2) WILD-TYPE       2        9       35       21        30
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 30(11Q23.2) MUTATED           8         1         21         12
  DEL PEAK 30(11Q23.2) WILD-TYPE        47         3         64         50
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 30(11Q23.2) MUTATED           10       13
  DEL PEAK 30(11Q23.2) WILD-TYPE         31       33
D66V3, multiclass
            clus
vv           DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE
  STAGE I                               1                              2
  STAGE IA                              5                              9
  STAGE IB                              6                             35
  STAGE II                             10                             21
  STAGE IIA                             8                             30
  STAGE IIB                             8                             47
  STAGE III                             1                              3
  STAGE IIIA                           21                             64
  STAGE IIIB                           12                             50
  STAGE IIIC                           10                             31
  STAGE IV                             13                             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 30(11Q23.2) MUTATED     7  21  44  24
  DEL PEAK 30(11Q23.2) WILD-TYPE  15  69 151  95
D66V4, multiclass
    clus
vv   DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE
  T1                            7                             15
  T2                           21                             69
  T3                           44                            151
  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    25  24  26  20
  DEL PEAK 30(11Q23.2) WILD-TYPE 104  94  58  69
D66V5, multiclass
    clus
vv   DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE
  N0                           25                            104
  N1                           24                             94
  N2                           26                             58
  N3                           20                             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"
D66V6, binary
                                cls
clus                               0   1
  DEL PEAK 30(11Q23.2) MUTATED    80   9
  DEL PEAK 30(11Q23.2) WILD-TYPE 307  21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11Q23.2) MUTATED     80    9
  DEL PEAK 30(11Q23.2) WILD-TYPE  307   21
   clus
vv  DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE
  0                           80                            307
  1                            9                             21
[1] 2 2
[1] FALSE
D66V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(11Q23.2) MUTATED    32  65
  DEL PEAK 30(11Q23.2) WILD-TYPE 126 213
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11Q23.2) MUTATED     32   65
  DEL PEAK 30(11Q23.2) WILD-TYPE  126  213
        clus
vv       DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE
  FEMALE                           32                            126
  MALE                             65                            213
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 30(11Q23.2) MUTATED                                      10
  DEL PEAK 30(11Q23.2) WILD-TYPE                                    61
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 30(11Q23.2) MUTATED                                                       34
  DEL PEAK 30(11Q23.2) WILD-TYPE                                                    128
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 30(11Q23.2) MUTATED                                                                  20
  DEL PEAK 30(11Q23.2) WILD-TYPE                                                                61
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 30(11Q23.2) MUTATED                                                 22
  DEL PEAK 30(11Q23.2) WILD-TYPE                                               56
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 30(11Q23.2) MUTATED                                                          6
  DEL PEAK 30(11Q23.2) WILD-TYPE                                                       15
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 30(11Q23.2) MUTATED                                                           2
  DEL PEAK 30(11Q23.2) WILD-TYPE                                                         6
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 30(11Q23.2) MUTATED                                          3
  DEL PEAK 30(11Q23.2) WILD-TYPE                                       10
D66V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 30(11Q23.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       10
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      34
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           20
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            22
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     3
                                                                   clus
vv                                                                  DEL PEAK 30(11Q23.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         61
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             61
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              56
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      10
[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"
D66V9, binary
                                cls
clus                               0   1
  DEL PEAK 30(11Q23.2) MUTATED     1  96
  DEL PEAK 30(11Q23.2) WILD-TYPE   5 334
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11Q23.2) MUTATED      1   96
  DEL PEAK 30(11Q23.2) WILD-TYPE    5  334
     clus
vv    DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE
  NO                             1                              5
  YES                           96                            334
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 30(11Q23.2) MUTATED    72   7   5   5
  DEL PEAK 30(11Q23.2) WILD-TYPE 275  11  14  20
D66V10, multiclass
    clus
vv   DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE
  R0                           72                            275
  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                         9
                                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      59
  DEL PEAK 30(11Q23.2) WILD-TYPE   215
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                                                               59
                                           clus
vv                                          DEL PEAK 30(11Q23.2) WILD-TYPE
  ASIAN                                                                 69
  BLACK OR AFRICAN AMERICAN                                              9
  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"
D66V13, binary
                                cls
clus                               0   1
  DEL PEAK 30(11Q23.2) MUTATED     1  66
  DEL PEAK 30(11Q23.2) WILD-TYPE   3 247
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11Q23.2) MUTATED      1   66
  DEL PEAK 30(11Q23.2) WILD-TYPE    3  247
                        clus
vv                       DEL PEAK 30(11Q23.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           66
                        clus
vv                       DEL PEAK 30(11Q23.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            247
[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  33
  DEL PEAK 31(12P13.1) WILD-TYPE 218 117
  DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE 
                            69                            335 
  DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE 
                            33                            117 
$`DEL PEAK 31(12P13.1) MUTATED`
TCGA-BR-4183 TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6709 TCGA-BR-7704 
        6.61         6.18        17.29        19.33        12.16        35.24 
TCGA-BR-7715 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8289 TCGA-BR-8362 TCGA-BR-8369 
       15.42         3.45        11.44         2.66        13.08        14.04 
TCGA-BR-8483 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-A4CQ TCGA-CD-5800 TCGA-CD-8524 
        5.39        11.54         9.86        22.26        13.15         0.07 
TCGA-CD-8527 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH 
        0.07         0.13         3.42        11.31        12.43        12.20 
TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4441 TCGA-CG-4477 TCGA-CG-5725 TCGA-CG-5732 
        3.02         7.99        14.01        30.97        15.02        69.04 
TCGA-D7-6519 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-A4YT TCGA-D7-A74A 
       20.55        15.22        12.79        12.33        14.27         7.40 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-HU-8245 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.62         7.99        72.23        12.59        23.84        12.30 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A7NU TCGA-IP-7968 TCGA-R5-A7O7 
        3.39        18.38         5.19         1.81         2.53        45.67 
TCGA-RD-A8MW TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8P3 TCGA-VQ-A8PJ 
       37.91        35.61         5.46        13.02        32.48         2.70 
TCGA-VQ-A8PM TCGA-VQ-A8PY TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X 
        1.87        14.33        18.74         1.71        36.16         9.50 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O 
       52.24         9.04         2.01         5.72        64.18        21.04 
TCGA-VQ-AA6D TCGA-VQ-AA6I TCGA-ZQ-A9CR 
       17.13        16.14         0.79 

$`DEL PEAK 31(12P13.1) WILD-TYPE`
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-4191 TCGA-BR-4201 TCGA-BR-4279 
        6.97         4.64         7.43        18.35        30.90         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        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        24.76        23.93        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73        12.43         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.56        12.95        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         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        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        0.26        15.85         3.72        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        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 
        7.53         0.49        15.81        16.44        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS 
       10.68        12.56        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 
       13.41        13.51        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        12.82         0.66        19.36        13.51         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 
        2.83         3.25        13.18         0.30         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI 
        0.13         0.10         9.34        11.61         6.58         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       12.62        20.02        27.02        15.95         1.02         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        29.98        47.05        19.07        12.03 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       21.99         0.00         9.01        18.97         7.07        12.00 
TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       22.98         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 
       17.19        10.26        15.98        10.55        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-A4YY TCGA-D7-A4Z0 
       20.91        16.44         5.92        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       13.71        11.24        11.31        11.44         9.76         2.96 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 
       15.65         8.38         4.34         7.13        16.24        14.47 
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-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        0.23        18.08        26.47         1.51         5.92        14.27 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
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-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       19.36         9.67         8.88         8.81        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
        3.45        18.81         5.36        13.08         1.41         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X 
        6.74        12.59         6.51         5.56         7.82        13.51 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        60.56        20.15        37.64         3.72        19.73 
TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
        9.86        18.21         8.52        61.25         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-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-A8DV 
       16.87        19.04         5.79         0.92        48.79        13.25 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P5 
       18.48        35.24        21.73        34.45        27.88         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       28.96        34.29        46.26        16.31        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       12.79        17.85         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       26.24        27.35        64.57        65.16        36.69        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91Y 
       11.93        61.22        20.81        22.68         7.36         9.73 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
       55.43         4.54         6.58         2.66        42.54        11.24 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       22.09        18.41        40.08        28.41        32.94        29.98 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        21.11        12.43        10.62 

  DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE 
                          0.07                           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 
                         12.33                          12.95 
[1] "0.1 - 72.2 (12.3)"  "0.0 - 122.3 (12.9)"
[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       10        5         6
  DEL PEAK 31(12P13.1) WILD-TYPE       2       13       31       26        32
                                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        48         4         67         53
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 31(12P13.1) MUTATED            4       11
  DEL PEAK 31(12P13.1) WILD-TYPE         37       35
D67V3, multiclass
            clus
vv           DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE
  STAGE I                               1                              2
  STAGE IA                              1                             13
  STAGE IB                             10                             31
  STAGE II                              5                             26
  STAGE IIA                             6                             32
  STAGE IIB                             7                             48
  STAGE III                             0                              4
  STAGE IIIA                           18                             67
  STAGE IIIB                            9                             53
  STAGE IIIC                            4                             37
  STAGE IV                             11                             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 31(12P13.1) MUTATED     1  22  34  15
  DEL PEAK 31(12P13.1) WILD-TYPE  21  68 161 104
D67V4, multiclass
    clus
vv   DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE
  T1                            1                             21
  T2                           22                             68
  T3                           34                            161
  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    21  21  14  16
  DEL PEAK 31(12P13.1) WILD-TYPE 108  97  70  73
D67V5, multiclass
    clus
vv   DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE
  N0                           21                            108
  N1                           21                             97
  N2                           14                             70
  N3                           16                             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"
D67V6, binary
                                cls
clus                               0   1
  DEL PEAK 31(12P13.1) MUTATED    64   6
  DEL PEAK 31(12P13.1) WILD-TYPE 323  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(12P13.1) MUTATED     64    6
  DEL PEAK 31(12P13.1) WILD-TYPE  323   24
   clus
vv  DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE
  0                           64                            323
  1                            6                             24
[1] 2 2
[1] FALSE
D67V7, binary
                                cls
clus                               0   1
  DEL PEAK 31(12P13.1) MUTATED    28  46
  DEL PEAK 31(12P13.1) WILD-TYPE 130 232
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(12P13.1) MUTATED     28   46
  DEL PEAK 31(12P13.1) WILD-TYPE  130  232
        clus
vv       DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE
  FEMALE                           28                            130
  MALE                             46                            232
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 31(12P13.1) MUTATED                                       3
  DEL PEAK 31(12P13.1) WILD-TYPE                                    68
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 31(12P13.1) MUTATED                                                       30
  DEL PEAK 31(12P13.1) WILD-TYPE                                                    132
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 31(12P13.1) MUTATED                                                                  15
  DEL PEAK 31(12P13.1) WILD-TYPE                                                                66
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 31(12P13.1) MUTATED                                                 20
  DEL PEAK 31(12P13.1) WILD-TYPE                                               58
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 31(12P13.1) MUTATED                                                          0
  DEL PEAK 31(12P13.1) WILD-TYPE                                                       21
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 31(12P13.1) MUTATED                                                           4
  DEL PEAK 31(12P13.1) WILD-TYPE                                                         4
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 31(12P13.1) MUTATED                                          2
  DEL PEAK 31(12P13.1) WILD-TYPE                                       11
D67V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 31(12P13.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      30
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           15
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
                                                                   clus
vv                                                                  DEL PEAK 31(12P13.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         68
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             66
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              58
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      11
[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"
D67V9, binary
                                cls
clus                               0   1
  DEL PEAK 31(12P13.1) MUTATED     3  71
  DEL PEAK 31(12P13.1) WILD-TYPE   3 359
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(12P13.1) MUTATED      3   71
  DEL PEAK 31(12P13.1) WILD-TYPE    3  359
     clus
vv    DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE
  NO                             3                              3
  YES                           71                            359
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 31(12P13.1) MUTATED    57   2   4   5
  DEL PEAK 31(12P13.1) WILD-TYPE 290  16  15  20
D67V10, multiclass
    clus
vv   DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE
  R0                           57                            290
  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                         8
                                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      44
  DEL PEAK 31(12P13.1) WILD-TYPE   230
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                                                               44
                                           clus
vv                                          DEL PEAK 31(12P13.1) WILD-TYPE
  ASIAN                                                                 74
  BLACK OR AFRICAN AMERICAN                                              8
  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"
D67V13, binary
                                cls
clus                               0   1
  DEL PEAK 31(12P13.1) MUTATED     1  47
  DEL PEAK 31(12P13.1) WILD-TYPE   3 266
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(12P13.1) MUTATED      1   47
  DEL PEAK 31(12P13.1) WILD-TYPE    3  266
                        clus
vv                       DEL PEAK 31(12P13.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           47
                        clus
vv                       DEL PEAK 31(12P13.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            266
[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  25
  DEL PEAK 32(12Q12) WILD-TYPE 223 125
  DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE 
                          56                          348 
  DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE 
                          25                          125 
$`DEL PEAK 32(12Q12) MUTATED`
TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 
        6.18        17.29        24.76        35.24        15.42        18.15 
TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8483 TCGA-BR-8682 TCGA-BR-8683 
        3.45        11.44        12.95         5.39        16.44         9.86 
TCGA-BR-8687 TCGA-BR-A4J6 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5802 
        8.22         0.66         1.15        13.64         2.83         0.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-5725 
       11.31        12.43        12.20        20.02         7.99        15.02 
TCGA-D7-6519 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-A4YY TCGA-D7-A6F2 TCGA-EQ-5647 
       20.55        13.35        15.22        13.78        15.65         0.62 
TCGA-EQ-8122 TCGA-F1-A72C TCGA-FP-8211 TCGA-HU-A4GH TCGA-HU-A4H2 TCGA-HU-A4H5 
        7.99        11.38        13.58        11.77        12.95        12.30 
TCGA-IN-7806 TCGA-KB-A93H TCGA-R5-A7O7 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DU 
       21.21        37.64        45.67        35.61         5.79         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A91Q TCGA-VQ-A91V 
       13.02        17.85        13.35        27.35        20.81        36.16 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6I 
       52.24         9.04        21.04        18.41        40.08        16.14 
TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       12.43         0.79 

$`DEL PEAK 32(12Q12) WILD-TYPE`
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-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
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-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        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7716 
       31.20        32.94        12.82         9.21        23.93        28.01 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73        12.43         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56         2.66        16.31         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        19.50        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        19.17        14.79         0.26        15.85         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        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.81        15.68        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        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        12.82        19.36 
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        11.57         5.13 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 
        3.25        13.15        13.18         0.07         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.13         0.13         0.10         3.42         9.34 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
       11.61         6.58         0.10        12.62         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       29.98        47.05        19.07        12.03        21.99         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
        9.01        18.97         7.07        12.00        22.98        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-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        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        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 
       19.13        18.84        18.54        18.61        17.85        17.19 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.98        12.79        10.55        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        15.16 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        13.71        11.24        11.31        11.44         9.76 
TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-A4SO 
        2.96         8.38         4.34         7.40         7.13        16.24 
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-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BF 
       22.29        17.06        59.54         5.03         0.56         5.52 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        0.23        18.08        26.47         1.51         5.92        14.27 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        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         6.25        10.19         0.26         2.10        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 
       23.84         9.67         8.88         8.81        27.42         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         5.36         5.19        13.08 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
        1.41         6.44         6.74        12.59         6.51         5.56 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        1.81         7.82        13.51         2.53         5.56        60.56 
TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       20.15         3.72        19.73         9.86        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       61.25         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-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        16.87        19.04 
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        35.24        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       34.45        27.88        32.48         7.73        28.96        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        26.24        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        65.16        36.69        11.70        11.93        61.22 
TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       18.74        22.68         1.71         7.36         9.50         9.73 
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        64.18 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA69 TCGA-VQ-AA6A 
        2.66        42.54        11.24        22.09        28.41        32.94 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-ZA-A8F6 
       29.98        17.13        54.12        26.04        21.11        10.62 

  DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE 
                         0.3                          0.0 
  DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE 
                       52.24                       122.30 
  DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE 
                      13.350                       12.775 
[1] "0.3 - 52.2 (13.3)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.3"
D68V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 32(12Q12) MUTATED         0        2        6        5         7
  DEL PEAK 32(12Q12) WILD-TYPE       3       12       35       26        31
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 32(12Q12) MUTATED           8         0          8          9
  DEL PEAK 32(12Q12) WILD-TYPE        47         4         77         53
                              vv
clus                           STAGE IIIC STAGE IV
  DEL PEAK 32(12Q12) MUTATED            6        6
  DEL PEAK 32(12Q12) WILD-TYPE         35       40
D68V3, multiclass
            clus
vv           DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE
  STAGE I                             0                            3
  STAGE IA                            2                           12
  STAGE IB                            6                           35
  STAGE II                            5                           26
  STAGE IIA                           7                           31
  STAGE IIB                           8                           47
  STAGE III                           0                            4
  STAGE IIIA                          8                           77
  STAGE IIIB                          9                           53
  STAGE IIIC                          6                           35
  STAGE IV                            6                           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 32(12Q12) MUTATED     2  10  31  14
  DEL PEAK 32(12Q12) WILD-TYPE  20  80 164 105
D68V4, multiclass
    clus
vv   DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE
  T1                          2                           20
  T2                         10                           80
  T3                         31                          164
  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  14  11  12
  DEL PEAK 32(12Q12) WILD-TYPE 109 104  73  77
D68V5, multiclass
    clus
vv   DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE
  N0                         20                          109
  N1                         14                          104
  N2                         11                           73
  N3                         12                           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"
D68V6, binary
                              cls
clus                             0   1
  DEL PEAK 32(12Q12) MUTATED    52   3
  DEL PEAK 32(12Q12) WILD-TYPE 335  27
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(12Q12) MUTATED     52    3
  DEL PEAK 32(12Q12) WILD-TYPE  335   27
   clus
vv  DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE
  0                         52                          335
  1                          3                           27
[1] 2 2
[1] FALSE
D68V7, binary
                              cls
clus                             0   1
  DEL PEAK 32(12Q12) MUTATED    19  39
  DEL PEAK 32(12Q12) WILD-TYPE 139 239
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(12Q12) MUTATED     19   39
  DEL PEAK 32(12Q12) WILD-TYPE  139  239
        clus
vv       DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE
  FEMALE                         19                          139
  MALE                           39                          239
[1] 2 2
[1] FALSE
                              vv
clus                           STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 32(12Q12) MUTATED                                       6
  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                                                    142
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 32(12Q12) MUTATED                                                                  10
  DEL PEAK 32(12Q12) WILD-TYPE                                                                71
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 32(12Q12) MUTATED                                                 15
  DEL PEAK 32(12Q12) WILD-TYPE                                               63
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 32(12Q12) MUTATED                                                          3
  DEL PEAK 32(12Q12) WILD-TYPE                                                       18
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 32(12Q12) MUTATED                                                           2
  DEL PEAK 32(12Q12) WILD-TYPE                                                         6
                              vv
clus                           STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 32(12Q12) MUTATED                                          2
  DEL PEAK 32(12Q12) WILD-TYPE                                       11
D68V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 32(12Q12) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    20
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         10
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                          15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                  2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   2
                                                                   clus
vv                                                                  DEL PEAK 32(12Q12) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       65
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     142
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           71
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            63
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    11
[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"
D68V9, binary
                              cls
clus                             0   1
  DEL PEAK 32(12Q12) MUTATED     0  58
  DEL PEAK 32(12Q12) WILD-TYPE   6 372
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(12Q12) MUTATED      0   58
  DEL PEAK 32(12Q12) WILD-TYPE    6  372
     clus
vv    DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE
  NO                           0                            6
  YES                         58                          372
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 32(12Q12) MUTATED    44   3   2   2
  DEL PEAK 32(12Q12) WILD-TYPE 303  15  17  23
D68V10, multiclass
    clus
vv   DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE
  R0                         44                          303
  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                         9
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 32(12Q12) MUTATED                                           0    36
  DEL PEAK 32(12Q12) WILD-TYPE                                         1   238
D68V12, multiclass
                                           clus
vv                                          DEL PEAK 32(12Q12) MUTATED
  ASIAN                                                             13
  BLACK OR AFRICAN AMERICAN                                          2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          0
  WHITE                                                             36
                                           clus
vv                                          DEL PEAK 32(12Q12) WILD-TYPE
  ASIAN                                                               75
  BLACK OR AFRICAN AMERICAN                                            9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  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"
D68V13, binary
                              cls
clus                             0   1
  DEL PEAK 32(12Q12) MUTATED     1  38
  DEL PEAK 32(12Q12) WILD-TYPE   3 275
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(12Q12) MUTATED      1   38
  DEL PEAK 32(12Q12) WILD-TYPE    3  275
                        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                                3
  NOT HISPANIC OR LATINO                          275
[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    30  24
  DEL PEAK 33(13Q12.11) WILD-TYPE 224 126
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                             54                             350 
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                             24                             126 
$`DEL PEAK 33(13Q12.11) MUTATED`
TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-6456 TCGA-BR-6564 TCGA-BR-6709 TCGA-BR-7715 
       19.56         6.97        17.29        26.10        12.16        15.42 
TCGA-BR-7716 TCGA-BR-7959 TCGA-BR-8289 TCGA-BR-8297 TCGA-BR-8683 TCGA-BR-A4CS 
       28.01        18.71         2.66         7.40         9.86         1.48 
TCGA-BR-A4IY TCGA-BR-A4J6 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-A486 TCGA-CG-4444 
       12.89         0.66         0.07         0.07         3.42        47.05 
TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5727 TCGA-D7-5579 
       18.97        22.98        12.03        15.02        79.07        11.93 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6818 TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A6F2 
       13.35        10.26        10.55        18.21        16.44        15.65 
TCGA-FP-7916 TCGA-HU-8243 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GU 
       14.07         5.92         3.25        25.81        11.77         6.25 
TCGA-HU-A4H2 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RR 
       12.95        18.81         3.39         5.36         5.19         6.74 
TCGA-IN-AB1X TCGA-RD-A7BS TCGA-RD-A8N1 TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8P5 
       13.51        11.05       115.69        13.25        13.02         7.73 
TCGA-VQ-A8PM TCGA-VQ-A91A TCGA-VQ-A91Q TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-AA6G 
        1.87        36.69        20.81         4.54        64.18        26.04 

$`DEL PEAK 33(13Q12.11) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        4.64         7.43        18.35        30.90         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        6.61        34.68        15.95        13.87        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12         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        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 
        9.21        24.76        35.24        23.93        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
       28.73        12.43         3.45         9.07        12.76        17.49 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56        12.95        16.31         2.20        15.58 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        19.50        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 
       19.17        14.79         0.26        15.85         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        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       15.81        16.44        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV 
       13.87         7.53         6.08        22.26        13.41        13.51 
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        12.82        19.36 
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        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 
        0.30         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.16         0.10         0.10         0.13         0.13         0.10 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        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 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       29.98        19.07        12.03        21.99         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-5726 TCGA-CG-5728 
        0.99         6.02         0.99       105.07        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        12.36        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-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 
       17.19        15.22        15.98        12.79        11.31        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-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27         5.92        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       13.71        11.24        11.31        11.44         9.76         2.96 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34         7.40         7.13         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
       16.24        14.47        72.23        21.27        11.38         3.48 
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-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        0.56         5.52         0.23        18.08        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       14.27        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
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-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
       10.19         0.26         2.10        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
        9.67         8.88         8.81        27.42        21.21         3.45 
TCGA-IN-A6RI TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR 
       18.38        13.08         1.41         6.44        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        5.56         1.81         7.82         2.53         5.56        60.56 
TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 
       20.15        37.64         3.72        19.73         9.86        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        61.25         6.08         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-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-A8E0 
       19.04         5.79         0.92        48.79         5.46        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       35.24        21.73        34.45        27.88        32.48        28.96 
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-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
        2.70        17.85         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D 
       26.24        27.35        64.57        14.33        65.16        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       11.93        61.22        18.74        22.68         1.71        36.16 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
        7.36         9.50         9.73        52.24         9.04         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-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       11.24        22.09        18.41        40.08        28.41        32.94 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       29.98        17.13        54.12        16.14        21.11        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                           0.07                            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 
                         12.920                          12.805 
[1] "0.1 - 115.7 (12.9)" "0.0 - 122.3 (12.8)"
[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        1        8        3         8
  DEL PEAK 33(13Q12.11) WILD-TYPE       3       13       33       28        30
                                 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        48         4         71         55
                                 vv
clus                              STAGE IIIC STAGE IV
  DEL PEAK 33(13Q12.11) MUTATED            5        6
  DEL PEAK 33(13Q12.11) WILD-TYPE         36       40
D69V3, multiclass
            clus
vv           DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  STAGE I                                0                               3
  STAGE IA                               1                              13
  STAGE IB                               8                              33
  STAGE II                               3                              28
  STAGE IIA                              8                              30
  STAGE IIB                              7                              48
  STAGE III                              0                               4
  STAGE IIIA                            14                              71
  STAGE IIIB                             7                              55
  STAGE IIIC                             5                              36
  STAGE IV                               6                              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 33(13Q12.11) MUTATED     2  17  29  12
  DEL PEAK 33(13Q12.11) WILD-TYPE  20  73 166 107
D69V4, multiclass
    clus
vv   DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  T1                             2                              20
  T2                            17                              73
  T3                            29                             166
  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    19  15  10  16
  DEL PEAK 33(13Q12.11) WILD-TYPE 110 103  74  73
D69V5, multiclass
    clus
vv   DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  N0                            19                             110
  N1                            15                             103
  N2                            10                              74
  N3                            16                              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"
D69V6, binary
                                 cls
clus                                0   1
  DEL PEAK 33(13Q12.11) MUTATED    55   3
  DEL PEAK 33(13Q12.11) WILD-TYPE 332  27
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q12.11) MUTATED     55    3
  DEL PEAK 33(13Q12.11) WILD-TYPE  332   27
   clus
vv  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  0                            55                             332
  1                             3                              27
[1] 2 2
[1] FALSE
D69V7, binary
                                 cls
clus                                0   1
  DEL PEAK 33(13Q12.11) MUTATED    14  47
  DEL PEAK 33(13Q12.11) WILD-TYPE 144 231
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q12.11) MUTATED     14   47
  DEL PEAK 33(13Q12.11) WILD-TYPE  144  231
        clus
vv       DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  FEMALE                            14                             144
  MALE                              47                             231
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 33(13Q12.11) MUTATED                                      12
  DEL PEAK 33(13Q12.11) WILD-TYPE                                    59
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 33(13Q12.11) MUTATED                                                       21
  DEL PEAK 33(13Q12.11) WILD-TYPE                                                    141
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 33(13Q12.11) MUTATED                                                                   8
  DEL PEAK 33(13Q12.11) WILD-TYPE                                                                73
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 33(13Q12.11) MUTATED                                                 12
  DEL PEAK 33(13Q12.11) WILD-TYPE                                               66
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 33(13Q12.11) MUTATED                                                          4
  DEL PEAK 33(13Q12.11) WILD-TYPE                                                       17
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 33(13Q12.11) MUTATED                                                           1
  DEL PEAK 33(13Q12.11) WILD-TYPE                                                         7
                                 vv
clus                              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 33(13Q12.11) MUTATED                                          2
  DEL PEAK 33(13Q12.11) WILD-TYPE                                       11
D69V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 33(13Q12.11) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       21
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             8
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      2
                                                                   clus
vv                                                                  DEL PEAK 33(13Q12.11) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        141
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              73
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               66
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       11
[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"
D69V9, binary
                                 cls
clus                                0   1
  DEL PEAK 33(13Q12.11) MUTATED     3  58
  DEL PEAK 33(13Q12.11) WILD-TYPE   3 372
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q12.11) MUTATED      3   58
  DEL PEAK 33(13Q12.11) WILD-TYPE    3  372
     clus
vv    DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  NO                              3                               3
  YES                            58                             372
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 33(13Q12.11) MUTATED    47   4   3   4
  DEL PEAK 33(13Q12.11) WILD-TYPE 300  14  16  21
D69V10, multiclass
    clus
vv   DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  R0                            47                             300
  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                        10
                                 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      39
  DEL PEAK 33(13Q12.11) WILD-TYPE   235
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                                                                39
                                           clus
vv                                          DEL PEAK 33(13Q12.11) WILD-TYPE
  ASIAN                                                                  76
  BLACK OR AFRICAN AMERICAN                                              10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 235
[1] 4 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     0  44
  DEL PEAK 33(13Q12.11) WILD-TYPE   4 269
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q12.11) MUTATED      0   44
  DEL PEAK 33(13Q12.11) WILD-TYPE    4  269
                        clus
vv                       DEL PEAK 33(13Q12.11) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            44
                        clus
vv                       DEL PEAK 33(13Q12.11) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             269
[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    75  51
  DEL PEAK 34(14Q23.3) WILD-TYPE 179  99
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                           126                            278 
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                            51                             99 
$`DEL PEAK 34(14Q23.3) MUTATED`
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4279 TCGA-BR-6456 
       19.56        11.01         9.44         6.61         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        15.42 
TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8286 
       28.01        28.73        18.71        17.49        11.44        12.95 
TCGA-BR-8289 TCGA-BR-8361 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8484 
        2.66        19.50        14.79         0.26         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8589 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-A452 TCGA-BR-A4CQ 
        9.21        15.81        11.54        15.68         7.53        22.26 
TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD 
        1.48         0.72         0.66        19.36         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         0.07         0.07         0.07         0.13 
TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4437 
        0.13        11.31        12.20        20.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5725 
       54.08         4.01        14.01        18.97        30.97        15.02 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       20.55        18.84        18.54        13.35        17.19        10.26 
TCGA-D7-6815 TCGA-D7-8576 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 
       15.98        14.66        16.44        11.31        11.44         2.96 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 
        7.99        16.24        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        12.59        14.17         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        12.30        27.42        21.21         5.19 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 
       13.08         6.44         6.74         1.81         2.53         5.56 
TCGA-KB-A93H TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 
       37.64        16.67       122.30        37.91       115.69         8.94 
TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
        0.92         5.46        13.25        13.02        18.48        35.24 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       32.48         7.73        46.26        12.79         2.70        17.85 
TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91N 
       13.35        27.35        64.57        14.33        65.16        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R 
       20.81        52.24         9.04        64.18        21.04        42.54 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-ZQ-A9CR 
       22.09        18.41        32.94        29.98        26.04         0.79 

$`DEL PEAK 34(14Q23.3) WILD-TYPE`
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-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         6.18         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.87        13.68        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        21.11        30.90        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 
       12.82         9.21        24.76        23.93        18.15        15.32 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8077 
       12.43         3.45         9.07        12.76        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 
       12.26         9.60        20.55         8.05         0.56        16.31 
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-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-8382 TCGA-BR-8384 TCGA-BR-8486 
        3.32        11.80        19.17        15.85         3.72        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 
        0.49        15.81        16.44         9.86         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       12.56        13.87         6.08        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4PE 
        8.98        14.17         0.53        12.82        13.51        20.42 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5802 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.30         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A 
        0.10         0.10         0.10         3.42         9.34        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
       11.61         6.58         0.10        12.62         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
       15.95         1.02        29.98        47.05        19.07        12.03 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
       21.99         0.00         9.01         7.07        12.00        22.98 
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-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        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        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 
       19.13        18.61        17.85        15.22        12.79        10.55 
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-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX 
       18.21        21.14        20.91        14.27         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F2 
       13.78        14.76        13.71        11.24         9.76        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 
        8.38         4.34         7.40         7.13         0.62        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 
       72.23        21.27         3.48        19.53        22.29        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8238 
        5.03        13.58         5.52         0.23        18.08         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        14.27        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF 
       24.30        12.30        11.84        24.20        22.75        25.81 
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         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        0.26        12.95        19.36        23.84         9.67         8.88 
TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
        8.81         3.45        18.81         3.39        18.38         5.36 
TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X 
        1.41        12.59         6.51         5.56         7.82        13.51 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 
       60.56        20.15         3.72        19.73         9.86        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        61.25         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        34.45        27.88        28.96        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 
       26.24        36.69        11.70        11.93        61.22        22.68 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A923 
        1.71        36.16         7.36         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 
       40.08        28.41        17.13        54.12        16.14        21.11 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        10.62 

  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                          0.07                           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 
                        14.040                         12.495 
[1] "0.1 - 122.3 (14.0)" "0.0 - 116.4 (12.5)"
[1] "hr=" "1"  
D70V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 34(14Q23.3) MUTATED         0        2       12       11        14
  DEL PEAK 34(14Q23.3) WILD-TYPE       3       12       29       20        24
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 34(14Q23.3) MUTATED          16         0         33         21
  DEL PEAK 34(14Q23.3) WILD-TYPE        39         4         52         41
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 34(14Q23.3) MUTATED           12        9
  DEL PEAK 34(14Q23.3) WILD-TYPE         29       37
D70V3, multiclass
            clus
vv           DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  STAGE I                               0                              3
  STAGE IA                              2                             12
  STAGE IB                             12                             29
  STAGE II                             11                             20
  STAGE IIA                            14                             24
  STAGE IIB                            16                             39
  STAGE III                             0                              4
  STAGE IIIA                           33                             52
  STAGE IIIB                           21                             41
  STAGE IIIC                           12                             29
  STAGE IV                              9                             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 34(14Q23.3) MUTATED     4  27  63  36
  DEL PEAK 34(14Q23.3) WILD-TYPE  18  63 132  83
D70V4, multiclass
    clus
vv   DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  T1                            4                             18
  T2                           27                             63
  T3                           63                            132
  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   37 35 34 22
  DEL PEAK 34(14Q23.3) WILD-TYPE 92 83 50 67
D70V5, multiclass
    clus
vv   DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  N0                           37                             92
  N1                           35                             83
  N2                           34                             50
  N3                           22                             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 266  26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q23.3) MUTATED    121    4
  DEL PEAK 34(14Q23.3) WILD-TYPE  266   26
   clus
vv  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  0                          121                            266
  1                            4                             26
[1] 2 2
[1] FALSE
D70V7, binary
                                cls
clus                               0   1
  DEL PEAK 34(14Q23.3) MUTATED    44  90
  DEL PEAK 34(14Q23.3) WILD-TYPE 114 188
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q23.3) MUTATED     44   90
  DEL PEAK 34(14Q23.3) WILD-TYPE  114  188
        clus
vv       DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  FEMALE                           44                            114
  MALE                             90                            188
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 34(14Q23.3) MUTATED                                      15
  DEL PEAK 34(14Q23.3) WILD-TYPE                                    56
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 34(14Q23.3) MUTATED                                                       48
  DEL PEAK 34(14Q23.3) WILD-TYPE                                                    114
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 34(14Q23.3) MUTATED                                                                  34
  DEL PEAK 34(14Q23.3) WILD-TYPE                                                                47
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 34(14Q23.3) MUTATED                                                 27
  DEL PEAK 34(14Q23.3) WILD-TYPE                                               51
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 34(14Q23.3) MUTATED                                                          2
  DEL PEAK 34(14Q23.3) WILD-TYPE                                                       19
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 34(14Q23.3) MUTATED                                                           3
  DEL PEAK 34(14Q23.3) WILD-TYPE                                                         5
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 34(14Q23.3) MUTATED                                          5
  DEL PEAK 34(14Q23.3) WILD-TYPE                                        8
D70V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 34(14Q23.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      48
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           34
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            27
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     5
                                                                   clus
vv                                                                  DEL PEAK 34(14Q23.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       114
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             47
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              51
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       8
[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"
D70V9, binary
                                cls
clus                               0   1
  DEL PEAK 34(14Q23.3) MUTATED     1 133
  DEL PEAK 34(14Q23.3) WILD-TYPE   5 297
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q23.3) MUTATED      1  133
  DEL PEAK 34(14Q23.3) WILD-TYPE    5  297
     clus
vv    DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  NO                             1                              5
  YES                          133                            297
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 34(14Q23.3) MUTATED   114   2   3   7
  DEL PEAK 34(14Q23.3) WILD-TYPE 233  16  16  18
D70V10, multiclass
    clus
vv   DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  R0                          114                            233
  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                         8
                                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      89
  DEL PEAK 34(14Q23.3) WILD-TYPE   185
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                                                               89
                                           clus
vv                                          DEL PEAK 34(14Q23.3) WILD-TYPE
  ASIAN                                                                 62
  BLACK OR AFRICAN AMERICAN                                              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  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"
D70V13, binary
                                cls
clus                               0   1
  DEL PEAK 34(14Q23.3) MUTATED     0  93
  DEL PEAK 34(14Q23.3) WILD-TYPE   4 220
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q23.3) MUTATED      0   93
  DEL PEAK 34(14Q23.3) WILD-TYPE    4  220
                        clus
vv                       DEL PEAK 34(14Q23.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           93
                        clus
vv                       DEL PEAK 34(14Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            220
[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    77  46
  DEL PEAK 35(14Q32.32) WILD-TYPE 177 104
  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                            123                             281 
  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                             46                             104 
$`DEL PEAK 35(14Q32.32) MUTATED`
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4279 TCGA-BR-6456 
       19.56        11.01         6.61        18.35         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 
       15.42        28.01        18.71        17.49        11.44         9.60 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8361 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 
       12.95         2.66        19.50        14.79         0.26         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8589 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-8690 
       25.18         9.21        15.81        11.54        15.68        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        19.36 
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         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MH 
        0.07         0.13         0.13        11.31        11.61        12.20 
TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       20.02         7.99        54.08        29.98        47.05        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-EQ-A4SO 
       11.31         9.76         2.96         7.40         7.99        16.24 
TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 TCGA-HJ-7597 TCGA-HU-8245 
       11.38        14.07        17.06         0.56        26.47        12.59 
TCGA-HU-8249 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H5 TCGA-HU-A4HD 
       14.17        11.77         8.98         2.10        12.30        27.42 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU 
       21.21        18.81         5.19         6.44         6.74         1.81 
TCGA-IP-7968 TCGA-KB-A93H TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N6 
        2.53        37.64        16.67       122.30        37.91         8.94 
TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PC 
       35.61         5.46        13.02        35.24         7.73        46.26 
TCGA-VQ-A8PH TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A 
       12.79        13.35        27.35        64.57        65.16        36.69 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A925 
       18.74        20.81        22.68         9.73        52.24         4.54 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA6A 
        5.72        64.18        21.04        22.09        18.41        32.94 
TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-ZQ-A9CR 
       29.98        26.04         0.79 

$`DEL PEAK 35(14Q32.32) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 
       26.70        11.70         9.47         9.44         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        7.43        30.90         6.18         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.87        13.68        39.12        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 
       19.89         8.98        21.11        30.90        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
        9.21        24.76        23.93        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8077 
       12.43         3.45         9.07        12.76        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 
       12.26        20.55         8.05         0.56        16.31         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-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-8382 TCGA-BR-8384 TCGA-BR-8486 TCGA-BR-8487 
       11.80        19.17        15.85         3.72        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U 
       15.81        16.44         9.86         8.22        12.56        13.87 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 
        6.08        22.26        13.41        13.51         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL 
        0.53        12.82        13.51        20.42        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8525 
        5.13         2.83         3.25        13.15         0.30         0.07 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI 
        0.10         3.42         9.34        12.43         6.58         0.10 
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-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
        4.01        14.01        12.03        21.99         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        12.00        22.98         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-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        79.07        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        12.36        12.66        11.93        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        10.55        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        15.16        14.76        13.71 
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-FP-A8CX 
       22.29        59.54         5.03        13.58         5.52         0.23 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 
       18.08         1.51         5.92        14.27        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
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-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 
        0.10         6.51         6.25        10.19         0.26        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 
       19.36        23.84         9.67         8.88         8.81         3.45 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RS 
        3.39        18.38         5.36        13.08         1.41        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 
        6.51         5.56         7.82        13.51         5.56        60.56 
TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       20.15         3.72        19.73         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        61.25         6.08         4.60         9.24        11.05 
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-A8DL TCGA-VQ-A8DT 
       57.44        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        18.48        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PJ 
       28.96        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-A8PT 
       17.85         1.87         9.27        23.41        15.65        26.24 
TCGA-VQ-A8PY TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91V 
       14.33        11.70        11.93        61.22         1.71        36.16 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
        7.36         9.50         9.04         2.01        55.43         6.58 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D 
        2.66        42.54        11.24        40.08        28.41        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        16.14        21.11        12.43        10.62 

  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                           0.07                            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 
                          14.07                           12.56 
[1] "0.1 - 122.3 (14.1)" "0.0 - 116.4 (12.6)"
[1] "hr=" "1.1"
D71V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 35(14Q32.32) MUTATED         0        3        9       12        13
  DEL PEAK 35(14Q32.32) WILD-TYPE       3       11       32       19        25
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 35(14Q32.32) MUTATED          17         0         33         20
  DEL PEAK 35(14Q32.32) WILD-TYPE        38         4         52         42
                                 vv
clus                              STAGE IIIC STAGE IV
  DEL PEAK 35(14Q32.32) MUTATED           13        7
  DEL PEAK 35(14Q32.32) WILD-TYPE         28       39
D71V3, multiclass
            clus
vv           DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  STAGE I                                0                               3
  STAGE IA                               3                              11
  STAGE IB                               9                              32
  STAGE II                              12                              19
  STAGE IIA                             13                              25
  STAGE IIB                             17                              38
  STAGE III                              0                               4
  STAGE IIIA                            33                              52
  STAGE IIIB                            20                              42
  STAGE IIIC                            13                              28
  STAGE IV                               7                              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 35(14Q32.32) MUTATED     4  28  62  33
  DEL PEAK 35(14Q32.32) WILD-TYPE  18  62 133  86
D71V4, multiclass
    clus
vv   DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  T1                             4                              18
  T2                            28                              62
  T3                            62                             133
  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 37 29 26
  DEL PEAK 35(14Q32.32) WILD-TYPE 94 81 55 63
D71V5, multiclass
    clus
vv   DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  N0                            35                              94
  N1                            37                              81
  N2                            29                              55
  N3                            26                              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"
D71V6, binary
                                 cls
clus                                0   1
  DEL PEAK 35(14Q32.32) MUTATED   120   2
  DEL PEAK 35(14Q32.32) WILD-TYPE 267  28
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(14Q32.32) MUTATED    120    2
  DEL PEAK 35(14Q32.32) WILD-TYPE  267   28
   clus
vv  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  0                           120                             267
  1                             2                              28
[1] 2 2
[1] FALSE
D71V7, binary
                                 cls
clus                                0   1
  DEL PEAK 35(14Q32.32) MUTATED    45  86
  DEL PEAK 35(14Q32.32) WILD-TYPE 113 192
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(14Q32.32) MUTATED     45   86
  DEL PEAK 35(14Q32.32) WILD-TYPE  113  192
        clus
vv       DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  FEMALE                            45                             113
  MALE                              86                             192
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 35(14Q32.32) MUTATED                                      15
  DEL PEAK 35(14Q32.32) WILD-TYPE                                    56
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 35(14Q32.32) MUTATED                                                       49
  DEL PEAK 35(14Q32.32) WILD-TYPE                                                    113
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 35(14Q32.32) MUTATED                                                                  28
  DEL PEAK 35(14Q32.32) WILD-TYPE                                                                53
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 35(14Q32.32) MUTATED                                                 24
  DEL PEAK 35(14Q32.32) WILD-TYPE                                               54
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 35(14Q32.32) MUTATED                                                          6
  DEL PEAK 35(14Q32.32) WILD-TYPE                                                       15
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 35(14Q32.32) MUTATED                                                           4
  DEL PEAK 35(14Q32.32) WILD-TYPE                                                         4
                                 vv
clus                              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 35(14Q32.32) MUTATED                                          5
  DEL PEAK 35(14Q32.32) WILD-TYPE                                        8
D71V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 35(14Q32.32) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       49
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            28
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             24
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      5
                                                                   clus
vv                                                                  DEL PEAK 35(14Q32.32) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        113
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              53
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               54
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                        8
[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"
D71V9, binary
                                 cls
clus                                0   1
  DEL PEAK 35(14Q32.32) MUTATED     2 129
  DEL PEAK 35(14Q32.32) WILD-TYPE   4 301
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(14Q32.32) MUTATED      2  129
  DEL PEAK 35(14Q32.32) WILD-TYPE    4  301
     clus
vv    DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  NO                              2                               4
  YES                           129                             301
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 35(14Q32.32) MUTATED   110   3   3   7
  DEL PEAK 35(14Q32.32) WILD-TYPE 237  15  16  18
D71V10, multiclass
    clus
vv   DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  R0                           110                             237
  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                         8
                                 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      88
  DEL PEAK 35(14Q32.32) WILD-TYPE   186
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                                                                88
                                           clus
vv                                          DEL PEAK 35(14Q32.32) WILD-TYPE
  ASIAN                                                                  61
  BLACK OR AFRICAN AMERICAN                                               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 186
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V13, binary
                                 cls
clus                                0   1
  DEL PEAK 35(14Q32.32) MUTATED     0  95
  DEL PEAK 35(14Q32.32) WILD-TYPE   4 218
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(14Q32.32) MUTATED      0   95
  DEL PEAK 35(14Q32.32) WILD-TYPE    4  218
                        clus
vv                       DEL PEAK 35(14Q32.32) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            95
                        clus
vv                       DEL PEAK 35(14Q32.32) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             218
[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    71  38
  DEL PEAK 36(15Q11.2) WILD-TYPE 183 112
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                           109                            295 
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                            38                            112 
$`DEL PEAK 36(15Q11.2) MUTATED`
TCGA-B7-A5TJ TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7703 TCGA-BR-7704 
       11.01        13.68        19.33         9.17        24.76        35.24 
TCGA-BR-7901 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8485 
        3.45        12.95         2.66        14.79         5.39         9.21 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4QI 
       15.68        10.68        22.26         0.72        20.65        13.64 
TCGA-CD-5801 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 
       13.18         0.07         0.07         0.07         0.13         0.16 
TCGA-CD-8535 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 
        0.13        12.43        11.61        12.20        20.02         7.99 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4466 TCGA-CG-5719 TCGA-CG-5724 
       54.08         4.01        47.05        18.97         1.02        12.03 
TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       15.02        69.04        12.66        19.13        20.55        18.84 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A 
       18.21        14.66        11.31         2.96        15.65         7.40 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 
        7.99        72.23        13.58         5.52         0.23        26.47 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH 
       12.59        14.17        12.10         3.25        25.81        11.77 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD 
        8.98         6.25         2.10        23.84         9.67        27.42 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A7NT TCGA-IN-A7NU 
       18.38         5.36         5.19         1.41         5.56         1.81 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-MX-A663 TCGA-R5-A7ZF TCGA-R5-A805 TCGA-RD-A7BS 
        2.53        60.56         9.86         8.52         9.24        11.05 
TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL 
       16.67        37.91       115.69        35.61         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E7 TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A8PZ 
       48.79         5.46        34.45        17.85        13.35        65.16 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       18.74        20.81         1.71         9.50         9.73        52.24 
TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6F 
       64.18        42.54        22.09        40.08        29.98        54.12 
TCGA-VQ-AA6I 
       16.14 

$`DEL PEAK 36(15Q11.2) WILD-TYPE`
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-4267 
        6.97         4.64         7.43        18.35        30.90         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-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10        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        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       12.82         9.21        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73        12.43         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       17.49        14.43        11.44         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
       20.55         8.05         0.56        16.31         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        19.50        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-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 
       11.80        19.17         0.26        15.85         3.72        25.18 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        9.86         8.22        12.56        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        13.41        13.51        12.89         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.53        12.82         0.66        19.36        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        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8528 TCGA-CD-8531 
       13.15         0.30         0.07         0.07         0.10         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        6.58         0.10        12.62         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
        1.02         8.05        14.01        29.98        19.07        12.03 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
       21.99         0.00         9.01         7.07        12.00        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       30.97         6.97        36.00         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 
      105.07        28.96        79.07        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        12.36        11.93        18.54        18.61        17.85 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        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 
       15.16        13.78        14.76        13.71        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO 
        9.76         8.38         4.34         7.13         0.62        16.24 
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-HF-A5NB 
       22.29        17.06        59.54         5.03         0.56        18.08 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
        1.51         5.92        14.27        11.41        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD 
       24.30         5.59        12.30        11.84        24.20        22.75 
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        10.19         0.26 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       12.95        19.36        12.30         8.88         8.81        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
        3.45        18.81         3.39        13.08         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A93G 
       12.59         6.51         7.82        13.51         5.56        20.15 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZI 
       37.64         3.72        19.73        45.67        18.21        61.25 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 
        6.08         4.60         8.61         5.13       122.30        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-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 
       13.25        13.02        18.48        35.24        21.73        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       32.48         7.73        28.96        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-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       23.41        15.65        26.24        27.35        64.57        14.33 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91V 
       36.69        11.70        11.93        61.22        22.68        36.16 
TCGA-VQ-A91W TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
        7.36         9.04         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 
        5.72        21.04         2.66        11.24        18.41        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       32.94        17.13        26.04        21.11        12.43        10.62 
TCGA-ZQ-A9CR 
        0.79 

  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                          0.07                           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 
                         12.95                          12.82 
[1] "0.1 - 115.7 (12.9)" "0.0 - 122.3 (12.8)"
[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        4       12        7        11
  DEL PEAK 36(15Q11.2) WILD-TYPE       2       10       29       24        27
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 36(15Q11.2) MUTATED          13         0         33         14
  DEL PEAK 36(15Q11.2) WILD-TYPE        42         4         52         48
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 36(15Q11.2) MUTATED            7       13
  DEL PEAK 36(15Q11.2) WILD-TYPE         34       33
D72V3, multiclass
            clus
vv           DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  STAGE I                               1                              2
  STAGE IA                              4                             10
  STAGE IB                             12                             29
  STAGE II                              7                             24
  STAGE IIA                            11                             27
  STAGE IIB                            13                             42
  STAGE III                             0                              4
  STAGE IIIA                           33                             52
  STAGE IIIB                           14                             48
  STAGE IIIC                            7                             34
  STAGE IV                             13                             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 36(15Q11.2) MUTATED     6  27  61  22
  DEL PEAK 36(15Q11.2) WILD-TYPE  16  63 134  97
D72V4, multiclass
    clus
vv   DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  T1                            6                             16
  T2                           27                             63
  T3                           61                            134
  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 31 27 21
  DEL PEAK 36(15Q11.2) WILD-TYPE 94 87 57 68
D72V5, multiclass
    clus
vv   DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  N0                           35                             94
  N1                           31                             87
  N2                           27                             57
  N3                           21                             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"
D72V6, binary
                                cls
clus                               0   1
  DEL PEAK 36(15Q11.2) MUTATED   106   7
  DEL PEAK 36(15Q11.2) WILD-TYPE 281  23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(15Q11.2) MUTATED    106    7
  DEL PEAK 36(15Q11.2) WILD-TYPE  281   23
   clus
vv  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  0                          106                            281
  1                            7                             23
[1] 2 2
[1] FALSE
D72V7, binary
                                cls
clus                               0   1
  DEL PEAK 36(15Q11.2) MUTATED    42  77
  DEL PEAK 36(15Q11.2) WILD-TYPE 116 201
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(15Q11.2) MUTATED     42   77
  DEL PEAK 36(15Q11.2) WILD-TYPE  116  201
        clus
vv       DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  FEMALE                           42                            116
  MALE                             77                            201
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 36(15Q11.2) MUTATED                                      14
  DEL PEAK 36(15Q11.2) WILD-TYPE                                    57
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 36(15Q11.2) MUTATED                                                       37
  DEL PEAK 36(15Q11.2) WILD-TYPE                                                    125
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 36(15Q11.2) MUTATED                                                                  27
  DEL PEAK 36(15Q11.2) WILD-TYPE                                                                54
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 36(15Q11.2) MUTATED                                                 29
  DEL PEAK 36(15Q11.2) WILD-TYPE                                               49
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 36(15Q11.2) MUTATED                                                          4
  DEL PEAK 36(15Q11.2) WILD-TYPE                                                       17
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 36(15Q11.2) MUTATED                                                           3
  DEL PEAK 36(15Q11.2) WILD-TYPE                                                         5
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 36(15Q11.2) MUTATED                                          5
  DEL PEAK 36(15Q11.2) WILD-TYPE                                        8
D72V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 36(15Q11.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       14
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      37
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           27
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            29
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     5
                                                                   clus
vv                                                                  DEL PEAK 36(15Q11.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         57
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             54
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              49
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       8
[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"
D72V9, binary
                                cls
clus                               0   1
  DEL PEAK 36(15Q11.2) MUTATED     4 115
  DEL PEAK 36(15Q11.2) WILD-TYPE   2 315
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(15Q11.2) MUTATED      4  115
  DEL PEAK 36(15Q11.2) WILD-TYPE    2  315
     clus
vv    DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  NO                             4                              2
  YES                          115                            315
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 36(15Q11.2) MUTATED    99   6   3   4
  DEL PEAK 36(15Q11.2) WILD-TYPE 248  12  16  21
D72V10, multiclass
    clus
vv   DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  R0                           99                            248
  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                         9
                                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      72
  DEL PEAK 36(15Q11.2) WILD-TYPE   202
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                                                               72
                                           clus
vv                                          DEL PEAK 36(15Q11.2) WILD-TYPE
  ASIAN                                                                 60
  BLACK OR AFRICAN AMERICAN                                              9
  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"
D72V13, binary
                                cls
clus                               0   1
  DEL PEAK 36(15Q11.2) MUTATED     0  85
  DEL PEAK 36(15Q11.2) WILD-TYPE   4 228
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(15Q11.2) MUTATED      0   85
  DEL PEAK 36(15Q11.2) WILD-TYPE    4  228
                        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                                  4
  NOT HISPANIC OR LATINO                            228
[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    70  41
  DEL PEAK 37(15Q15.1) WILD-TYPE 184 109
  DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE 
                           111                            293 
  DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE 
                            41                            109 
$`DEL PEAK 37(15Q15.1) MUTATED`
TCGA-B7-A5TJ TCGA-BR-4267 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7704 TCGA-BR-7901 
       11.01         6.18         9.17        12.16        35.24         3.45 
TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8686 
        0.69        12.95         2.66        14.79         5.39        15.68 
TCGA-BR-8690 TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-5801 
       10.68        22.26         0.72        20.65        13.64        13.18 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8535 
        0.07         0.07         0.07         0.13         0.16         0.13 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4438 
       12.43        11.61        12.20        20.02         7.99        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5719 
        4.01        14.01        47.05        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         2.96        15.65         7.40 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7998 TCGA-FP-8211 TCGA-FP-A4BF 
        7.99        16.24        72.23        22.29        13.58         5.52 
TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GD 
        0.23        26.47        12.59        14.17        12.10        22.75 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
        8.98         6.25         2.10        12.95        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        9.67        27.42        18.81        18.38         5.36         5.19 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-MX-A663 
        1.41         6.44         5.56         1.81         2.53         9.86 
TCGA-R5-A7ZF TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 
        8.52         9.24        11.05        16.67        37.91       115.69 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8PK 
       35.61         5.79        48.79         5.46        18.48        17.85 
TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A8PZ TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U 
       13.35        27.35        65.16        18.74        20.81         1.71 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A92D TCGA-VQ-A94R 
        9.50         9.73        52.24         9.04        64.18        42.54 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6B 
       18.41        40.08        29.98 

$`DEL PEAK 37(15Q15.1) WILD-TYPE`
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-4279 
        6.97         4.64         7.43        18.35        30.90         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-6566 TCGA-BR-6705 TCGA-BR-6706 
       19.33        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        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       12.82         9.21        24.76        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73        12.43         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43        11.44        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
       20.55         8.05         0.56        16.31         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        19.50        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-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 
       11.80        19.17         0.26        15.85         3.72        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        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       16.44         9.86         8.22        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08         1.48        13.41        13.51        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        12.82         0.66        19.36        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.42         1.15        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8528 
        3.25        13.15         0.30         0.07         0.07         0.10 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
       11.31         6.58         0.10        12.62         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       15.95         1.02         8.05        29.98        19.07        12.03 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
       21.99         0.00         9.01         7.07        12.00        22.98 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         0.99         6.02         0.99       105.07 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 
       15.02        28.96        79.07        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        12.36        11.93        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        10.55        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 
       15.16        13.78        14.76        13.71        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 
        9.76         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-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 
       59.54         5.03         0.56        18.08         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.27        11.41        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        11.84        24.20         3.25        25.81        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        10.19         0.26 
TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 
       19.36         8.88         8.81        21.21         3.45         3.39 
TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X 
       13.08         6.74        12.59         6.51         7.82        13.51 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        60.56        20.15        37.64         3.72        19.73 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BT 
       45.67        18.21        61.25         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-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        8.94        16.87        19.04         0.92        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       35.24        21.73        34.45        27.88        32.48         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       28.96        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-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       26.24        64.57        14.33        36.69        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A924 
       61.22        22.68        36.16         7.36         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-A94U TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       22.09        28.41        32.94        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        21.11        12.43        10.62         0.79 

  DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE 
                          0.07                           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 
                         12.66                          12.89 
[1] "0.1 - 115.7 (12.7)" "0.0 - 122.3 (12.9)"
[1] "hr=" "1"  
D73V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 37(15Q15.1) MUTATED         1        2       14        7         8
  DEL PEAK 37(15Q15.1) WILD-TYPE       2       12       27       24        30
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 37(15Q15.1) MUTATED          11         0         35         17
  DEL PEAK 37(15Q15.1) WILD-TYPE        44         4         50         45
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 37(15Q15.1) MUTATED            8       13
  DEL PEAK 37(15Q15.1) WILD-TYPE         33       33
D73V3, multiclass
            clus
vv           DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE
  STAGE I                               1                              2
  STAGE IA                              2                             12
  STAGE IB                             14                             27
  STAGE II                              7                             24
  STAGE IIA                             8                             30
  STAGE IIB                            11                             44
  STAGE III                             0                              4
  STAGE IIIA                           35                             50
  STAGE IIIB                           17                             45
  STAGE IIIC                            8                             33
  STAGE IV                             13                             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 37(15Q15.1) MUTATED     4  31  59  24
  DEL PEAK 37(15Q15.1) WILD-TYPE  18  59 136  95
D73V4, multiclass
    clus
vv   DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE
  T1                            4                             18
  T2                           31                             59
  T3                           59                            136
  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   32 32 28 23
  DEL PEAK 37(15Q15.1) WILD-TYPE 97 86 56 66
D73V5, multiclass
    clus
vv   DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE
  N0                           32                             97
  N1                           32                             86
  N2                           28                             56
  N3                           23                             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"
D73V6, binary
                                cls
clus                               0   1
  DEL PEAK 37(15Q15.1) MUTATED   106   6
  DEL PEAK 37(15Q15.1) WILD-TYPE 281  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(15Q15.1) MUTATED    106    6
  DEL PEAK 37(15Q15.1) WILD-TYPE  281   24
   clus
vv  DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE
  0                          106                            281
  1                            6                             24
[1] 2 2
[1] FALSE
D73V7, binary
                                cls
clus                               0   1
  DEL PEAK 37(15Q15.1) MUTATED    42  79
  DEL PEAK 37(15Q15.1) WILD-TYPE 116 199
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(15Q15.1) MUTATED     42   79
  DEL PEAK 37(15Q15.1) WILD-TYPE  116  199
        clus
vv       DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE
  FEMALE                           42                            116
  MALE                             79                            199
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 37(15Q15.1) MUTATED                                      14
  DEL PEAK 37(15Q15.1) WILD-TYPE                                    57
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 37(15Q15.1) MUTATED                                                       38
  DEL PEAK 37(15Q15.1) WILD-TYPE                                                    124
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 37(15Q15.1) MUTATED                                                                  29
  DEL PEAK 37(15Q15.1) WILD-TYPE                                                                52
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 37(15Q15.1) MUTATED                                                 29
  DEL PEAK 37(15Q15.1) WILD-TYPE                                               49
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 37(15Q15.1) MUTATED                                                          4
  DEL PEAK 37(15Q15.1) WILD-TYPE                                                       17
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 37(15Q15.1) MUTATED                                                           3
  DEL PEAK 37(15Q15.1) WILD-TYPE                                                         5
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 37(15Q15.1) MUTATED                                          4
  DEL PEAK 37(15Q15.1) WILD-TYPE                                        9
D73V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 37(15Q15.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       14
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      38
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           29
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            29
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     4
                                                                   clus
vv                                                                  DEL PEAK 37(15Q15.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         57
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             52
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              49
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       9
[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"
D73V9, binary
                                cls
clus                               0   1
  DEL PEAK 37(15Q15.1) MUTATED     4 117
  DEL PEAK 37(15Q15.1) WILD-TYPE   2 313
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(15Q15.1) MUTATED      4  117
  DEL PEAK 37(15Q15.1) WILD-TYPE    2  313
     clus
vv    DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE
  NO                             4                              2
  YES                          117                            313
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 37(15Q15.1) MUTATED    98   7   3   6
  DEL PEAK 37(15Q15.1) WILD-TYPE 249  11  16  19
D73V10, multiclass
    clus
vv   DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE
  R0                           98                            249
  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                         8
                                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      73
  DEL PEAK 37(15Q15.1) WILD-TYPE   201
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                                                               73
                                           clus
vv                                          DEL PEAK 37(15Q15.1) WILD-TYPE
  ASIAN                                                                 61
  BLACK OR AFRICAN AMERICAN                                              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  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"
D73V13, binary
                                cls
clus                               0   1
  DEL PEAK 37(15Q15.1) MUTATED     1  87
  DEL PEAK 37(15Q15.1) WILD-TYPE   3 226
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(15Q15.1) MUTATED      1   87
  DEL PEAK 37(15Q15.1) WILD-TYPE    3  226
                        clus
vv                       DEL PEAK 37(15Q15.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           87
                        clus
vv                       DEL PEAK 37(15Q15.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            226
[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    54  30
  DEL PEAK 38(16P13.3) WILD-TYPE 200 120
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                            84                            320 
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                            30                            120 
$`DEL PEAK 38(16P13.3) MUTATED`
TCGA-BR-4183 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7901 
        6.61         9.21        35.24        15.42        28.01         3.45 
TCGA-BR-7959 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8365 TCGA-BR-8373 
       18.71        12.95         2.66        16.31        17.52        14.79 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 
        0.49        11.54         7.53        22.26         1.48         0.72 
TCGA-BR-A4PF TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8530 
        1.15         0.07         0.07         0.07         0.07         0.16 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        0.13         3.42         9.34        12.43        11.61        12.20 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-5724 TCGA-D7-5579 TCGA-D7-6528 
       47.05        19.07        12.03        12.03        11.93        15.22 
TCGA-D7-6822 TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-6875 
       12.33        11.31         2.96         7.40         7.99        72.23 
TCGA-FP-8211 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4GD 
       13.58         5.92        12.59        12.10         0.76        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD 
       25.81        11.77        23.84        12.30         9.67        27.42 
TCGA-IN-8663 TCGA-IN-A6RR TCGA-IN-A6RS TCGA-KB-A6F5 TCGA-KB-A93H TCGA-R5-A7ZR 
        3.39         6.74        12.59         5.56        37.64         6.08 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT 
        9.24        11.05        16.67        35.61         5.79        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8PC TCGA-VQ-A8PH 
        5.46        13.25        13.02        18.48        46.26        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91Z 
        2.70        17.85         1.87        27.35        64.57        52.24 
TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6J 
        9.04        21.04        40.08        32.94        17.13        21.11 

$`DEL PEAK 38(16P13.3) WILD-TYPE`
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-4191 TCGA-BR-4201 TCGA-BR-4267 
        6.97         4.64         7.43        18.35        30.90         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        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        32.94        12.82        24.76        23.93 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73        12.43         9.07        12.76 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       17.49        14.43        11.44         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       20.55         8.05         0.56         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 
        6.18        19.50        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        19.17 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         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        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        6.28         7.53        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU 
        8.22        10.68        12.56        13.87         6.08        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       13.51        12.89         8.98        14.17         0.53        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.66        19.36        13.51         0.46        20.65        20.42 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 
       13.18         0.30         0.07         0.10         0.13         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI 
        0.10         0.13         0.10        11.31         6.58         0.10 
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-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       21.99         0.00         9.01        18.97         7.07        12.00 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        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-5727 
        6.02         0.99       105.07        15.02        28.96        79.07 
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        12.36 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.66        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        17.19        10.26        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       10.55        11.31        24.72        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-A6EV 
        5.92        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       11.44         9.76        15.65         8.38         4.34         7.13 
TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62        16.24        14.47        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-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        0.56         5.52         0.23        18.08        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.27        14.17        11.41        10.62        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GN 
       12.30        11.84        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         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
        2.10        12.95        19.36         8.88         8.81        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45        18.81        18.38         5.36         5.19        13.08 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        1.41         6.44         6.51         5.56         1.81         7.82 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ 
       13.51         2.53        60.56        20.15         3.72        19.73 
TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
        9.86        45.67        18.21         8.52        61.25         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        35.24        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
        7.73        28.96        34.29        16.31        22.19         2.50 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PY 
        9.27        23.41        15.65        13.35        26.24        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       65.16        36.69        11.70        11.93        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       20.81        22.68         1.71        36.16         7.36         9.50 
TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        9.73         2.01        55.43         4.54         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 
       64.18         2.66        42.54        11.24        22.09        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K 
       28.41        29.98        54.12        26.04        16.14        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                          0.07                           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 
                        12.150                         13.265 
[1] "0.1 - 72.2 (12.1)"  "0.0 - 122.3 (13.3)"
[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        9         8
  DEL PEAK 38(16P13.3) WILD-TYPE       3        9       34       22        30
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 38(16P13.3) MUTATED          11         1         27          7
  DEL PEAK 38(16P13.3) WILD-TYPE        44         3         58         55
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 38(16P13.3) MUTATED            6        7
  DEL PEAK 38(16P13.3) WILD-TYPE         35       39
D74V3, multiclass
            clus
vv           DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  STAGE I                               0                              3
  STAGE IA                              5                              9
  STAGE IB                              7                             34
  STAGE II                              9                             22
  STAGE IIA                             8                             30
  STAGE IIB                            11                             44
  STAGE III                             1                              3
  STAGE IIIA                           27                             58
  STAGE IIIB                            7                             55
  STAGE IIIC                            6                             35
  STAGE IV                              7                             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 38(16P13.3) MUTATED     4  16  49  20
  DEL PEAK 38(16P13.3) WILD-TYPE  18  74 146  99
D74V4, multiclass
    clus
vv   DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  T1                            4                             18
  T2                           16                             74
  T3                           49                            146
  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    26  31  16  15
  DEL PEAK 38(16P13.3) WILD-TYPE 103  87  68  74
D74V5, multiclass
    clus
vv   DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  N0                           26                            103
  N1                           31                             87
  N2                           16                             68
  N3                           15                             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"
D74V6, binary
                                cls
clus                               0   1
  DEL PEAK 38(16P13.3) MUTATED    86   4
  DEL PEAK 38(16P13.3) WILD-TYPE 301  26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16P13.3) MUTATED     86    4
  DEL PEAK 38(16P13.3) WILD-TYPE  301   26
   clus
vv  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  0                           86                            301
  1                            4                             26
[1] 2 2
[1] FALSE
D74V7, binary
                                cls
clus                               0   1
  DEL PEAK 38(16P13.3) MUTATED    30  62
  DEL PEAK 38(16P13.3) WILD-TYPE 128 216
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16P13.3) MUTATED     30   62
  DEL PEAK 38(16P13.3) WILD-TYPE  128  216
        clus
vv       DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  FEMALE                           30                            128
  MALE                             62                            216
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 38(16P13.3) MUTATED                                       8
  DEL PEAK 38(16P13.3) WILD-TYPE                                    63
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 38(16P13.3) MUTATED                                                       31
  DEL PEAK 38(16P13.3) WILD-TYPE                                                    131
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 38(16P13.3) MUTATED                                                                  17
  DEL PEAK 38(16P13.3) WILD-TYPE                                                                64
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 38(16P13.3) MUTATED                                                 24
  DEL PEAK 38(16P13.3) WILD-TYPE                                               54
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 38(16P13.3) MUTATED                                                          7
  DEL PEAK 38(16P13.3) WILD-TYPE                                                       14
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 38(16P13.3) MUTATED                                                           2
  DEL PEAK 38(16P13.3) WILD-TYPE                                                         6
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 38(16P13.3) MUTATED                                          3
  DEL PEAK 38(16P13.3) WILD-TYPE                                       10
D74V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 38(16P13.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      31
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            24
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     3
                                                                   clus
vv                                                                  DEL PEAK 38(16P13.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             64
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              54
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      10
[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"
D74V9, binary
                                cls
clus                               0   1
  DEL PEAK 38(16P13.3) MUTATED     2  90
  DEL PEAK 38(16P13.3) WILD-TYPE   4 340
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16P13.3) MUTATED      2   90
  DEL PEAK 38(16P13.3) WILD-TYPE    4  340
     clus
vv    DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  NO                             2                              4
  YES                           90                            340
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 38(16P13.3) MUTATED    70   5   3   6
  DEL PEAK 38(16P13.3) WILD-TYPE 277  13  16  19
D74V10, multiclass
    clus
vv   DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  R0                           70                            277
  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      26                         6
  DEL PEAK 38(16P13.3) WILD-TYPE    62                         5
                                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      48
  DEL PEAK 38(16P13.3) WILD-TYPE   226
D74V12, multiclass
                                           clus
vv                                          DEL PEAK 38(16P13.3) MUTATED
  ASIAN                                                               26
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               48
                                           clus
vv                                          DEL PEAK 38(16P13.3) WILD-TYPE
  ASIAN                                                                 62
  BLACK OR AFRICAN AMERICAN                                              5
  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"
D74V13, binary
                                cls
clus                               0   1
  DEL PEAK 38(16P13.3) MUTATED     0  65
  DEL PEAK 38(16P13.3) WILD-TYPE   4 248
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16P13.3) MUTATED      0   65
  DEL PEAK 38(16P13.3) WILD-TYPE    4  248
                        clus
vv                       DEL PEAK 38(16P13.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           65
                        clus
vv                       DEL PEAK 38(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            248
[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   105  62
  DEL PEAK 39(16Q23.1) WILD-TYPE 149  88
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                           167                            237 
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                            62                             88 
$`DEL PEAK 39(16Q23.1) MUTATED`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        19.56        11.01         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6456 TCGA-BR-6458 
        6.97        18.35         9.57         6.61        17.29        19.33 
TCGA-BR-6564 TCGA-BR-6706 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 
       26.10        18.05        24.76        35.24        15.42        18.15 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       28.73         3.45        18.71        11.44         0.69         9.60 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8361 TCGA-BR-8362 
        0.56        12.95         2.66        16.31        19.50        13.08 
TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8677 
        0.26        17.52        19.17        14.79        25.18         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ 
       11.54        16.44         8.22        13.87         7.53        22.26 
TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5800 
        0.72        20.65        20.42         1.15        13.64        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8535 
        0.30         0.07         0.07         0.07         0.16         0.13 
TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4305 TCGA-CG-4436 
        3.42        12.43        11.61        12.20        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4469 
        8.05        54.08        47.05        19.07        12.03         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5727 
       22.98        30.97       105.07        12.03        15.02        79.07 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 
       12.36        12.66        11.93        13.35        17.19        15.22 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-A4YT TCGA-D7-A4YX 
       12.79        10.55        19.50        18.21        14.27        15.16 
TCGA-D7-A4YY TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       13.78        11.24        11.31         2.96        15.65         8.38 
TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-A4BF TCGA-HF-A5NB 
       16.24        72.23        14.07        22.29         5.52        18.08 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G3 
        1.51         5.92        12.59        12.10         0.76         5.59 
TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GX 
       12.30        22.75        11.77         8.98         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD 
        0.26         2.10        23.84        12.30         9.67        27.42 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NR 
        3.45        18.81        18.38        13.08         6.44         6.51 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G 
        1.81         7.82        13.51         5.56        60.56        20.15 
TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7C1 
       37.64         9.86         6.08         9.24        11.05        16.67 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
        8.94        35.61         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PK 
       13.02         7.73        46.26        22.19        12.79        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PP TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91E 
        1.87        23.41        64.57        14.33        36.69        11.93 
TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       61.22        22.68         1.71         9.50         9.73        52.24 
TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA68 
        9.04         4.54         5.72        42.54        22.09        40.08 
TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-ZQ-A9CR 
       32.94        17.13        54.12        26.04         0.79 

$`DEL PEAK 39(16Q23.1) WILD-TYPE`
TCGA-B7-A5TK TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-6452 
        9.47         4.64         7.43        30.90         6.18        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 
       15.95        13.87        13.68        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        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7716 
       31.20        32.94        12.82         9.21        23.93        28.01 
TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 
       15.32        12.43         9.07        12.76        17.49        14.43 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.26        20.55         8.05         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
        6.18        22.19         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
        3.32        11.80         0.26        15.85         3.72         5.39 
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        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 
       13.45         6.28         7.53        15.81         9.86        15.68 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       10.68        12.56         6.08         1.48        13.41        13.51 
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        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       19.36        13.51         0.46        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        3.25        13.18         0.07         0.07         0.10         0.13 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.10         0.13         0.10         9.34        11.31 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4460 TCGA-CG-4462 
        1.02         4.01        14.01        29.98        21.99         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        9.01        18.97        12.00         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99         6.02         0.99        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       69.04        21.07         7.99        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6820 
       18.54        18.61        17.85        10.26        15.98        11.31 
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-A4YU TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY 
       20.91        16.44         5.92        14.76        13.71        11.44 
TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        9.76         4.34         7.40         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 
       14.47        21.27        11.38         3.48        19.53        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HJ-7597 
       59.54         5.03        13.58         0.56         0.23        26.47 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G8 
       14.27        14.17        11.41        10.62        24.30        11.84 
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-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
        6.51        12.95        19.36         8.88         8.81        21.21 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS 
        3.39         5.36         5.19         1.41         6.74        12.59 
TCGA-IN-A7NT TCGA-IP-7968 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE 
        5.56         2.53         3.72        19.73        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV 
        8.52        61.25         4.60         8.61         5.13       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-A8NB TCGA-SW-A7EA TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       16.87        19.04        13.25        18.48        35.24        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       34.45        27.88        32.48        28.96        34.29        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        2.50         2.70         9.27        15.65        13.35        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V 
       27.35        65.16        11.70        18.74        20.81        36.16 
TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O 
        7.36         2.01        55.43         6.58        64.18        21.04 
TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6I 
        2.66        11.24        18.41        28.41        29.98        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       21.11        12.43        10.62 

  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                          0.07                           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 
                         12.79                          12.89 
[1] "0.1 - 105.1 (12.8)" "0.0 - 122.3 (12.9)"
[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       16       17        15
  DEL PEAK 39(16Q23.1) WILD-TYPE       2        7       25       14        23
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 39(16Q23.1) MUTATED          23         3         42         17
  DEL PEAK 39(16Q23.1) WILD-TYPE        32         1         43         45
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 39(16Q23.1) MUTATED           22       13
  DEL PEAK 39(16Q23.1) WILD-TYPE         19       33
D75V3, multiclass
            clus
vv           DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  STAGE I                               1                              2
  STAGE IA                              7                              7
  STAGE IB                             16                             25
  STAGE II                             17                             14
  STAGE IIA                            15                             23
  STAGE IIB                            23                             32
  STAGE III                             3                              1
  STAGE IIIA                           42                             43
  STAGE IIIB                           17                             45
  STAGE IIIC                           22                             19
  STAGE IV                             13                             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 39(16Q23.1) MUTATED    10  40  82  46
  DEL PEAK 39(16Q23.1) WILD-TYPE  12  50 113  73
D75V4, multiclass
    clus
vv   DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  T1                           10                             12
  T2                           40                             50
  T3                           82                            113
  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   51 52 30 41
  DEL PEAK 39(16Q23.1) WILD-TYPE 78 66 54 48
D75V5, multiclass
    clus
vv   DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  N0                           51                             78
  N1                           52                             66
  N2                           30                             54
  N3                           41                             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   169   5
  DEL PEAK 39(16Q23.1) WILD-TYPE 218  25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(16Q23.1) MUTATED    169    5
  DEL PEAK 39(16Q23.1) WILD-TYPE  218   25
   clus
vv  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  0                          169                            218
  1                            5                             25
[1] 2 2
[1] FALSE
D75V7, binary
                                cls
clus                               0   1
  DEL PEAK 39(16Q23.1) MUTATED    60 120
  DEL PEAK 39(16Q23.1) WILD-TYPE  98 158
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(16Q23.1) MUTATED     60  120
  DEL PEAK 39(16Q23.1) WILD-TYPE   98  158
        clus
vv       DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  FEMALE                           60                             98
  MALE                            120                            158
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 39(16Q23.1) MUTATED                                      23
  DEL PEAK 39(16Q23.1) WILD-TYPE                                    48
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 39(16Q23.1) MUTATED                                                       64
  DEL PEAK 39(16Q23.1) WILD-TYPE                                                     98
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 39(16Q23.1) MUTATED                                                                  31
  DEL PEAK 39(16Q23.1) WILD-TYPE                                                                50
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 39(16Q23.1) MUTATED                                                 38
  DEL PEAK 39(16Q23.1) WILD-TYPE                                               40
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 39(16Q23.1) MUTATED                                                         11
  DEL PEAK 39(16Q23.1) WILD-TYPE                                                       10
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 39(16Q23.1) MUTATED                                                           6
  DEL PEAK 39(16Q23.1) WILD-TYPE                                                         2
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 39(16Q23.1) MUTATED                                          6
  DEL PEAK 39(16Q23.1) WILD-TYPE                                        7
D75V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 39(16Q23.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       23
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      64
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           31
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     6
                                                                   clus
vv                                                                  DEL PEAK 39(16Q23.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        98
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             50
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              40
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       7
[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"
D75V9, binary
                                cls
clus                               0   1
  DEL PEAK 39(16Q23.1) MUTATED     5 175
  DEL PEAK 39(16Q23.1) WILD-TYPE   1 255
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(16Q23.1) MUTATED      5  175
  DEL PEAK 39(16Q23.1) WILD-TYPE    1  255
     clus
vv    DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  NO                             5                              1
  YES                          175                            255
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 39(16Q23.1) MUTATED   144   9   4  10
  DEL PEAK 39(16Q23.1) WILD-TYPE 203   9  15  15
D75V10, multiclass
    clus
vv   DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  R0                          144                            203
  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                         7
                                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     112
  DEL PEAK 39(16Q23.1) WILD-TYPE   162
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                                                              112
                                           clus
vv                                          DEL PEAK 39(16Q23.1) WILD-TYPE
  ASIAN                                                                 51
  BLACK OR AFRICAN AMERICAN                                              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  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"
D75V13, binary
                                cls
clus                               0   1
  DEL PEAK 39(16Q23.1) MUTATED     1 124
  DEL PEAK 39(16Q23.1) WILD-TYPE   3 189
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(16Q23.1) MUTATED      1  124
  DEL PEAK 39(16Q23.1) WILD-TYPE    3  189
                        clus
vv                       DEL PEAK 39(16Q23.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          124
                        clus
vv                       DEL PEAK 39(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            189
[1] 2 2
[1] FALSE

Clustering(76) Variable = DEL PEAK 40(17P13.3) MUTATION ANALYSIS
D76V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 40(17P13.3) MUTATED    99  64
  DEL PEAK 40(17P13.3) WILD-TYPE 155  86
  DEL PEAK 40(17P13.3) MUTATED DEL PEAK 40(17P13.3) WILD-TYPE 
                           163                            241 
  DEL PEAK 40(17P13.3) MUTATED DEL PEAK 40(17P13.3) WILD-TYPE 
                            64                             86 
$`DEL PEAK 40(17P13.3) MUTATED`
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4267 
       11.70        19.56        11.01         9.44         6.61         6.18 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7197 
       17.29        13.68        19.33         9.17        12.16         9.21 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 
       35.24        15.42        28.73        18.71        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 
        9.60        12.95         2.66        16.31        15.58         7.40 
TCGA-BR-8362 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8678 
       13.08        14.04        14.79         5.39        25.18        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ 
       16.44         9.86        10.68        13.87         7.53        22.26 
TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        1.48         0.72        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 
       13.64         3.25        13.15         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 
        0.10         0.13         0.13         0.13         3.42        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 
       12.43        11.61        20.02         3.02        27.02         7.99 
TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4475 
        4.01        29.98        47.05        19.07         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5579 
       30.97         1.02        79.07         4.01        69.04        11.93 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       20.55        18.84        18.54        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8576 TCGA-D7-A4YU 
       15.22        12.79        11.31        12.33        14.66        16.44 
TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C 
       11.31        15.65         7.40         7.99        72.23        11.38 
TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 
       14.07        17.06        13.58         5.52         0.23        26.47 
TCGA-HU-8238 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4GH 
        1.51        12.59        14.17        12.10        22.75        11.77 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 
        8.98         6.25         0.26         2.10        12.95        12.30 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL 
       27.42        21.21        18.81         3.39        18.38         5.19 
TCGA-IN-A6RO TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 
        1.41         6.51         1.81         7.82         2.53         5.56 
TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A805 TCGA-RD-A7BT 
       37.64        45.67        18.21         8.52         9.24         8.61 
TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV 
       16.67       115.69         8.94         0.92         5.46        13.25 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH 
       18.48        35.24         7.73        46.26        22.19        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
        2.70         1.87        13.35        27.35        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y 
       65.16        18.74        20.81        36.16         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A928 TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA68 
       52.24         9.04         5.72        11.24        22.09        40.08 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       29.98        54.12        26.04        16.14        21.11        12.43 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK 40(17P13.3) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       26.70         9.47         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
       30.90         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10        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        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 
       24.76        23.93        28.01        18.15        15.32        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 
        3.45         9.07        12.76        17.49        14.43        12.26 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 
       20.55         8.05         0.56         2.20         6.18        19.50 
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        19.17         0.26        15.85         3.72 
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        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8686 
       13.45         6.28         7.53         0.49        15.81        15.68 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        8.22        12.56         6.08        13.41        13.51        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        12.82         0.66        19.36 
TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 
        0.46        11.57         5.13         2.83        13.18         0.30 
TCGA-CD-5803 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 
        0.07         0.07         0.16         0.10         0.10         0.10 
TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4305 
        9.34         6.58        12.20         0.10        12.62        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4460 
        1.02         8.05        54.08        14.01        12.03        21.99 
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-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        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        12.36        12.66 
TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-8570 
       19.13        18.61        17.85        15.98        10.55        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-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 
       11.24        11.44         9.76         2.96         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 
        7.13         0.62        16.24        14.47        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HF-A5NB 
       19.53        22.29        59.54         5.03         0.56        18.08 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
        5.92        14.27        11.41        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
        5.59        12.30        11.84        24.20         3.25        25.81 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 
       21.37        29.98         0.10         6.51        10.19        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-A6RJ 
       23.84         9.67         8.88         8.81         3.45         5.36 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-AB1X 
       13.08         6.44         6.74        12.59         5.56        13.51 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZI 
       60.56        20.15         3.72        19.73         9.86        61.25 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
        6.08         4.60        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-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       19.04         5.79        48.79        13.02        21.73        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF 
       27.88        32.48        28.96        34.29        16.31         2.50 
TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A91A 
       17.85         9.27        23.41        15.65        26.24        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W 
       11.70        11.93        61.22        22.68         1.71         7.36 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O 
        2.01        55.43         4.54         6.58        64.18        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D 
        2.66        42.54        18.41        28.41        32.94        17.13 
TCGA-ZA-A8F6 
       10.62 

  DEL PEAK 40(17P13.3) MUTATED DEL PEAK 40(17P13.3) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 40(17P13.3) MUTATED DEL PEAK 40(17P13.3) WILD-TYPE 
                        115.69                         122.30 
  DEL PEAK 40(17P13.3) MUTATED DEL PEAK 40(17P13.3) WILD-TYPE 
                         12.59                          13.02 
[1] "0.1 - 115.7 (12.6)" "0.0 - 122.3 (13.0)"
[1] "hr=" "1.2"
D76V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 40(17P13.3) MUTATED         1        6       16       13        15
  DEL PEAK 40(17P13.3) WILD-TYPE       2        8       25       18        23
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 40(17P13.3) MUTATED          22         0         38         25
  DEL PEAK 40(17P13.3) WILD-TYPE        33         4         47         37
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 40(17P13.3) MUTATED           14       19
  DEL PEAK 40(17P13.3) WILD-TYPE         27       27
D76V3, multiclass
            clus
vv           DEL PEAK 40(17P13.3) MUTATED DEL PEAK 40(17P13.3) WILD-TYPE
  STAGE I                               1                              2
  STAGE IA                              6                              8
  STAGE IB                             16                             25
  STAGE II                             13                             18
  STAGE IIA                            15                             23
  STAGE IIB                            22                             33
  STAGE III                             0                              4
  STAGE IIIA                           38                             47
  STAGE IIIB                           25                             37
  STAGE IIIC                           14                             27
  STAGE IV                             19                             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 40(17P13.3) MUTATED     6  39  84  41
  DEL PEAK 40(17P13.3) WILD-TYPE  16  51 111  78
D76V4, multiclass
    clus
vv   DEL PEAK 40(17P13.3) MUTATED DEL PEAK 40(17P13.3) WILD-TYPE
  T1                            6                             16
  T2                           39                             51
  T3                           84                            111
  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 40(17P13.3) MUTATED   52 44 35 37
  DEL PEAK 40(17P13.3) WILD-TYPE 77 74 49 52
D76V5, multiclass
    clus
vv   DEL PEAK 40(17P13.3) MUTATED DEL PEAK 40(17P13.3) WILD-TYPE
  N0                           52                             77
  N1                           44                             74
  N2                           35                             49
  N3                           37                             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"
D76V6, binary
                                cls
clus                               0   1
  DEL PEAK 40(17P13.3) MUTATED   153  10
  DEL PEAK 40(17P13.3) WILD-TYPE 234  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17P13.3) MUTATED    153   10
  DEL PEAK 40(17P13.3) WILD-TYPE  234   20
   clus
vv  DEL PEAK 40(17P13.3) MUTATED DEL PEAK 40(17P13.3) WILD-TYPE
  0                          153                            234
  1                           10                             20
[1] 2 2
[1] FALSE
D76V7, binary
                                cls
clus                               0   1
  DEL PEAK 40(17P13.3) MUTATED    56 116
  DEL PEAK 40(17P13.3) WILD-TYPE 102 162
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17P13.3) MUTATED     56  116
  DEL PEAK 40(17P13.3) WILD-TYPE  102  162
        clus
vv       DEL PEAK 40(17P13.3) MUTATED DEL PEAK 40(17P13.3) WILD-TYPE
  FEMALE                           56                            102
  MALE                            116                            162
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 40(17P13.3) MUTATED                                      18
  DEL PEAK 40(17P13.3) WILD-TYPE                                    53
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 40(17P13.3) MUTATED                                                       55
  DEL PEAK 40(17P13.3) WILD-TYPE                                                    107
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 40(17P13.3) MUTATED                                                                  36
  DEL PEAK 40(17P13.3) WILD-TYPE                                                                45
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 40(17P13.3) MUTATED                                                 40
  DEL PEAK 40(17P13.3) WILD-TYPE                                               38
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 40(17P13.3) MUTATED                                                          9
  DEL PEAK 40(17P13.3) WILD-TYPE                                                       12
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 40(17P13.3) MUTATED                                                           5
  DEL PEAK 40(17P13.3) WILD-TYPE                                                         3
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 40(17P13.3) MUTATED                                          8
  DEL PEAK 40(17P13.3) WILD-TYPE                                        5
D76V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 40(17P13.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       18
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      55
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            40
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     8
                                                                   clus
vv                                                                  DEL PEAK 40(17P13.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         53
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       107
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             45
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       5
[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"
D76V9, binary
                                cls
clus                               0   1
  DEL PEAK 40(17P13.3) MUTATED     5 167
  DEL PEAK 40(17P13.3) WILD-TYPE   1 263
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17P13.3) MUTATED      5  167
  DEL PEAK 40(17P13.3) WILD-TYPE    1  263
     clus
vv    DEL PEAK 40(17P13.3) MUTATED DEL PEAK 40(17P13.3) WILD-TYPE
  NO                             5                              1
  YES                          167                            263
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 40(17P13.3) MUTATED   137  10   6   5
  DEL PEAK 40(17P13.3) WILD-TYPE 210   8  13  20
D76V10, multiclass
    clus
vv   DEL PEAK 40(17P13.3) MUTATED DEL PEAK 40(17P13.3) WILD-TYPE
  R0                          137                            210
  R1                           10                              8
  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"
D76V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 40(17P13.3) MUTATED      35                         4
  DEL PEAK 40(17P13.3) WILD-TYPE    53                         7
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 40(17P13.3) MUTATED                                           1
  DEL PEAK 40(17P13.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 40(17P13.3) MUTATED     105
  DEL PEAK 40(17P13.3) WILD-TYPE   169
D76V12, multiclass
                                           clus
vv                                          DEL PEAK 40(17P13.3) MUTATED
  ASIAN                                                               35
  BLACK OR AFRICAN AMERICAN                                            4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              105
                                           clus
vv                                          DEL PEAK 40(17P13.3) WILD-TYPE
  ASIAN                                                                 53
  BLACK OR AFRICAN AMERICAN                                              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  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"
D76V13, binary
                                cls
clus                               0   1
  DEL PEAK 40(17P13.3) MUTATED     1 117
  DEL PEAK 40(17P13.3) WILD-TYPE   3 196
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17P13.3) MUTATED      1  117
  DEL PEAK 40(17P13.3) WILD-TYPE    3  196
                        clus
vv                       DEL PEAK 40(17P13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          117
                        clus
vv                       DEL PEAK 40(17P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            196
[1] 2 2
[1] FALSE

Clustering(77) Variable = DEL PEAK 41(17P12) MUTATION ANALYSIS
D77V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 41(17P12) MUTATED   102  67
  DEL PEAK 41(17P12) WILD-TYPE 152  83
  DEL PEAK 41(17P12) MUTATED DEL PEAK 41(17P12) WILD-TYPE 
                         169                          235 
  DEL PEAK 41(17P12) MUTATED DEL PEAK 41(17P12) WILD-TYPE 
                          67                           83 
$`DEL PEAK 41(17P12) MUTATED`
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4267 TCGA-BR-6456 
       11.70        11.01         9.44         6.61         6.18        17.29 
TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 
       19.33         9.17        12.16         9.21        35.24        15.42 
TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 
       28.73        18.71        11.44         0.69         9.60        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8369 
        2.66        16.31        15.58        19.50        13.08        14.04 
TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
       14.79         5.39        25.18        11.54        16.44         9.86 
TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 
       10.68        13.87         7.53        22.26         1.48         0.72 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5800 
       13.51        20.65        20.42         1.15         3.25        13.15 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8533 
        0.07         0.07         0.07         0.10         0.13         0.13 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        0.13         3.42        11.31        12.43        11.61        12.20 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       20.02         3.02        27.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4477 
        4.01        29.98        47.05        19.07         7.07        30.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5725 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 
       36.00         1.02        15.02        79.07         4.01        69.04 
TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 
       11.93        20.55        18.84        18.54        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8576 
       10.26        15.22        15.98        11.31        12.33        14.66 
TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-8122 TCGA-EQ-A4SO 
       16.44        11.31        15.65         7.40         7.99        16.24 
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-A8CX TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
        0.23        26.47         1.51        12.59        14.17        12.10 
TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 
       22.75        11.77         8.98         6.25         2.10        12.95 
TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       12.30        27.42        21.21        18.81         3.39        18.38 
TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NU TCGA-IN-AB1V 
        5.19         1.41         6.44        12.59         1.81         7.82 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
        2.53         5.56        37.64         9.86        45.67        18.21 
TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-VQ-A8DL 
        9.24         8.61        16.67       115.69         8.94         0.92 
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        35.24         7.73 
TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PS 
       46.26        12.79         2.70        17.85         1.87        13.35 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91N TCGA-VQ-A91Q 
       27.35        64.57        14.33        65.16        18.74        20.81 
TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 
       36.16         9.50         9.73        52.24         9.04         4.54 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6B 
       64.18        11.24        22.09        18.41        40.08        29.98 
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        21.11        12.43 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK 41(17P12) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        19.56         9.47         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         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        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 
       32.94        12.82        24.76        23.93        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
       15.32        12.43         3.45         9.07        12.76        17.49 
TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8295 
       14.43        12.26        20.55         8.05         0.56         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         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-8381 
       26.33         4.31         3.32        11.80        19.17         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
       15.85         3.72         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 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU 
       15.81        15.68         8.22        12.56         6.08        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       13.51        12.89         8.98        14.17         0.53        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
        0.66        19.36         0.46        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8526 TCGA-CD-8530 
        2.83        13.18         0.30         0.07         0.07         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MI 
        0.10         0.10         0.10         9.34         6.58         0.10 
TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4460 
       12.62        15.95         1.02        14.01        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 
        0.00         9.01        18.97        12.00        22.98         6.97 
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-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 
       65.10        21.07         7.99        12.36        12.66        19.13 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-8570 TCGA-D7-8572 
       18.61        17.85        12.79        10.55        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        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       11.44         9.76         2.96         8.38         4.34         7.13 
TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
        0.62        14.47        21.27         3.48        19.53        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HU-8243 TCGA-HU-8244 
       59.54         5.03         5.52        18.08         5.92        14.27 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       11.41        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       11.84        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        10.19         0.26        19.36        23.84 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-A6RJ TCGA-IN-A6RN 
        9.67         8.88         8.81         3.45         5.36        13.08 
TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-KB-A93G 
        6.74         6.51         5.56        13.51        60.56        20.15 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
        3.72        19.73         8.52        61.25         6.08         4.60 
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-A8DT TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       48.79        21.73        34.45        27.88        32.48        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PP 
       34.29        16.31        22.19         2.50         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       15.65        26.24        36.69        11.70        11.93        61.22 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
       22.68         1.71         7.36         2.01        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA69 TCGA-VQ-AA6A 
        5.72        21.04         2.66        42.54        28.41        32.94 
TCGA-ZA-A8F6 
       10.62 

  DEL PEAK 41(17P12) MUTATED DEL PEAK 41(17P12) WILD-TYPE 
                        0.07                         0.00 
  DEL PEAK 41(17P12) MUTATED DEL PEAK 41(17P12) WILD-TYPE 
                      115.69                       122.30 
  DEL PEAK 41(17P12) MUTATED DEL PEAK 41(17P12) WILD-TYPE 
                       12.95                        12.82 
[1] "0.1 - 115.7 (12.9)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D77V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 41(17P12) MUTATED         1        7       17       15        15
  DEL PEAK 41(17P12) WILD-TYPE       2        7       24       16        23
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 41(17P12) MUTATED          22         0         38         27
  DEL PEAK 41(17P12) WILD-TYPE        33         4         47         35
                              vv
clus                           STAGE IIIC STAGE IV
  DEL PEAK 41(17P12) MUTATED           14       18
  DEL PEAK 41(17P12) WILD-TYPE         27       28
D77V3, multiclass
            clus
vv           DEL PEAK 41(17P12) MUTATED DEL PEAK 41(17P12) WILD-TYPE
  STAGE I                             1                            2
  STAGE IA                            7                            7
  STAGE IB                           17                           24
  STAGE II                           15                           16
  STAGE IIA                          15                           23
  STAGE IIB                          22                           33
  STAGE III                           0                            4
  STAGE IIIA                         38                           47
  STAGE IIIB                         27                           35
  STAGE IIIC                         14                           27
  STAGE IV                           18                           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 41(17P12) MUTATED     8  42  83  42
  DEL PEAK 41(17P12) WILD-TYPE  14  48 112  77
D77V4, multiclass
    clus
vv   DEL PEAK 41(17P12) MUTATED DEL PEAK 41(17P12) WILD-TYPE
  T1                          8                           14
  T2                         42                           48
  T3                         83                          112
  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 41(17P12) MUTATED   54 45 40 34
  DEL PEAK 41(17P12) WILD-TYPE 75 73 44 55
D77V5, multiclass
    clus
vv   DEL PEAK 41(17P12) MUTATED DEL PEAK 41(17P12) WILD-TYPE
  N0                         54                           75
  N1                         45                           73
  N2                         40                           44
  N3                         34                           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"
D77V6, binary
                              cls
clus                             0   1
  DEL PEAK 41(17P12) MUTATED   157   9
  DEL PEAK 41(17P12) WILD-TYPE 230  21
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 41(17P12) MUTATED    157    9
  DEL PEAK 41(17P12) WILD-TYPE  230   21
   clus
vv  DEL PEAK 41(17P12) MUTATED DEL PEAK 41(17P12) WILD-TYPE
  0                        157                          230
  1                          9                           21
[1] 2 2
[1] FALSE
D77V7, binary
                              cls
clus                             0   1
  DEL PEAK 41(17P12) MUTATED    56 121
  DEL PEAK 41(17P12) WILD-TYPE 102 157
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 41(17P12) MUTATED     56  121
  DEL PEAK 41(17P12) WILD-TYPE  102  157
        clus
vv       DEL PEAK 41(17P12) MUTATED DEL PEAK 41(17P12) WILD-TYPE
  FEMALE                         56                          102
  MALE                          121                          157
[1] 2 2
[1] FALSE
                              vv
clus                           STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 41(17P12) MUTATED                                      15
  DEL PEAK 41(17P12) WILD-TYPE                                    56
                              vv
clus                           STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 41(17P12) MUTATED                                                       58
  DEL PEAK 41(17P12) WILD-TYPE                                                    104
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 41(17P12) MUTATED                                                                  42
  DEL PEAK 41(17P12) WILD-TYPE                                                                39
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 41(17P12) MUTATED                                                 41
  DEL PEAK 41(17P12) WILD-TYPE                                               37
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 41(17P12) MUTATED                                                          9
  DEL PEAK 41(17P12) WILD-TYPE                                                       12
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 41(17P12) MUTATED                                                           4
  DEL PEAK 41(17P12) WILD-TYPE                                                         4
                              vv
clus                           STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 41(17P12) MUTATED                                          8
  DEL PEAK 41(17P12) WILD-TYPE                                        5
D77V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 41(17P12) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    58
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         42
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                          41
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                  4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   8
                                                                   clus
vv                                                                  DEL PEAK 41(17P12) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     104
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     5
[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"
D77V9, binary
                              cls
clus                             0   1
  DEL PEAK 41(17P12) MUTATED     4 173
  DEL PEAK 41(17P12) WILD-TYPE   2 257
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 41(17P12) MUTATED      4  173
  DEL PEAK 41(17P12) WILD-TYPE    2  257
     clus
vv    DEL PEAK 41(17P12) MUTATED DEL PEAK 41(17P12) WILD-TYPE
  NO                           4                            2
  YES                        173                          257
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 41(17P12) MUTATED   142   9   8   5
  DEL PEAK 41(17P12) WILD-TYPE 205   9  11  20
D77V10, multiclass
    clus
vv   DEL PEAK 41(17P12) MUTATED DEL PEAK 41(17P12) WILD-TYPE
  R0                        142                          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"
D77V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 41(17P12) MUTATED      35                         4
  DEL PEAK 41(17P12) WILD-TYPE    53                         7
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 41(17P12) MUTATED                                           1   106
  DEL PEAK 41(17P12) WILD-TYPE                                         0   168
D77V12, multiclass
                                           clus
vv                                          DEL PEAK 41(17P12) MUTATED
  ASIAN                                                             35
  BLACK OR AFRICAN AMERICAN                                          4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                            106
                                           clus
vv                                          DEL PEAK 41(17P12) WILD-TYPE
  ASIAN                                                               53
  BLACK OR AFRICAN AMERICAN                                            7
  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"
D77V13, binary
                              cls
clus                             0   1
  DEL PEAK 41(17P12) MUTATED     1 115
  DEL PEAK 41(17P12) WILD-TYPE   3 198
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 41(17P12) MUTATED      1  115
  DEL PEAK 41(17P12) WILD-TYPE    3  198
                        clus
vv                       DEL PEAK 41(17P12) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                        115
                        clus
vv                       DEL PEAK 41(17P12) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          198
[1] 2 2
[1] FALSE

Clustering(78) Variable = DEL PEAK 42(17Q24.3) MUTATION ANALYSIS
D78V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 42(17Q24.3) MUTATED    40  29
  DEL PEAK 42(17Q24.3) WILD-TYPE 214 121
  DEL PEAK 42(17Q24.3) MUTATED DEL PEAK 42(17Q24.3) WILD-TYPE 
                            69                            335 
  DEL PEAK 42(17Q24.3) MUTATED DEL PEAK 42(17Q24.3) WILD-TYPE 
                            29                            121 
$`DEL PEAK 42(17Q24.3) MUTATED`
TCGA-B7-A5TJ TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7959 
       11.01        19.33         9.17        35.24        15.42        18.71 
TCGA-BR-8077 TCGA-BR-8291 TCGA-BR-8361 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8485 
        0.69        16.31        19.50        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        13.64         0.07         0.10         0.13        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-4444 TCGA-CG-4469 TCGA-CG-5730 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6528 
       47.05         7.07         4.01        11.93        17.19        15.22 
TCGA-D7-8576 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A74A TCGA-EQ-A4SO TCGA-FP-A8CX 
       14.66        16.44        11.31         7.40        16.24         0.23 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GP TCGA-HU-A4H2 TCGA-IN-8462 
        5.92        12.59        14.17         8.98        12.95        18.81 
TCGA-IN-8663 TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7O7 TCGA-RD-A7BT TCGA-RD-A7C1 
        3.39        37.64         9.86        45.67         8.61        16.67 
TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8PC TCGA-VQ-A8PH 
      115.69         8.94         5.79         5.46        46.26        12.79 
TCGA-VQ-A8PX TCGA-VQ-A91N TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A925 TCGA-VQ-A928 
       64.57        18.74         9.50         9.73         4.54         5.72 
TCGA-VQ-A94U TCGA-VQ-AA6I TCGA-ZQ-A9CR 
       22.09        16.14         0.79 

$`DEL PEAK 42(17Q24.3) WILD-TYPE`
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-4267 
        6.97         4.64         7.43        18.35        30.90         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        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 
       32.94        12.82         9.21        24.76        23.93        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       18.15        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 
       12.76        17.49        14.43        11.44        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 
       20.55         8.05         0.56        12.95         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-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-8381 TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8484 
       11.80        19.17         0.26        15.85         5.39        25.18 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4CQ 
       15.68         8.22        10.68        12.56         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        1.48        13.41        13.51        12.89         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE 
        0.53        12.82         0.66        19.36         0.46        20.42 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 
        0.30         0.07         0.07         0.07         0.07         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 
        9.34        12.43         6.58         0.10        12.62         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4443 
       27.02        15.95         1.02         7.99         8.05        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       19.07        12.03        21.99         0.00         9.01        18.97 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       12.00        22.98        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-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07        65.10        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.36        12.66        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-D7-8573 
       10.55        11.31        12.33        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 
       15.16        13.78        14.76        13.71        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
        9.76         2.96        15.65         8.38         4.34         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         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-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HJ-7597 
        5.03        13.58         0.56         5.52        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        1.51        14.27        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
       22.75        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         6.25        10.19         0.26         2.10        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        12.30         9.67         8.88         8.81        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       21.21         3.45        18.38         5.36         5.19        13.08 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
        1.41         6.44         6.74        12.59         6.51         5.56 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        1.81         7.82        13.51         2.53         5.56        60.56 
TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       20.15         3.72        19.73        18.21         8.52        61.25 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV 
        6.08         4.60         9.24        11.05         5.13       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
       37.91        40.64       116.38        71.38        57.44        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       16.87        19.04         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        35.24        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
        7.73        28.96        34.29        16.31        22.19         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-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       13.35        26.24        27.35        14.33        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       11.70        11.93        61.22        20.81        22.68         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
       36.16         7.36        52.24         9.04         2.01        55.43 
TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
        6.58        64.18        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        40.08        28.41        32.94        29.98        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        21.11        12.43        10.62 

  DEL PEAK 42(17Q24.3) MUTATED DEL PEAK 42(17Q24.3) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 42(17Q24.3) MUTATED DEL PEAK 42(17Q24.3) WILD-TYPE 
                        115.69                         122.30 
  DEL PEAK 42(17Q24.3) MUTATED DEL PEAK 42(17Q24.3) WILD-TYPE 
                         12.20                          12.95 
[1] "0.1 - 115.7 (12.2)" "0.0 - 122.3 (12.9)"
[1] "hr=" "1.3"
D78V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 42(17Q24.3) MUTATED         0        1        2        3         7
  DEL PEAK 42(17Q24.3) WILD-TYPE       3       13       39       28        31
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 42(17Q24.3) MUTATED          10         0         18         14
  DEL PEAK 42(17Q24.3) WILD-TYPE        45         4         67         48
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 42(17Q24.3) MUTATED            7        9
  DEL PEAK 42(17Q24.3) WILD-TYPE         34       37
D78V3, multiclass
            clus
vv           DEL PEAK 42(17Q24.3) MUTATED DEL PEAK 42(17Q24.3) WILD-TYPE
  STAGE I                               0                              3
  STAGE IA                              1                             13
  STAGE IB                              2                             39
  STAGE II                              3                             28
  STAGE IIA                             7                             31
  STAGE IIB                            10                             45
  STAGE III                             0                              4
  STAGE IIIA                           18                             67
  STAGE IIIB                           14                             48
  STAGE IIIC                            7                             34
  STAGE IV                              9                             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 42(17Q24.3) MUTATED     1  10  37  24
  DEL PEAK 42(17Q24.3) WILD-TYPE  21  80 158  95
D78V4, multiclass
    clus
vv   DEL PEAK 42(17Q24.3) MUTATED DEL PEAK 42(17Q24.3) WILD-TYPE
  T1                            1                             21
  T2                           10                             80
  T3                           37                            158
  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 42(17Q24.3) MUTATED    17  16  21  17
  DEL PEAK 42(17Q24.3) WILD-TYPE 112 102  63  72
D78V5, multiclass
    clus
vv   DEL PEAK 42(17Q24.3) MUTATED DEL PEAK 42(17Q24.3) WILD-TYPE
  N0                           17                            112
  N1                           16                            102
  N2                           21                             63
  N3                           17                             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"
D78V6, binary
                                cls
clus                               0   1
  DEL PEAK 42(17Q24.3) MUTATED    69   4
  DEL PEAK 42(17Q24.3) WILD-TYPE 318  26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(17Q24.3) MUTATED     69    4
  DEL PEAK 42(17Q24.3) WILD-TYPE  318   26
   clus
vv  DEL PEAK 42(17Q24.3) MUTATED DEL PEAK 42(17Q24.3) WILD-TYPE
  0                           69                            318
  1                            4                             26
[1] 2 2
[1] FALSE
D78V7, binary
                                cls
clus                               0   1
  DEL PEAK 42(17Q24.3) MUTATED    29  47
  DEL PEAK 42(17Q24.3) WILD-TYPE 129 231
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(17Q24.3) MUTATED     29   47
  DEL PEAK 42(17Q24.3) WILD-TYPE  129  231
        clus
vv       DEL PEAK 42(17Q24.3) MUTATED DEL PEAK 42(17Q24.3) WILD-TYPE
  FEMALE                           29                            129
  MALE                             47                            231
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 42(17Q24.3) MUTATED                                       7
  DEL PEAK 42(17Q24.3) WILD-TYPE                                    64
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 42(17Q24.3) MUTATED                                                       27
  DEL PEAK 42(17Q24.3) WILD-TYPE                                                    135
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 42(17Q24.3) MUTATED                                                                  15
  DEL PEAK 42(17Q24.3) WILD-TYPE                                                                66
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 42(17Q24.3) MUTATED                                                 19
  DEL PEAK 42(17Q24.3) WILD-TYPE                                               59
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 42(17Q24.3) MUTATED                                                          3
  DEL PEAK 42(17Q24.3) WILD-TYPE                                                       18
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 42(17Q24.3) MUTATED                                                           2
  DEL PEAK 42(17Q24.3) WILD-TYPE                                                         6
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 42(17Q24.3) MUTATED                                          3
  DEL PEAK 42(17Q24.3) WILD-TYPE                                       10
D78V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 42(17Q24.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      27
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           15
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     3
                                                                   clus
vv                                                                  DEL PEAK 42(17Q24.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         64
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       135
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             66
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              59
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      10
[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"
D78V9, binary
                                cls
clus                               0   1
  DEL PEAK 42(17Q24.3) MUTATED     0  76
  DEL PEAK 42(17Q24.3) WILD-TYPE   6 354
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(17Q24.3) MUTATED      0   76
  DEL PEAK 42(17Q24.3) WILD-TYPE    6  354
     clus
vv    DEL PEAK 42(17Q24.3) MUTATED DEL PEAK 42(17Q24.3) WILD-TYPE
  NO                             0                              6
  YES                           76                            354
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 42(17Q24.3) MUTATED    55   4   6   6
  DEL PEAK 42(17Q24.3) WILD-TYPE 292  14  13  19
D78V10, multiclass
    clus
vv   DEL PEAK 42(17Q24.3) MUTATED DEL PEAK 42(17Q24.3) WILD-TYPE
  R0                           55                            292
  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"
D78V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 42(17Q24.3) MUTATED      15                         0
  DEL PEAK 42(17Q24.3) WILD-TYPE    73                        11
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 42(17Q24.3) MUTATED                                           1
  DEL PEAK 42(17Q24.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 42(17Q24.3) MUTATED      50
  DEL PEAK 42(17Q24.3) WILD-TYPE   224
D78V12, multiclass
                                           clus
vv                                          DEL PEAK 42(17Q24.3) MUTATED
  ASIAN                                                               15
  BLACK OR AFRICAN AMERICAN                                            0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               50
                                           clus
vv                                          DEL PEAK 42(17Q24.3) WILD-TYPE
  ASIAN                                                                 73
  BLACK OR AFRICAN AMERICAN                                             11
  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"
D78V13, binary
                                cls
clus                               0   1
  DEL PEAK 42(17Q24.3) MUTATED     1  55
  DEL PEAK 42(17Q24.3) WILD-TYPE   3 258
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(17Q24.3) MUTATED      1   55
  DEL PEAK 42(17Q24.3) WILD-TYPE    3  258
                        clus
vv                       DEL PEAK 42(17Q24.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           55
                        clus
vv                       DEL PEAK 42(17Q24.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            258
[1] 2 2
[1] FALSE

Clustering(79) Variable = DEL PEAK 43(18Q12.2) MUTATION ANALYSIS
D79V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 43(18Q12.2) MUTATED   108  60
  DEL PEAK 43(18Q12.2) WILD-TYPE 146  90
  DEL PEAK 43(18Q12.2) MUTATED DEL PEAK 43(18Q12.2) WILD-TYPE 
                           168                            236 
  DEL PEAK 43(18Q12.2) MUTATED DEL PEAK 43(18Q12.2) WILD-TYPE 
                            60                             90 
$`DEL PEAK 43(18Q12.2) MUTATED`
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-4267 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6564 TCGA-BR-6709 
        6.18         9.57        17.29        13.68        26.10        12.16 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       35.24        15.42        15.32        28.73         3.45         9.07 
TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8369 
       11.44        12.95        16.31        22.19         0.95        14.04 
TCGA-BR-8370 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8677 TCGA-BR-8683 TCGA-BR-8686 
        3.32        20.22        15.81         0.49         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4IY 
        8.22        10.68        13.87         7.53        22.26        12.89 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 
        0.66        13.51        13.64         3.25        13.18         0.30 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.07         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         0.10         0.13         3.42        12.43        11.61 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       12.20        20.02         3.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
        4.01        47.05        19.07        18.97         7.07        12.00 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5730 TCGA-CG-5732 
       22.98        30.97         1.02        12.03         4.01        69.04 
TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 
       12.36        19.13        20.55        18.54        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6822 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 
       10.26        15.98        12.33        19.50        18.21        14.66 
TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EV TCGA-D7-A6EZ 
       21.14        14.27        16.44        15.16        11.24         9.76 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-A72C 
        2.96        15.65         7.40         0.62         7.99        11.38 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 
       19.53        14.07        22.29        17.06        13.58         0.56 
TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 
        5.52         5.92        14.17        12.10        10.62        24.30 
TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 
       12.30        22.75        11.77         8.98         6.25         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RL 
       12.95        23.84         9.67         3.45        18.38         5.19 
TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 
        1.41         6.74         5.56         1.81        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE 
        5.56        60.56        20.15        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        35.24         7.73        22.19         2.50        17.85 
TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 
       13.35        27.35        36.16         9.50        52.24         9.04 
TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U 
        2.01         4.54        64.18        42.54        11.24        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       18.41        32.94        29.98        26.04        12.43         0.79 

$`DEL PEAK 43(18Q12.2) WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       26.70         6.97         4.64         7.43        18.35        30.90 
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-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-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7851 TCGA-BR-7958 
       24.76        23.93        28.01        18.15        12.43        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 
       20.55         8.05         0.56         2.66         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8365 
        7.40         6.18        19.50        13.08         0.26        17.52 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       26.33         4.31        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 
       15.85         3.72         5.39        25.18         9.21         1.12 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8678 
       12.79         9.34        13.45         6.28         7.53        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       15.81        16.44        12.56         6.08         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       13.51         8.98         0.72        14.17         0.53        12.82 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL 
       19.36         0.46        20.65        20.42         1.15        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8535 
        5.13         2.83        13.15         0.16         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.10         9.34        11.31         6.58         0.10        12.62 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 
       27.02        15.95         1.02        14.01        29.98        12.03 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 
       21.99         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-5727 
        6.02         0.99       105.07        15.02        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 
       65.10        21.07         7.99        12.66        11.93        18.84 
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        10.55        11.31 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YY 
       24.72        16.80        17.19        20.91         5.92        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A747 TCGA-D7-A748 
       14.76        13.71        11.31        11.44         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.13        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       59.54         5.03         0.23        18.08        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 
       14.27        12.59        11.41         0.76         5.59        11.84 
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        10.19         0.26        19.36        12.30         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ 
        8.81        27.42        21.21        18.81         3.39         5.36 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-MX-A5UG 
       13.08         6.44        12.59         6.51         7.82         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT 
       19.73         9.86        61.25         4.60        11.05         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-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        8.94        16.87        19.04        13.02        21.73        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       27.88        32.48        28.96        34.29        46.26        16.31 
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-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       26.24        64.57        14.33        65.16        36.69        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       11.93        61.22        18.74        20.81        22.68         1.71 
TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O 
        7.36         9.73        55.43         6.58         5.72        21.04 
TCGA-VQ-A94P TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6I 
        2.66        40.08        28.41        17.13        54.12        16.14 
TCGA-VQ-AA6J TCGA-ZA-A8F6 
       21.11        10.62 

  DEL PEAK 43(18Q12.2) MUTATED DEL PEAK 43(18Q12.2) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 43(18Q12.2) MUTATED DEL PEAK 43(18Q12.2) WILD-TYPE 
                        115.69                         122.30 
  DEL PEAK 43(18Q12.2) MUTATED DEL PEAK 43(18Q12.2) WILD-TYPE 
                        12.345                         13.080 
[1] "0.1 - 115.7 (12.3)" "0.0 - 122.3 (13.1)"
[1] "hr=" "1.1"
D79V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 43(18Q12.2) MUTATED         1        4       14       15        18
  DEL PEAK 43(18Q12.2) WILD-TYPE       2       10       27       16        20
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 43(18Q12.2) MUTATED          22         2         41         29
  DEL PEAK 43(18Q12.2) WILD-TYPE        33         2         44         33
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 43(18Q12.2) MUTATED           12       17
  DEL PEAK 43(18Q12.2) WILD-TYPE         29       29
D79V3, multiclass
            clus
vv           DEL PEAK 43(18Q12.2) MUTATED DEL PEAK 43(18Q12.2) WILD-TYPE
  STAGE I                               1                              2
  STAGE IA                              4                             10
  STAGE IB                             14                             27
  STAGE II                             15                             16
  STAGE IIA                            18                             20
  STAGE IIB                            22                             33
  STAGE III                             2                              2
  STAGE IIIA                           41                             44
  STAGE IIIB                           29                             33
  STAGE IIIC                           12                             29
  STAGE IV                             17                             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 43(18Q12.2) MUTATED     6  37 101  33
  DEL PEAK 43(18Q12.2) WILD-TYPE  16  53  94  86
D79V4, multiclass
    clus
vv   DEL PEAK 43(18Q12.2) MUTATED DEL PEAK 43(18Q12.2) WILD-TYPE
  T1                            6                             16
  T2                           37                             53
  T3                          101                             94
  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 43(18Q12.2) MUTATED   48 50 39 36
  DEL PEAK 43(18Q12.2) WILD-TYPE 81 68 45 53
D79V5, multiclass
    clus
vv   DEL PEAK 43(18Q12.2) MUTATED DEL PEAK 43(18Q12.2) WILD-TYPE
  N0                           48                             81
  N1                           50                             68
  N2                           39                             45
  N3                           36                             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"
D79V6, binary
                                cls
clus                               0   1
  DEL PEAK 43(18Q12.2) MUTATED   160  11
  DEL PEAK 43(18Q12.2) WILD-TYPE 227  19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(18Q12.2) MUTATED    160   11
  DEL PEAK 43(18Q12.2) WILD-TYPE  227   19
   clus
vv  DEL PEAK 43(18Q12.2) MUTATED DEL PEAK 43(18Q12.2) WILD-TYPE
  0                          160                            227
  1                           11                             19
[1] 2 2
[1] FALSE
D79V7, binary
                                cls
clus                               0   1
  DEL PEAK 43(18Q12.2) MUTATED    60 120
  DEL PEAK 43(18Q12.2) WILD-TYPE  98 158
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(18Q12.2) MUTATED     60  120
  DEL PEAK 43(18Q12.2) WILD-TYPE   98  158
        clus
vv       DEL PEAK 43(18Q12.2) MUTATED DEL PEAK 43(18Q12.2) WILD-TYPE
  FEMALE                           60                             98
  MALE                            120                            158
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 43(18Q12.2) MUTATED                                      27
  DEL PEAK 43(18Q12.2) WILD-TYPE                                    44
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 43(18Q12.2) MUTATED                                                       60
  DEL PEAK 43(18Q12.2) WILD-TYPE                                                    102
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 43(18Q12.2) MUTATED                                                                  38
  DEL PEAK 43(18Q12.2) WILD-TYPE                                                                43
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 43(18Q12.2) MUTATED                                                 41
  DEL PEAK 43(18Q12.2) WILD-TYPE                                               37
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 43(18Q12.2) MUTATED                                                          6
  DEL PEAK 43(18Q12.2) WILD-TYPE                                                       15
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 43(18Q12.2) MUTATED                                                           2
  DEL PEAK 43(18Q12.2) WILD-TYPE                                                         6
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 43(18Q12.2) MUTATED                                          4
  DEL PEAK 43(18Q12.2) WILD-TYPE                                        9
D79V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 43(18Q12.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       27
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      60
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            41
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     4
                                                                   clus
vv                                                                  DEL PEAK 43(18Q12.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         44
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       102
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             43
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       9
[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"
D79V9, binary
                                cls
clus                               0   1
  DEL PEAK 43(18Q12.2) MUTATED     2 178
  DEL PEAK 43(18Q12.2) WILD-TYPE   4 252
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(18Q12.2) MUTATED      2  178
  DEL PEAK 43(18Q12.2) WILD-TYPE    4  252
     clus
vv    DEL PEAK 43(18Q12.2) MUTATED DEL PEAK 43(18Q12.2) WILD-TYPE
  NO                             2                              4
  YES                          178                            252
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 43(18Q12.2) MUTATED   136  10   6   9
  DEL PEAK 43(18Q12.2) WILD-TYPE 211   8  13  16
D79V10, multiclass
    clus
vv   DEL PEAK 43(18Q12.2) MUTATED DEL PEAK 43(18Q12.2) WILD-TYPE
  R0                          136                            211
  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"
D79V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 43(18Q12.2) MUTATED      42                         3
  DEL PEAK 43(18Q12.2) WILD-TYPE    46                         8
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 43(18Q12.2) MUTATED                                           0
  DEL PEAK 43(18Q12.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 43(18Q12.2) MUTATED     108
  DEL PEAK 43(18Q12.2) WILD-TYPE   166
D79V12, multiclass
                                           clus
vv                                          DEL PEAK 43(18Q12.2) MUTATED
  ASIAN                                                               42
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              108
                                           clus
vv                                          DEL PEAK 43(18Q12.2) WILD-TYPE
  ASIAN                                                                 46
  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"
D79V13, binary
                                cls
clus                               0   1
  DEL PEAK 43(18Q12.2) MUTATED     2 127
  DEL PEAK 43(18Q12.2) WILD-TYPE   2 186
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(18Q12.2) MUTATED      2  127
  DEL PEAK 43(18Q12.2) WILD-TYPE    2  186
                        clus
vv                       DEL PEAK 43(18Q12.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          127
                        clus
vv                       DEL PEAK 43(18Q12.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            186
[1] 2 2
[1] FALSE

Clustering(80) Variable = DEL PEAK 44(18Q21.2) MUTATION ANALYSIS
D80V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 44(18Q21.2) MUTATED   124  66
  DEL PEAK 44(18Q21.2) WILD-TYPE 130  84
  DEL PEAK 44(18Q21.2) MUTATED DEL PEAK 44(18Q21.2) WILD-TYPE 
                           190                            214 
  DEL PEAK 44(18Q21.2) MUTATED DEL PEAK 44(18Q21.2) WILD-TYPE 
                            66                             84 
$`DEL PEAK 44(18Q21.2) MUTATED`
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-4267 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 
        6.18         9.57        17.29        13.68        19.33        26.10 
TCGA-BR-6709 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       12.16        35.24        15.42        28.01        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        3.45         9.07        11.44        12.95         2.66        16.31 
TCGA-BR-8297 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8483 
        7.40        22.19         0.95        14.04         3.32         5.39 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8683 
       20.22         1.12        15.81         0.49        15.81         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ 
       15.68         8.22        10.68        13.87         7.53        22.26 
TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4QI 
        1.48        12.89         0.66        13.51        20.42        13.64 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        3.25        13.15        13.18         0.30         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8532 
        0.07         0.07         0.07         0.10         0.13         0.10 
TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4301 
        0.13         3.42        12.43        11.61        12.20         3.02 
TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 
       27.02         7.99         8.05        54.08         4.01        47.05 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5718 
       18.97         7.07        12.00        22.98        30.97        36.00 
TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-5579 
        1.02        12.03         4.01        69.04        12.36        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       19.13        20.55        18.54        13.35        17.19        10.26 
TCGA-D7-6815 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 
       15.98        12.33        24.72        19.50        18.21        14.66 
TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EV TCGA-D7-A6EZ 
       21.14        14.27        16.44        15.16        11.24         9.76 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
        2.96        15.65         7.40         0.62         7.99        16.24 
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-FP-A8CX TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8604 
        0.56         5.52         0.23         5.92        14.17        12.10 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GP 
       10.62        24.30        12.30        22.75        11.77         8.98 
TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        6.25         2.10        12.95        23.84        12.30         9.67 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP 
        3.45        18.81        18.38         5.19         1.41         6.44 
TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        6.74         5.56         1.81        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       60.56        20.15        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        35.24 
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-A8PU TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X 
       13.35        27.35        61.22         1.71        36.16         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A92D 
        9.73        52.24         9.04         2.01         4.54        64.18 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       42.54        11.24        22.09        18.41        32.94        29.98 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       17.13        26.04        12.43         0.79 

$`DEL PEAK 44(18Q21.2) WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       26.70         6.97         4.64         7.43        18.35        30.90 
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        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7851 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       23.93        18.15        12.43        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        0.56         2.20        15.58         6.18        19.50        13.08 
TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8371 TCGA-BR-8372 
        0.26        17.52        26.33         4.31        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 
       14.79         0.26        15.85         3.72        25.18         9.21 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8678 
       12.79         9.34        13.45         6.28         7.53        11.54 
TCGA-BR-8682 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
       16.44        12.56         6.08        13.41        13.51         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 
        0.72        14.17         0.53        12.82        19.36         0.46 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-8530 
       20.65         1.15        11.57         5.13         2.83         0.16 
TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG 
        0.10         0.13         0.10         9.34        11.31         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 
        0.10        12.62        20.02        15.95         1.02        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       29.98        19.07        12.03        21.99         0.00         9.01 
TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 
        6.97         0.99         6.02         0.99       105.07        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 
       28.96        79.07        65.10        21.07         7.99        12.66 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 
       18.84        18.61        17.85        15.22        12.79        10.55 
TCGA-D7-6820 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YY 
       11.31        16.80        17.19        20.91         5.92        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A747 TCGA-D7-A748 
       14.76        13.71        11.31        11.44         8.38         4.34 
TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-8209 
        7.13        14.47        72.23        21.27         3.48        59.54 
TCGA-FP-8210 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
        5.03        18.08        26.47         1.51        14.27        12.59 
TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       11.41         0.76         5.59        11.84        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        10.19 
TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
        0.26        19.36         8.88         8.81        27.42        21.21 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V 
        3.39         5.36        13.08        12.59         6.51         7.82 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS 
        3.72        19.73         9.86        61.25         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-A8DU TCGA-VQ-A8DZ 
       57.44         8.94        16.87        19.04         5.46        13.02 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       34.45        27.88        32.48        28.96        34.29        46.26 
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-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       26.24        64.57        14.33        65.16        36.69        11.70 
TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A924 
       11.93        18.74        20.81        22.68         7.36        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-AA68 TCGA-VQ-AA69 
        6.58         5.72        21.04         2.66        40.08        28.41 
TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       54.12        16.14        21.11        10.62 

  DEL PEAK 44(18Q21.2) MUTATED DEL PEAK 44(18Q21.2) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 44(18Q21.2) MUTATED DEL PEAK 44(18Q21.2) WILD-TYPE 
                        115.69                         122.30 
  DEL PEAK 44(18Q21.2) MUTATED DEL PEAK 44(18Q21.2) WILD-TYPE 
                        12.395                         13.050 
[1] "0.1 - 115.7 (12.4)" "0.0 - 122.3 (13.1)"
[1] "hr=" "1"  
D80V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 44(18Q21.2) MUTATED         1        4       17       16        20
  DEL PEAK 44(18Q21.2) WILD-TYPE       2       10       24       15        18
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 44(18Q21.2) MUTATED          25         2         45         30
  DEL PEAK 44(18Q21.2) WILD-TYPE        30         2         40         32
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 44(18Q21.2) MUTATED           18       19
  DEL PEAK 44(18Q21.2) WILD-TYPE         23       27
D80V3, multiclass
            clus
vv           DEL PEAK 44(18Q21.2) MUTATED DEL PEAK 44(18Q21.2) WILD-TYPE
  STAGE I                               1                              2
  STAGE IA                              4                             10
  STAGE IB                             17                             24
  STAGE II                             16                             15
  STAGE IIA                            20                             18
  STAGE IIB                            25                             30
  STAGE III                             2                              2
  STAGE IIIA                           45                             40
  STAGE IIIB                           30                             32
  STAGE IIIC                           18                             23
  STAGE IV                             19                             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(18Q21.2) MUTATED     7  42 109  42
  DEL PEAK 44(18Q21.2) WILD-TYPE  15  48  86  77
D80V4, multiclass
    clus
vv   DEL PEAK 44(18Q21.2) MUTATED DEL PEAK 44(18Q21.2) WILD-TYPE
  T1                            7                             15
  T2                           42                             48
  T3                          109                             86
  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 44(18Q21.2) MUTATED   54 57 40 44
  DEL PEAK 44(18Q21.2) WILD-TYPE 75 61 44 45
D80V5, multiclass
    clus
vv   DEL PEAK 44(18Q21.2) MUTATED DEL PEAK 44(18Q21.2) WILD-TYPE
  N0                           54                             75
  N1                           57                             61
  N2                           40                             44
  N3                           44                             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V6, binary
                                cls
clus                               0   1
  DEL PEAK 44(18Q21.2) MUTATED   179  13
  DEL PEAK 44(18Q21.2) WILD-TYPE 208  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(18Q21.2) MUTATED    179   13
  DEL PEAK 44(18Q21.2) WILD-TYPE  208   17
   clus
vv  DEL PEAK 44(18Q21.2) MUTATED DEL PEAK 44(18Q21.2) WILD-TYPE
  0                          179                            208
  1                           13                             17
[1] 2 2
[1] FALSE
D80V7, binary
                                cls
clus                               0   1
  DEL PEAK 44(18Q21.2) MUTATED    68 135
  DEL PEAK 44(18Q21.2) WILD-TYPE  90 143
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(18Q21.2) MUTATED     68  135
  DEL PEAK 44(18Q21.2) WILD-TYPE   90  143
        clus
vv       DEL PEAK 44(18Q21.2) MUTATED DEL PEAK 44(18Q21.2) WILD-TYPE
  FEMALE                           68                             90
  MALE                            135                            143
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 44(18Q21.2) MUTATED                                      28
  DEL PEAK 44(18Q21.2) WILD-TYPE                                    43
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 44(18Q21.2) MUTATED                                                       70
  DEL PEAK 44(18Q21.2) WILD-TYPE                                                     92
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 44(18Q21.2) MUTATED                                                                  44
  DEL PEAK 44(18Q21.2) WILD-TYPE                                                                37
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 44(18Q21.2) MUTATED                                                 44
  DEL PEAK 44(18Q21.2) WILD-TYPE                                               34
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 44(18Q21.2) MUTATED                                                          6
  DEL PEAK 44(18Q21.2) WILD-TYPE                                                       15
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 44(18Q21.2) MUTATED                                                           4
  DEL PEAK 44(18Q21.2) WILD-TYPE                                                         4
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 44(18Q21.2) MUTATED                                          5
  DEL PEAK 44(18Q21.2) WILD-TYPE                                        8
D80V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 44(18Q21.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       28
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      70
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           44
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            44
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     5
                                                                   clus
vv                                                                  DEL PEAK 44(18Q21.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         43
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        92
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       8
[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"
D80V9, binary
                                cls
clus                               0   1
  DEL PEAK 44(18Q21.2) MUTATED     2 201
  DEL PEAK 44(18Q21.2) WILD-TYPE   4 229
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(18Q21.2) MUTATED      2  201
  DEL PEAK 44(18Q21.2) WILD-TYPE    4  229
     clus
vv    DEL PEAK 44(18Q21.2) MUTATED DEL PEAK 44(18Q21.2) WILD-TYPE
  NO                             2                              4
  YES                          201                            229
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 44(18Q21.2) MUTATED   156  11   7  10
  DEL PEAK 44(18Q21.2) WILD-TYPE 191   7  12  15
D80V10, multiclass
    clus
vv   DEL PEAK 44(18Q21.2) MUTATED DEL PEAK 44(18Q21.2) WILD-TYPE
  R0                          156                            191
  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"
D80V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 44(18Q21.2) MUTATED      46                         3
  DEL PEAK 44(18Q21.2) WILD-TYPE    42                         8
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 44(18Q21.2) MUTATED                                           0
  DEL PEAK 44(18Q21.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 44(18Q21.2) MUTATED     126
  DEL PEAK 44(18Q21.2) WILD-TYPE   148
D80V12, multiclass
                                           clus
vv                                          DEL PEAK 44(18Q21.2) MUTATED
  ASIAN                                                               46
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              126
                                           clus
vv                                          DEL PEAK 44(18Q21.2) WILD-TYPE
  ASIAN                                                                 42
  BLACK OR AFRICAN AMERICAN                                              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                148
[1] 4 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(18Q21.2) MUTATED     2 145
  DEL PEAK 44(18Q21.2) WILD-TYPE   2 168
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(18Q21.2) MUTATED      2  145
  DEL PEAK 44(18Q21.2) WILD-TYPE    2  168
                        clus
vv                       DEL PEAK 44(18Q21.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          145
                        clus
vv                       DEL PEAK 44(18Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            168
[1] 2 2
[1] FALSE

Clustering(81) Variable = DEL PEAK 45(19P13.3) MUTATION ANALYSIS
D81V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 45(19P13.3) MUTATED    87  60
  DEL PEAK 45(19P13.3) WILD-TYPE 167  90
  DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE 
                           147                            257 
  DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE 
                            60                             90 
$`DEL PEAK 45(19P13.3) MUTATED`
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-6458 TCGA-BR-6565 
       19.56        11.01         9.44         6.61        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        28.01        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        12.95         2.66        16.31         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        11.54        10.68        22.26 
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         3.25 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.15         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
        0.13         0.16         0.13         0.13         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 
       11.31        12.43        11.61        12.20        20.02         7.99 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4466 
       54.08         4.01        29.98        19.07        21.99        18.97 
TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 
       22.98        36.00        12.03        15.02         4.01        69.04 
TCGA-D7-5578 TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
       12.66        18.84        13.35        10.26        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-8578 TCGA-D7-A6F0 TCGA-D7-A6F2 
       10.55        11.31        19.50        21.14         2.96        15.65 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 
        7.99        72.23        11.38        14.07        17.06         0.56 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 
        5.92        12.59        11.77         8.98         6.25         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 
       12.95        23.84        12.30         9.67        27.42        21.21 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RR 
       18.81         3.39        18.38         5.19         1.41         6.74 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       12.59         5.56         1.81         2.53         5.56        60.56 
TCGA-KB-A93G TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-R5-A805 
       20.15        37.64        45.67        18.21         6.08         9.24 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DL 
        8.61         5.13        37.91         8.94         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        35.24 
TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       34.45         7.73        22.19        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y 
        1.87        27.35         1.71        36.16         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A94O 
       52.24         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        40.08        32.94        17.13        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       21.11        12.43         0.79 

$`DEL PEAK 45(19P13.3) WILD-TYPE`
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-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         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-7703 
       21.11        30.90        31.20        32.94        12.82        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 
       23.93        15.42        18.15        15.32        12.43         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 
       12.76        18.71        17.49        14.43        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       20.55         8.05         0.56        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       19.50        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-8381 
       26.33         4.31         3.32        11.80        19.17         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 
       15.85         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 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T 
       15.81        16.44         9.86        15.68         8.22        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
       13.87         7.53         6.08        13.41        13.51         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        12.82         0.66        19.36        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.42        13.64        11.57         5.13         2.83 
TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8528 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 
       13.18         0.07         0.10         0.10         0.10         0.10 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        6.58         0.10        12.62         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4462 
        1.02         8.05        14.01        47.05        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 
        9.01         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-5727 
        0.99         6.02         0.99       105.07        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 
       65.10        21.07         7.99        12.36        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6528 
       20.55        18.54        18.61        17.85        17.19        15.22 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       12.33        24.72        16.80        17.19        18.21        14.66 
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        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        13.71        11.24        11.31        11.44         9.76 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO 
        8.38         4.34         7.40         7.13         0.62        16.24 
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-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 
        5.03        13.58         5.52         0.23        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        1.51        14.27        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
        3.25        22.75        25.81        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        10.19         0.26        19.36         8.88         8.81 
TCGA-IN-7808 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-AB1V 
        3.45         5.36        13.08         6.44         6.51         7.82 
TCGA-IN-AB1X TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZF TCGA-R5-A7ZI 
       13.51         3.72        19.73         9.86         8.52        61.25 
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        27.88        32.48        28.96        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 
       26.24        64.57        14.33        65.16        36.69        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91W 
       11.93        61.22        18.74        20.81        22.68         7.36 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
       55.43         6.58        64.18         2.66        42.54        11.24 
TCGA-VQ-A94U TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-ZA-A8F6 
       22.09        28.41        29.98        54.12        10.62 

  DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE 
                         72.23                         122.30 
  DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE 
                         12.03                          13.51 
[1] "0.1 - 72.2 (12.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D81V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 45(19P13.3) MUTATED         1        6       13       13        13
  DEL PEAK 45(19P13.3) WILD-TYPE       2        8       28       18        25
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 45(19P13.3) MUTATED          23         1         33         19
  DEL PEAK 45(19P13.3) WILD-TYPE        32         3         52         43
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 45(19P13.3) MUTATED           14       17
  DEL PEAK 45(19P13.3) WILD-TYPE         27       29
D81V3, multiclass
            clus
vv           DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE
  STAGE I                               1                              2
  STAGE IA                              6                              8
  STAGE IB                             13                             28
  STAGE II                             13                             18
  STAGE IIA                            13                             25
  STAGE IIB                            23                             32
  STAGE III                             1                              3
  STAGE IIIA                           33                             52
  STAGE IIIB                           19                             43
  STAGE IIIC                           14                             27
  STAGE IV                             17                             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 45(19P13.3) MUTATED     7  34  78  35
  DEL PEAK 45(19P13.3) WILD-TYPE  15  56 117  84
D81V4, multiclass
    clus
vv   DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE
  T1                            7                             15
  T2                           34                             56
  T3                           78                            117
  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 45(19P13.3) MUTATED   44 44 29 34
  DEL PEAK 45(19P13.3) WILD-TYPE 85 74 55 55
D81V5, multiclass
    clus
vv   DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE
  N0                           44                             85
  N1                           44                             74
  N2                           29                             55
  N3                           34                             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"
D81V6, binary
                                cls
clus                               0   1
  DEL PEAK 45(19P13.3) MUTATED   140  10
  DEL PEAK 45(19P13.3) WILD-TYPE 247  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(19P13.3) MUTATED    140   10
  DEL PEAK 45(19P13.3) WILD-TYPE  247   20
   clus
vv  DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE
  0                          140                            247
  1                           10                             20
[1] 2 2
[1] FALSE
D81V7, binary
                                cls
clus                               0   1
  DEL PEAK 45(19P13.3) MUTATED    48 110
  DEL PEAK 45(19P13.3) WILD-TYPE 110 168
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(19P13.3) MUTATED     48  110
  DEL PEAK 45(19P13.3) WILD-TYPE  110  168
        clus
vv       DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE
  FEMALE                           48                            110
  MALE                            110                            168
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 45(19P13.3) MUTATED                                      15
  DEL PEAK 45(19P13.3) WILD-TYPE                                    56
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 45(19P13.3) MUTATED                                                       53
  DEL PEAK 45(19P13.3) WILD-TYPE                                                    109
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 45(19P13.3) MUTATED                                                                  41
  DEL PEAK 45(19P13.3) WILD-TYPE                                                                40
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 45(19P13.3) MUTATED                                                 34
  DEL PEAK 45(19P13.3) WILD-TYPE                                               44
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 45(19P13.3) MUTATED                                                          5
  DEL PEAK 45(19P13.3) WILD-TYPE                                                       16
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 45(19P13.3) MUTATED                                                           5
  DEL PEAK 45(19P13.3) WILD-TYPE                                                         3
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 45(19P13.3) MUTATED                                          4
  DEL PEAK 45(19P13.3) WILD-TYPE                                        9
D81V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 45(19P13.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      53
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           41
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     4
                                                                   clus
vv                                                                  DEL PEAK 45(19P13.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       109
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              44
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       9
[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"
D81V9, binary
                                cls
clus                               0   1
  DEL PEAK 45(19P13.3) MUTATED     5 153
  DEL PEAK 45(19P13.3) WILD-TYPE   1 277
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(19P13.3) MUTATED      5  153
  DEL PEAK 45(19P13.3) WILD-TYPE    1  277
     clus
vv    DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE
  NO                             5                              1
  YES                          153                            277
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 45(19P13.3) MUTATED   123   4   9   6
  DEL PEAK 45(19P13.3) WILD-TYPE 224  14  10  19
D81V10, multiclass
    clus
vv   DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE
  R0                          123                            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"
D81V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 45(19P13.3) MUTATED      37                         6
  DEL PEAK 45(19P13.3) WILD-TYPE    51                         5
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 45(19P13.3) MUTATED                                           1
  DEL PEAK 45(19P13.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 45(19P13.3) MUTATED      89
  DEL PEAK 45(19P13.3) WILD-TYPE   185
D81V12, multiclass
                                           clus
vv                                          DEL PEAK 45(19P13.3) MUTATED
  ASIAN                                                               37
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               89
                                           clus
vv                                          DEL PEAK 45(19P13.3) WILD-TYPE
  ASIAN                                                                 51
  BLACK OR AFRICAN AMERICAN                                              5
  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"
D81V13, binary
                                cls
clus                               0   1
  DEL PEAK 45(19P13.3) MUTATED     1 102
  DEL PEAK 45(19P13.3) WILD-TYPE   3 211
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(19P13.3) MUTATED      1  102
  DEL PEAK 45(19P13.3) WILD-TYPE    3  211
                        clus
vv                       DEL PEAK 45(19P13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          102
                        clus
vv                       DEL PEAK 45(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            211
[1] 2 2
[1] FALSE

Clustering(82) Variable = DEL PEAK 46(19Q13.11) MUTATION ANALYSIS
D82V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 46(19Q13.11) MUTATED    45  27
  DEL PEAK 46(19Q13.11) WILD-TYPE 209 123
  DEL PEAK 46(19Q13.11) MUTATED DEL PEAK 46(19Q13.11) WILD-TYPE 
                             72                             332 
  DEL PEAK 46(19Q13.11) MUTATED DEL PEAK 46(19Q13.11) WILD-TYPE 
                             27                             123 
$`DEL PEAK 46(19Q13.11) MUTATED`
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 
       11.01         9.44         6.61         9.21        35.24        15.42 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8369 
       28.73         3.45        11.44         0.69         2.66        14.04 
TCGA-BR-8678 TCGA-BR-A4CS TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8527 
       11.54         1.48         1.15         3.25        13.15         0.07 
TCGA-CD-8529 TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A489 TCGA-CG-4300 TCGA-CG-4440 
        0.13         0.13         3.42        11.31        20.02         4.01 
TCGA-CG-4466 TCGA-CG-5724 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 
       18.97        12.03        17.19        10.26        15.22        12.79 
TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-A4YY TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.31        19.50        13.78        11.31         2.96        15.65 
TCGA-EQ-5647 TCGA-FP-8099 TCGA-FP-8631 TCGA-HU-8243 TCGA-HU-A4GH TCGA-HU-A4GP 
        0.62        17.06         0.56         5.92        11.77         8.98 
TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RS 
        6.25        12.95        23.84        27.42        18.38        12.59 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A93H TCGA-R5-A7O7 TCGA-RD-A8MW TCGA-VQ-A8DU 
        5.56         1.81        37.64        45.67        37.91         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8P3 TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PU 
       13.02        18.48        32.48        12.79        17.85        27.35 
TCGA-VQ-A91N TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 
       18.74        36.16         9.50        52.24         9.04         4.54 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-AA6D TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       64.18        21.04        17.13        16.14        21.11         0.79 

$`DEL PEAK 46(19Q13.11) WILD-TYPE`
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-4267 TCGA-BR-4279 TCGA-BR-4280 
        7.43        18.35        30.90         6.18         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-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        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 
       32.94        12.82        24.76        23.93        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       15.32        12.43         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       14.43        12.26         9.60        20.55         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       12.95        16.31         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 
       19.50        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        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         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        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08        22.26        13.41        13.51        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        12.82         0.66        19.36 
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        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        5.13         2.83        13.18         0.30         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.07         0.10         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        0.13         0.10         9.34        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20         0.10        12.62         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 
        1.02         7.99         8.05        54.08        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       47.05        19.07        12.03        21.99         0.00         9.01 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        7.07        12.00        22.98        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-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        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        12.36        12.66        11.93        19.13        20.55 
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-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 
       10.55        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-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ 
       15.16        14.76        13.71        11.24        11.44         9.76 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO 
        8.38         4.34         7.40         7.13         7.99        16.24 
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-A4BF 
       14.07        22.29        59.54         5.03        13.58         5.52 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
        0.23        18.08        26.47         1.51        14.27        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        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        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        0.26         2.10        19.36        12.30         9.67         8.88 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ 
        8.81        21.21         3.45        18.81         3.39         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR 
        5.19        13.08         1.41         6.44         6.74         6.51 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G 
        7.82        13.51         2.53         5.56        60.56        20.15 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        19.73         9.86        18.21         8.52        61.25 
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-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-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        0.92        48.79        13.25        35.24        21.73        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       27.88         7.73        28.96        34.29        46.26        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       22.19         2.50         2.70         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        13.35        26.24        64.57        14.33        65.16 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S 
       36.69        11.70        11.93        61.22        20.81        22.68 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
        1.71         7.36         9.73         2.01        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 
        5.72         2.66        42.54        11.24        22.09        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       40.08        28.41        32.94        29.98        54.12        26.04 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        10.62 

  DEL PEAK 46(19Q13.11) MUTATED DEL PEAK 46(19Q13.11) WILD-TYPE 
                           0.07                            0.00 
  DEL PEAK 46(19Q13.11) MUTATED DEL PEAK 46(19Q13.11) WILD-TYPE 
                          64.18                          122.30 
  DEL PEAK 46(19Q13.11) MUTATED DEL PEAK 46(19Q13.11) WILD-TYPE 
                         12.310                          13.015 
[1] "0.1 - 64.2 (12.3)"  "0.0 - 122.3 (13.0)"
[1] "hr=" "1.1"
D82V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 46(19Q13.11) MUTATED         1        2        6        7         6
  DEL PEAK 46(19Q13.11) WILD-TYPE       2       12       35       24        32
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 46(19Q13.11) MUTATED           8         0         15         13
  DEL PEAK 46(19Q13.11) WILD-TYPE        47         4         70         49
                                 vv
clus                              STAGE IIIC STAGE IV
  DEL PEAK 46(19Q13.11) MUTATED            6        9
  DEL PEAK 46(19Q13.11) WILD-TYPE         35       37
D82V3, multiclass
            clus
vv           DEL PEAK 46(19Q13.11) MUTATED DEL PEAK 46(19Q13.11) WILD-TYPE
  STAGE I                                1                               2
  STAGE IA                               2                              12
  STAGE IB                               6                              35
  STAGE II                               7                              24
  STAGE IIA                              6                              32
  STAGE IIB                              8                              47
  STAGE III                              0                               4
  STAGE IIIA                            15                              70
  STAGE IIIB                            13                              49
  STAGE IIIC                             6                              35
  STAGE IV                               9                              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 46(19Q13.11) MUTATED     3  14  37  19
  DEL PEAK 46(19Q13.11) WILD-TYPE  19  76 158 100
D82V4, multiclass
    clus
vv   DEL PEAK 46(19Q13.11) MUTATED DEL PEAK 46(19Q13.11) WILD-TYPE
  T1                             3                              19
  T2                            14                              76
  T3                            37                             158
  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 46(19Q13.11) MUTATED    19  17  15  20
  DEL PEAK 46(19Q13.11) WILD-TYPE 110 101  69  69
D82V5, multiclass
    clus
vv   DEL PEAK 46(19Q13.11) MUTATED DEL PEAK 46(19Q13.11) WILD-TYPE
  N0                            19                             110
  N1                            17                             101
  N2                            15                              69
  N3                            20                              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"
D82V6, binary
                                 cls
clus                                0   1
  DEL PEAK 46(19Q13.11) MUTATED    65   7
  DEL PEAK 46(19Q13.11) WILD-TYPE 322  23
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 46(19Q13.11) MUTATED     65    7
  DEL PEAK 46(19Q13.11) WILD-TYPE  322   23
   clus
vv  DEL PEAK 46(19Q13.11) MUTATED DEL PEAK 46(19Q13.11) WILD-TYPE
  0                            65                             322
  1                             7                              23
[1] 2 2
[1] FALSE
D82V7, binary
                                 cls
clus                                0   1
  DEL PEAK 46(19Q13.11) MUTATED    25  50
  DEL PEAK 46(19Q13.11) WILD-TYPE 133 228
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 46(19Q13.11) MUTATED     25   50
  DEL PEAK 46(19Q13.11) WILD-TYPE  133  228
        clus
vv       DEL PEAK 46(19Q13.11) MUTATED DEL PEAK 46(19Q13.11) WILD-TYPE
  FEMALE                            25                             133
  MALE                              50                             228
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 46(19Q13.11) MUTATED                                       5
  DEL PEAK 46(19Q13.11) WILD-TYPE                                    66
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 46(19Q13.11) MUTATED                                                       24
  DEL PEAK 46(19Q13.11) WILD-TYPE                                                    138
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 46(19Q13.11) MUTATED                                                                  17
  DEL PEAK 46(19Q13.11) WILD-TYPE                                                                64
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 46(19Q13.11) MUTATED                                                 25
  DEL PEAK 46(19Q13.11) WILD-TYPE                                               53
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 46(19Q13.11) MUTATED                                                          1
  DEL PEAK 46(19Q13.11) WILD-TYPE                                                       20
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 46(19Q13.11) MUTATED                                                           2
  DEL PEAK 46(19Q13.11) WILD-TYPE                                                         6
                                 vv
clus                              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 46(19Q13.11) MUTATED                                          1
  DEL PEAK 46(19Q13.11) WILD-TYPE                                       12
D82V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 46(19Q13.11) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       24
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             25
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      1
                                                                   clus
vv                                                                  DEL PEAK 46(19Q13.11) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          66
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        138
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              64
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               53
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       12
[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"
D82V9, binary
                                 cls
clus                                0   1
  DEL PEAK 46(19Q13.11) MUTATED     1  74
  DEL PEAK 46(19Q13.11) WILD-TYPE   5 356
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 46(19Q13.11) MUTATED      1   74
  DEL PEAK 46(19Q13.11) WILD-TYPE    5  356
     clus
vv    DEL PEAK 46(19Q13.11) MUTATED DEL PEAK 46(19Q13.11) WILD-TYPE
  NO                              1                               5
  YES                            74                             356
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 46(19Q13.11) MUTATED    60   1   5   3
  DEL PEAK 46(19Q13.11) WILD-TYPE 287  17  14  22
D82V10, multiclass
    clus
vv   DEL PEAK 46(19Q13.11) MUTATED DEL PEAK 46(19Q13.11) WILD-TYPE
  R0                            60                             287
  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"
D82V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 46(19Q13.11) MUTATED      15                         4
  DEL PEAK 46(19Q13.11) WILD-TYPE    73                         7
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 46(19Q13.11) MUTATED                                           0
  DEL PEAK 46(19Q13.11) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 46(19Q13.11) MUTATED      47
  DEL PEAK 46(19Q13.11) WILD-TYPE   227
D82V12, multiclass
                                           clus
vv                                          DEL PEAK 46(19Q13.11) MUTATED
  ASIAN                                                                15
  BLACK OR AFRICAN AMERICAN                                             4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                47
                                           clus
vv                                          DEL PEAK 46(19Q13.11) WILD-TYPE
  ASIAN                                                                  73
  BLACK OR AFRICAN AMERICAN                                               7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 227
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V13, binary
                                 cls
clus                                0   1
  DEL PEAK 46(19Q13.11) MUTATED     1  50
  DEL PEAK 46(19Q13.11) WILD-TYPE   3 263
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 46(19Q13.11) MUTATED      1   50
  DEL PEAK 46(19Q13.11) WILD-TYPE    3  263
                        clus
vv                       DEL PEAK 46(19Q13.11) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            50
                        clus
vv                       DEL PEAK 46(19Q13.11) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             263
[1] 2 2
[1] FALSE

Clustering(83) Variable = DEL PEAK 47(20P12.1) MUTATION ANALYSIS
D83V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 47(20P12.1) MUTATED    17  19
  DEL PEAK 47(20P12.1) WILD-TYPE 237 131
  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                            36                            368 
  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                            19                            131 
$`DEL PEAK 47(20P12.1) MUTATED`
TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6564 TCGA-BR-7723 TCGA-BR-8289 TCGA-BR-A4IY 
        6.18        17.29        26.10        28.73         2.66        12.89 
TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-8525 TCGA-CD-A48C TCGA-CG-4301 TCGA-CG-5717 
       20.65        13.64         0.07        11.61         3.02         6.97 
TCGA-CG-5725 TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-8575 TCGA-D7-8576 
       15.02        20.55        17.19        10.26        18.21        14.66 
TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-HU-8249 TCGA-HU-A4GF TCGA-IN-A6RJ TCGA-IN-A6RO 
        0.62        16.24        14.17        25.81         5.36         1.41 
TCGA-IN-AB1V TCGA-IP-7968 TCGA-RD-A8MW TCGA-SW-A7EA TCGA-VQ-A8DU TCGA-VQ-A8E0 
        7.82         2.53        37.91        19.04         5.46        18.48 
TCGA-VQ-A8P3 TCGA-VQ-A8PC TCGA-VQ-A8PK TCGA-VQ-A925 TCGA-VQ-AA68 TCGA-VQ-AA6D 
       32.48        46.26        17.85         4.54        40.08        17.13 

$`DEL PEAK 47(20P12.1) WILD-TYPE`
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-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
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-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-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       32.94        12.82         9.21        24.76        35.24        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 
       15.42        28.01        18.15        15.32        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        12.76        18.71        17.49        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        12.26         9.60        20.55         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       12.95        16.31         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 
       19.50        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        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         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        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       13.51         8.98         0.72        14.17         0.53        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36        13.51         0.46        20.42         1.15 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.30         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
        0.13         0.16         0.10         0.10         0.13         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG 
        0.10         3.42         9.34        11.31        12.43         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 
       12.20         0.10        12.62        20.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       29.98        47.05        19.07        12.03        21.99         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
        9.01        18.97         7.07        12.00        22.98        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-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        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        12.36        12.66        11.93        19.13 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 
       18.84        18.54        18.61        17.85        13.35        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        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        15.16        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44         9.76         2.96        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 
        8.38         4.34         7.40         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-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        5.52         0.23        18.08        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       14.27        12.59        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        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         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       19.36        23.84        12.30         9.67         8.88         8.81 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       27.42        21.21         3.45        18.81         3.39        18.38 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
        5.19        13.08         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G 
        5.56         1.81        13.51         5.56        60.56        20.15 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       37.64         3.72        19.73         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        61.25         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        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        34.45        27.88         7.73        28.96        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-A8PU 
        9.27        23.41        15.65        13.35        26.24        27.35 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        65.16        36.69        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       61.22        18.74        20.81        22.68         1.71        36.16 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
        7.36         9.50         9.73        52.24         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P 
       55.43         6.58         5.72        64.18        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       42.54        11.24        22.09        18.41        28.41        32.94 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       29.98        54.12        26.04        16.14        21.11        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                         46.26                         122.30 
  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                        14.840                         12.775 
[1] "0.1 - 46.3 (14.8)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.5"
D83V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 47(20P12.1) MUTATED         0        2        5        2         2
  DEL PEAK 47(20P12.1) WILD-TYPE       3       12       36       29        36
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 47(20P12.1) MUTATED           4         0         11          7
  DEL PEAK 47(20P12.1) WILD-TYPE        51         4         74         55
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 47(20P12.1) MUTATED            1        4
  DEL PEAK 47(20P12.1) WILD-TYPE         40       42
D83V3, multiclass
            clus
vv           DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE
  STAGE I                               0                              3
  STAGE IA                              2                             12
  STAGE IB                              5                             36
  STAGE II                              2                             29
  STAGE IIA                             2                             36
  STAGE IIB                             4                             51
  STAGE III                             0                              4
  STAGE IIIA                           11                             74
  STAGE IIIB                            7                             55
  STAGE IIIC                            1                             40
  STAGE IV                              4                             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 47(20P12.1) MUTATED     3   8  18   9
  DEL PEAK 47(20P12.1) WILD-TYPE  19  82 177 110
D83V4, multiclass
    clus
vv   DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE
  T1                            3                             19
  T2                            8                             82
  T3                           18                            177
  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 47(20P12.1) MUTATED    11  11   9   7
  DEL PEAK 47(20P12.1) WILD-TYPE 118 107  75  82
D83V5, multiclass
    clus
vv   DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE
  N0                           11                            118
  N1                           11                            107
  N2                            9                             75
  N3                            7                             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"
D83V6, binary
                                cls
clus                               0   1
  DEL PEAK 47(20P12.1) MUTATED    32   3
  DEL PEAK 47(20P12.1) WILD-TYPE 355  27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(20P12.1) MUTATED     32    3
  DEL PEAK 47(20P12.1) WILD-TYPE  355   27
   clus
vv  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE
  0                           32                            355
  1                            3                             27
[1] 2 2
[1] FALSE
D83V7, binary
                                cls
clus                               0   1
  DEL PEAK 47(20P12.1) MUTATED    16  22
  DEL PEAK 47(20P12.1) WILD-TYPE 142 256
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(20P12.1) MUTATED     16   22
  DEL PEAK 47(20P12.1) WILD-TYPE  142  256
        clus
vv       DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE
  FEMALE                           16                            142
  MALE                             22                            256
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 47(20P12.1) MUTATED                                       3
  DEL PEAK 47(20P12.1) WILD-TYPE                                    68
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 47(20P12.1) MUTATED                                                       17
  DEL PEAK 47(20P12.1) WILD-TYPE                                                    145
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 47(20P12.1) MUTATED                                                                   4
  DEL PEAK 47(20P12.1) WILD-TYPE                                                                77
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 47(20P12.1) MUTATED                                                 10
  DEL PEAK 47(20P12.1) WILD-TYPE                                               68
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 47(20P12.1) MUTATED                                                          2
  DEL PEAK 47(20P12.1) WILD-TYPE                                                       19
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 47(20P12.1) MUTATED                                                           1
  DEL PEAK 47(20P12.1) WILD-TYPE                                                         7
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 47(20P12.1) MUTATED                                          1
  DEL PEAK 47(20P12.1) WILD-TYPE                                       12
D83V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 47(20P12.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      17
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     1
                                                                   clus
vv                                                                  DEL PEAK 47(20P12.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         68
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       145
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             77
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              68
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      12
[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"
D83V9, binary
                                cls
clus                               0   1
  DEL PEAK 47(20P12.1) MUTATED     2  36
  DEL PEAK 47(20P12.1) WILD-TYPE   4 394
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(20P12.1) MUTATED      2   36
  DEL PEAK 47(20P12.1) WILD-TYPE    4  394
     clus
vv    DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE
  NO                             2                              4
  YES                           36                            394
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 47(20P12.1) MUTATED    32   1   3   1
  DEL PEAK 47(20P12.1) WILD-TYPE 315  17  16  24
D83V10, multiclass
    clus
vv   DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE
  R0                           32                            315
  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"
D83V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 47(20P12.1) MUTATED       6                         1
  DEL PEAK 47(20P12.1) WILD-TYPE    82                        10
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 47(20P12.1) MUTATED                                           0
  DEL PEAK 47(20P12.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 47(20P12.1) MUTATED      25
  DEL PEAK 47(20P12.1) WILD-TYPE   249
D83V12, multiclass
                                           clus
vv                                          DEL PEAK 47(20P12.1) MUTATED
  ASIAN                                                                6
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               25
                                           clus
vv                                          DEL PEAK 47(20P12.1) WILD-TYPE
  ASIAN                                                                 82
  BLACK OR AFRICAN AMERICAN                                             10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                249
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V13, binary
                                cls
clus                               0   1
  DEL PEAK 47(20P12.1) MUTATED     0  25
  DEL PEAK 47(20P12.1) WILD-TYPE   4 288
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(20P12.1) MUTATED      0   25
  DEL PEAK 47(20P12.1) WILD-TYPE    4  288
                        clus
vv                       DEL PEAK 47(20P12.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           25
                        clus
vv                       DEL PEAK 47(20P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            288
[1] 2 2
[1] FALSE

Clustering(84) Variable = DEL PEAK 48(21Q11.2) MUTATION ANALYSIS
D84V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 48(21Q11.2) MUTATED   101  69
  DEL PEAK 48(21Q11.2) WILD-TYPE 153  81
  DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE 
                           170                            234 
  DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE 
                            69                             81 
$`DEL PEAK 48(21Q11.2) MUTATED`
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-6457 TCGA-BR-6458 
       11.70        11.01         9.44         6.97        13.68        19.33 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6803 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       26.10         9.17        31.20        35.24        15.42        28.01 
TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       28.73        18.71        11.44        12.26         9.60         8.05 
TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8361 TCGA-BR-8365 TCGA-BR-8368 TCGA-BR-8369 
       16.31        15.58        19.50        17.52         4.31        14.04 
TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 
       14.79         5.39        25.18         9.21        20.22        11.54 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ 
        9.86        15.68         8.22        10.68         7.53        22.26 
TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
        1.48        12.89         0.72        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 
       20.42         1.15        13.64         0.07         0.07         0.07 
TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.16         0.13         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4455 
       12.20        20.02        54.08         4.01        47.05        12.03 
TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97        22.98        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        11.93        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-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 
       21.14        16.44        11.31        15.65         0.62         7.99 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 
       72.23        11.38        19.53         5.52         0.23        26.47 
TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GP 
        1.51        14.17        12.10        11.84         3.25         8.98 
TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 
        0.26        19.36        12.30         9.67        27.42        21.21 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO 
       18.81         3.39        18.38         5.36         5.19         1.41 
TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 
        6.74         5.56         1.81         7.82         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       60.56        20.15        37.64         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A8MV TCGA-RD-A8MW 
        8.52        61.25         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-A8PU 
       22.19         2.70        17.85         1.87        23.41        27.35 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       64.57        14.33        36.69        61.22        18.74        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
        1.71        36.16         9.50         9.73        52.24         9.04 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T 
        2.01        55.43         4.54        21.04        42.54        11.24 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       22.09        18.41        40.08        29.98        54.12        26.04 
TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       12.43         0.79 

$`DEL PEAK 48(21Q11.2) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       26.70        19.56         9.47         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         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        21.11        30.90 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 
       32.94        12.82         9.21        24.76        23.93        18.15 
TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
       15.32        12.43         3.45         9.07        12.76        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       14.43         0.69        20.55         0.56        12.95         2.66 
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-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 
        0.95        26.33         3.32        11.80        19.17         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       15.85         3.72         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        15.81        16.44 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
       12.56        13.87         6.08        13.41        13.51         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4QL 
       14.17         0.53        12.82         0.66        19.36        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.07         0.10         0.13         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.13         0.10         3.42         6.58         0.10        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-4449 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        21.99         0.00         9.01 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        7.07        12.00         0.99         6.02         0.99       105.07 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        28.96        79.07        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       12.36        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        10.55        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       17.19        18.21        14.66        20.91        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
       15.16        13.78        14.76        13.71        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
        9.76         2.96         8.38         4.34         7.40         7.13 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
       16.24        14.47        21.27         3.48        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-A5NB 
       17.06        59.54         5.03        13.58         0.56        18.08 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
        5.92        14.27        12.59        11.41        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF 
       24.30         5.59        12.30        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         6.25 
TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-HU-A4HB 
       10.19         2.10        12.95        23.84         8.88         8.81 
TCGA-IN-7808 TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1X 
        3.45        13.08         6.44        12.59         6.51        13.51 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        3.72        19.73         4.60        11.05         8.61         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-A8DU TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
        5.46        35.24        34.45        27.88        32.48        28.96 
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-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E 
       15.65        13.35        26.24        65.16        11.70        11.93 
TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P 
       22.68         7.36         6.58         5.72        64.18         2.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       28.41        32.94        17.13        16.14        21.11        10.62 

  DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE 
                        122.30                         116.38 
  DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE 
                        12.955                         12.805 
[1] "0.1 - 122.3 (13.0)" "0.0 - 116.4 (12.8)"
[1] "hr=" "1"  
D84V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 48(21Q11.2) MUTATED         1        5       18        9        17
  DEL PEAK 48(21Q11.2) WILD-TYPE       2        9       23       22        21
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 48(21Q11.2) MUTATED          24         1         44         24
  DEL PEAK 48(21Q11.2) WILD-TYPE        31         3         41         38
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 48(21Q11.2) MUTATED           16       18
  DEL PEAK 48(21Q11.2) WILD-TYPE         25       28
D84V3, multiclass
            clus
vv           DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE
  STAGE I                               1                              2
  STAGE IA                              5                              9
  STAGE IB                             18                             23
  STAGE II                              9                             22
  STAGE IIA                            17                             21
  STAGE IIB                            24                             31
  STAGE III                             1                              3
  STAGE IIIA                           44                             41
  STAGE IIIB                           24                             38
  STAGE IIIC                           16                             25
  STAGE IV                             18                             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 48(21Q11.2) MUTATED     7  37  88  46
  DEL PEAK 48(21Q11.2) WILD-TYPE  15  53 107  73
D84V4, multiclass
    clus
vv   DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE
  T1                            7                             15
  T2                           37                             53
  T3                           88                            107
  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 48(21Q11.2) MUTATED   49 52 42 32
  DEL PEAK 48(21Q11.2) WILD-TYPE 80 66 42 57
D84V5, multiclass
    clus
vv   DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE
  N0                           49                             80
  N1                           52                             66
  N2                           42                             42
  N3                           32                             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"
D84V6, binary
                                cls
clus                               0   1
  DEL PEAK 48(21Q11.2) MUTATED   163  10
  DEL PEAK 48(21Q11.2) WILD-TYPE 224  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(21Q11.2) MUTATED    163   10
  DEL PEAK 48(21Q11.2) WILD-TYPE  224   20
   clus
vv  DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE
  0                          163                            224
  1                           10                             20
[1] 2 2
[1] FALSE
D84V7, binary
                                cls
clus                               0   1
  DEL PEAK 48(21Q11.2) MUTATED    70 111
  DEL PEAK 48(21Q11.2) WILD-TYPE  88 167
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(21Q11.2) MUTATED     70  111
  DEL PEAK 48(21Q11.2) WILD-TYPE   88  167
        clus
vv       DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE
  FEMALE                           70                             88
  MALE                            111                            167
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 48(21Q11.2) MUTATED                                      23
  DEL PEAK 48(21Q11.2) WILD-TYPE                                    48
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 48(21Q11.2) MUTATED                                                       61
  DEL PEAK 48(21Q11.2) WILD-TYPE                                                    101
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 48(21Q11.2) MUTATED                                                                  41
  DEL PEAK 48(21Q11.2) WILD-TYPE                                                                40
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 48(21Q11.2) MUTATED                                                 37
  DEL PEAK 48(21Q11.2) WILD-TYPE                                               41
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 48(21Q11.2) MUTATED                                                          9
  DEL PEAK 48(21Q11.2) WILD-TYPE                                                       12
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 48(21Q11.2) MUTATED                                                           1
  DEL PEAK 48(21Q11.2) WILD-TYPE                                                         7
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 48(21Q11.2) MUTATED                                          8
  DEL PEAK 48(21Q11.2) WILD-TYPE                                        5
D84V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 48(21Q11.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       23
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      61
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           41
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     8
                                                                   clus
vv                                                                  DEL PEAK 48(21Q11.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       101
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              41
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       5
[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"
D84V9, binary
                                cls
clus                               0   1
  DEL PEAK 48(21Q11.2) MUTATED     4 177
  DEL PEAK 48(21Q11.2) WILD-TYPE   2 253
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(21Q11.2) MUTATED      4  177
  DEL PEAK 48(21Q11.2) WILD-TYPE    2  253
     clus
vv    DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE
  NO                             4                              2
  YES                          177                            253
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 48(21Q11.2) MUTATED   145   9   8   6
  DEL PEAK 48(21Q11.2) WILD-TYPE 202   9  11  19
D84V10, multiclass
    clus
vv   DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE
  R0                          145                            202
  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"
D84V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 48(21Q11.2) MUTATED      32                         6
  DEL PEAK 48(21Q11.2) WILD-TYPE    56                         5
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 48(21Q11.2) MUTATED                                           0
  DEL PEAK 48(21Q11.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 48(21Q11.2) MUTATED     113
  DEL PEAK 48(21Q11.2) WILD-TYPE   161
D84V12, multiclass
                                           clus
vv                                          DEL PEAK 48(21Q11.2) MUTATED
  ASIAN                                                               32
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              113
                                           clus
vv                                          DEL PEAK 48(21Q11.2) WILD-TYPE
  ASIAN                                                                 56
  BLACK OR AFRICAN AMERICAN                                              5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                161
[1] 4 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(21Q11.2) MUTATED     2 119
  DEL PEAK 48(21Q11.2) WILD-TYPE   2 194
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(21Q11.2) MUTATED      2  119
  DEL PEAK 48(21Q11.2) WILD-TYPE    2  194
                        clus
vv                       DEL PEAK 48(21Q11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          119
                        clus
vv                       DEL PEAK 48(21Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            194
[1] 2 2
[1] FALSE

Clustering(85) Variable = DEL PEAK 49(21Q22.3) MUTATION ANALYSIS
D85V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 49(21Q22.3) MUTATED   110  69
  DEL PEAK 49(21Q22.3) WILD-TYPE 144  81
  DEL PEAK 49(21Q22.3) MUTATED DEL PEAK 49(21Q22.3) WILD-TYPE 
                           179                            225 
  DEL PEAK 49(21Q22.3) MUTATED DEL PEAK 49(21Q22.3) WILD-TYPE 
                            69                             81 
$`DEL PEAK 49(21Q22.3) MUTATED`
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-6457 
       11.70        11.01         9.44         6.97        18.35        13.68 
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        15.42 
TCGA-BR-7716 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8284 
       28.01        18.71        14.43        11.44         9.60         8.05 
TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8369 
       16.31        15.58         7.40        19.50         4.31        14.04 
TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8683 
       14.79         5.39        25.18         9.21        11.54         9.86 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY 
       15.68        10.68         7.53        22.26         1.48        12.89 
TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI 
        0.72        13.51         0.46        20.65         1.15        13.64 
TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8535 
        0.07         0.07         0.07         0.10         0.16         0.13 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4437 
       11.31        12.43        11.61        12.20        20.02         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 
       54.08         4.01        47.05        19.07        12.03        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5724 
        7.07        22.98        30.97         6.97         1.02        12.03 
TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5579 TCGA-D7-6518 
       15.02        65.10         4.01        69.04        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
       20.55        13.35        17.19        10.26        15.98        12.79 
TCGA-D7-6820 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 
       11.31        21.14        14.27        16.44        11.31        15.65 
TCGA-D7-A74A TCGA-EQ-5647 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-8099 
        7.40         0.62        72.23        11.38        19.53        17.06 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8604 
        5.52         0.23        26.47         1.51        14.17        12.10 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H2 
       11.84         3.25         8.98         6.25         0.26        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-8462 
       19.36        23.84        12.30         9.67        21.21        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RR 
        3.39        18.38         5.36         5.19         1.41         6.74 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 
        6.51         5.56         1.81         7.82         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       60.56        20.15        37.64         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7C1 TCGA-RD-A8MV 
        8.52        61.25         6.08         9.24        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
       37.91       115.69        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E7 
        5.79         0.92        48.79        13.25        18.48        34.45 
TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PP 
        7.73        46.26        22.19        17.85         1.87        23.41 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91K TCGA-VQ-A91N 
       27.35        64.57        14.33        36.69        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       20.81         1.71        36.16         9.50         9.73        52.24 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T 
        2.01        55.43         4.54        21.04        42.54        11.24 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       22.09        18.41        40.08        29.98        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       26.04        16.14        21.11        12.43         0.79 

$`DEL PEAK 49(21Q22.3) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       26.70        19.56         9.47         6.61         4.64         7.43 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         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        21.11        30.90        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 
       12.82         9.21        24.76        23.93        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
       28.73        12.43         3.45         9.07        12.76        17.49 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.69        12.26        20.55         0.56        12.95         2.66 
TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         6.18        13.08         0.26        22.19        17.52 
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        19.17         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       15.85         3.72        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        9.34        13.45         6.28         7.53         0.49        15.81 
TCGA-BR-8682 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU 
       16.44         8.22        12.56        13.87         6.08        13.41 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       13.51         8.98        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       19.36        20.42        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8529 
       13.15        13.18         0.30         0.07         0.07         0.13 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        6.58         0.10        12.62         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4460 TCGA-CG-4462 
        1.02         7.99        14.01        29.98        21.99         0.00 
TCGA-CG-4465 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        9.01        12.00        36.00         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
      105.07        28.96        79.07        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6528 
       12.66        18.84        18.54        18.61        17.85        15.22 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       10.55        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       18.21        14.66        20.91         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        13.71        11.24        11.44         9.76         2.96 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
        8.38         4.34         7.13         7.99        16.24        14.47 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
       21.27         3.48        14.07        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-A5NB TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       13.58         0.56        18.08         5.92        14.27        12.59 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       11.41        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H8 TCGA-HU-A4HB 
        0.10         6.51        10.19         2.10         8.88         8.81 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-AB1X 
       27.42         3.45        13.08         6.44        12.59        13.51 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        3.72        19.73         4.60        11.05         8.61         5.13 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-VQ-A8DU TCGA-VQ-A8DZ 
       40.64       116.38        71.38        16.87         5.46        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       35.24        21.73        27.88        32.48        28.96        34.29 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PQ 
       16.31         2.50        12.79         2.70         9.27        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91S 
       13.35        26.24        65.16        11.70        11.93        22.68 
TCGA-VQ-A91W TCGA-VQ-A922 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P 
        7.36         9.04         6.58         5.72        64.18         2.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-ZA-A8F6 
       28.41        32.94        10.62 

  DEL PEAK 49(21Q22.3) MUTATED DEL PEAK 49(21Q22.3) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 49(21Q22.3) MUTATED DEL PEAK 49(21Q22.3) WILD-TYPE 
                        122.30                         116.38 
  DEL PEAK 49(21Q22.3) MUTATED DEL PEAK 49(21Q22.3) WILD-TYPE 
                         13.51                          12.66 
[1] "0.1 - 122.3 (13.5)" "0.0 - 116.4 (12.7)"
[1] "hr=" "1.1"
D85V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 49(21Q22.3) MUTATED         1        4       19       11        17
  DEL PEAK 49(21Q22.3) WILD-TYPE       2       10       22       20        21
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 49(21Q22.3) MUTATED          23         2         47         26
  DEL PEAK 49(21Q22.3) WILD-TYPE        32         2         38         36
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 49(21Q22.3) MUTATED           16       19
  DEL PEAK 49(21Q22.3) WILD-TYPE         25       27
D85V3, multiclass
            clus
vv           DEL PEAK 49(21Q22.3) MUTATED DEL PEAK 49(21Q22.3) WILD-TYPE
  STAGE I                               1                              2
  STAGE IA                              4                             10
  STAGE IB                             19                             22
  STAGE II                             11                             20
  STAGE IIA                            17                             21
  STAGE IIB                            23                             32
  STAGE III                             2                              2
  STAGE IIIA                           47                             38
  STAGE IIIB                           26                             36
  STAGE IIIC                           16                             25
  STAGE IV                             19                             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 49(21Q22.3) MUTATED     6  43  91  46
  DEL PEAK 49(21Q22.3) WILD-TYPE  16  47 104  73
D85V4, multiclass
    clus
vv   DEL PEAK 49(21Q22.3) MUTATED DEL PEAK 49(21Q22.3) WILD-TYPE
  T1                            6                             16
  T2                           43                             47
  T3                           91                            104
  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 49(21Q22.3) MUTATED   49 56 42 37
  DEL PEAK 49(21Q22.3) WILD-TYPE 80 62 42 52
D85V5, multiclass
    clus
vv   DEL PEAK 49(21Q22.3) MUTATED DEL PEAK 49(21Q22.3) WILD-TYPE
  N0                           49                             80
  N1                           56                             62
  N2                           42                             42
  N3                           37                             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"
D85V6, binary
                                cls
clus                               0   1
  DEL PEAK 49(21Q22.3) MUTATED   173  10
  DEL PEAK 49(21Q22.3) WILD-TYPE 214  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 49(21Q22.3) MUTATED    173   10
  DEL PEAK 49(21Q22.3) WILD-TYPE  214   20
   clus
vv  DEL PEAK 49(21Q22.3) MUTATED DEL PEAK 49(21Q22.3) WILD-TYPE
  0                          173                            214
  1                           10                             20
[1] 2 2
[1] FALSE
D85V7, binary
                                cls
clus                               0   1
  DEL PEAK 49(21Q22.3) MUTATED    70 121
  DEL PEAK 49(21Q22.3) WILD-TYPE  88 157
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 49(21Q22.3) MUTATED     70  121
  DEL PEAK 49(21Q22.3) WILD-TYPE   88  157
        clus
vv       DEL PEAK 49(21Q22.3) MUTATED DEL PEAK 49(21Q22.3) WILD-TYPE
  FEMALE                           70                             88
  MALE                            121                            157
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 49(21Q22.3) MUTATED                                      26
  DEL PEAK 49(21Q22.3) WILD-TYPE                                    45
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 49(21Q22.3) MUTATED                                                       61
  DEL PEAK 49(21Q22.3) WILD-TYPE                                                    101
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 49(21Q22.3) MUTATED                                                                  44
  DEL PEAK 49(21Q22.3) WILD-TYPE                                                                37
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 49(21Q22.3) MUTATED                                                 39
  DEL PEAK 49(21Q22.3) WILD-TYPE                                               39
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 49(21Q22.3) MUTATED                                                         10
  DEL PEAK 49(21Q22.3) WILD-TYPE                                                       11
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 49(21Q22.3) MUTATED                                                           2
  DEL PEAK 49(21Q22.3) WILD-TYPE                                                         6
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 49(21Q22.3) MUTATED                                          8
  DEL PEAK 49(21Q22.3) WILD-TYPE                                        5
D85V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 49(21Q22.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       26
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      61
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           44
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            39
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     8
                                                                   clus
vv                                                                  DEL PEAK 49(21Q22.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         45
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       101
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              39
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       5
[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"
D85V9, binary
                                cls
clus                               0   1
  DEL PEAK 49(21Q22.3) MUTATED     4 187
  DEL PEAK 49(21Q22.3) WILD-TYPE   2 243
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 49(21Q22.3) MUTATED      4  187
  DEL PEAK 49(21Q22.3) WILD-TYPE    2  243
     clus
vv    DEL PEAK 49(21Q22.3) MUTATED DEL PEAK 49(21Q22.3) WILD-TYPE
  NO                             4                              2
  YES                          187                            243
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 49(21Q22.3) MUTATED   156   9   6   8
  DEL PEAK 49(21Q22.3) WILD-TYPE 191   9  13  17
D85V10, multiclass
    clus
vv   DEL PEAK 49(21Q22.3) MUTATED DEL PEAK 49(21Q22.3) WILD-TYPE
  R0                          156                            191
  R1                            9                              9
  R2                            6                             13
  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(21Q22.3) MUTATED      33                         6
  DEL PEAK 49(21Q22.3) WILD-TYPE    55                         5
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 49(21Q22.3) MUTATED                                           0
  DEL PEAK 49(21Q22.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 49(21Q22.3) MUTATED     119
  DEL PEAK 49(21Q22.3) WILD-TYPE   155
D85V12, multiclass
                                           clus
vv                                          DEL PEAK 49(21Q22.3) MUTATED
  ASIAN                                                               33
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              119
                                           clus
vv                                          DEL PEAK 49(21Q22.3) WILD-TYPE
  ASIAN                                                                 55
  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"
D85V13, binary
                                cls
clus                               0   1
  DEL PEAK 49(21Q22.3) MUTATED     2 124
  DEL PEAK 49(21Q22.3) WILD-TYPE   2 189
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 49(21Q22.3) MUTATED      2  124
  DEL PEAK 49(21Q22.3) WILD-TYPE    2  189
                        clus
vv                       DEL PEAK 49(21Q22.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          124
                        clus
vv                       DEL PEAK 49(21Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            189
[1] 2 2
[1] FALSE

Clustering(86) Variable = DEL PEAK 50(22Q13.31) MUTATION ANALYSIS
D86V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 50(22Q13.31) MUTATED    88  59
  DEL PEAK 50(22Q13.31) WILD-TYPE 166  91
  DEL PEAK 50(22Q13.31) MUTATED DEL PEAK 50(22Q13.31) WILD-TYPE 
                            147                             257 
  DEL PEAK 50(22Q13.31) MUTATED DEL PEAK 50(22Q13.31) WILD-TYPE 
                             59                              91 
$`DEL PEAK 50(22Q13.31) MUTATED`
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6456 
       11.01         9.44         6.61        18.35         6.18        17.29 
TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7715 
       19.33        26.10         9.17        12.16         9.21        15.42 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8295 
       17.49        14.43        11.44         0.69         9.60         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8369 TCGA-BR-8484 TCGA-BR-8677 
        7.40         6.18        19.50        14.04        25.18         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A4CQ 
       11.54        16.44         9.86         8.22        10.68        22.26 
TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI 
       12.89         0.72        19.36        20.65         1.15        13.64 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8533 
        3.25        13.15         0.07         0.07         0.16         0.13 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        3.42         9.34        11.31        12.43        11.61        12.20 
TCGA-CG-4301 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 
        3.02         8.05        54.08         4.01        14.01        47.05 
TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5724 TCGA-CG-5725 
       19.07        21.99        18.97        30.97        12.03        15.02 
TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6525 TCGA-D7-6526 
       69.04        12.66        11.93        20.55        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       10.26        15.22        12.79        11.31        12.33        24.72 
TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 
       19.50        18.21        21.14        16.44        11.31        15.65 
TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8631 
        7.40         0.62        16.24        19.53        17.06         0.56 
TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4GY 
        5.52         5.92        14.17        22.75         8.98         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-8663 
        2.10        12.95        23.84         9.67        27.42         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38         5.36         5.19        13.08         6.44         6.74 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93G TCGA-MX-A663 
        1.81         7.82         2.53         5.56        20.15         9.86 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 
       45.67        18.21         6.08         8.61        16.67       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-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P3 TCGA-VQ-A8PC TCGA-VQ-A8PE 
       13.02        18.48        35.24        32.48        46.26        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A91A 
       12.79        17.85         1.87        27.35        14.33        36.69 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y 
       18.74        20.81         1.71        36.16         9.50         9.73 
TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 
        9.04         4.54        64.18        11.24        22.09        18.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-ZQ-A9CR 
       32.94        29.98         0.79 

$`DEL PEAK 50(22Q13.31) WILD-TYPE`
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-4201 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        7.43        30.90         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.87        13.68        39.12        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        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 
       12.82        24.76        35.24        23.93        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       18.71        12.26        20.55         8.05         0.56        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        2.66        16.31        15.58        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 
       19.17        14.79         0.26        15.85         3.72         5.39 
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        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-A44T 
       13.45         6.28         7.53        15.81        15.68        12.56 
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        13.41        13.51 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 
        8.98        14.17         0.53        12.82         0.66        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 
        0.46        20.42        11.57         5.13         2.83        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.30         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MI 
        0.10         0.10         0.13         0.10         6.58         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02        27.02        15.95         1.02         7.99 
TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 
       29.98        12.03         0.00         9.01         7.07        12.00 
TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       22.98         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        28.96        79.07        65.10         4.01 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
       21.07         7.99        12.36        19.13        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-8572 TCGA-D7-8574 
       18.61        17.85        15.98        10.55        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        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        13.71        11.24        11.44         9.76         2.96 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
        8.38         4.34         7.13         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
       21.27        11.38         3.48        14.07        22.29        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        5.03        13.58         0.23        18.08        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       14.27        12.59        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        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-A4GU TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB 
        6.25        10.19        19.36        12.30         8.88         8.81 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NR 
       21.21         3.45        18.81         1.41        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        13.51        60.56        37.64         3.72        19.73 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW 
        8.52        61.25         4.60         9.24        11.05         5.13 
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-A8NB TCGA-SW-A7EA TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        8.94        16.87        19.04        21.73        34.45        27.88 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PJ 
        7.73        28.96        34.29        16.31         2.50         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        26.24        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91W 
       65.16        11.70        11.93        61.22        22.68         7.36 
TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O 
       52.24         2.01        55.43         6.58         5.72        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F 
        2.66        42.54        40.08        28.41        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        21.11        12.43        10.62 

  DEL PEAK 50(22Q13.31) MUTATED DEL PEAK 50(22Q13.31) WILD-TYPE 
                           0.07                            0.00 
  DEL PEAK 50(22Q13.31) MUTATED DEL PEAK 50(22Q13.31) WILD-TYPE 
                         115.69                          122.30 
  DEL PEAK 50(22Q13.31) MUTATED DEL PEAK 50(22Q13.31) WILD-TYPE 
                          12.79                           12.95 
[1] "0.1 - 115.7 (12.8)" "0.0 - 122.3 (12.9)"
[1] "hr=" "1.2"
D86V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 50(22Q13.31) MUTATED         1        1       16       11        12
  DEL PEAK 50(22Q13.31) WILD-TYPE       2       13       25       20        26
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 50(22Q13.31) MUTATED          19         2         38         25
  DEL PEAK 50(22Q13.31) WILD-TYPE        36         2         47         37
                                 vv
clus                              STAGE IIIC STAGE IV
  DEL PEAK 50(22Q13.31) MUTATED           13       15
  DEL PEAK 50(22Q13.31) WILD-TYPE         28       31
D86V3, multiclass
            clus
vv           DEL PEAK 50(22Q13.31) MUTATED DEL PEAK 50(22Q13.31) WILD-TYPE
  STAGE I                                1                               2
  STAGE IA                               1                              13
  STAGE IB                              16                              25
  STAGE II                              11                              20
  STAGE IIA                             12                              26
  STAGE IIB                             19                              36
  STAGE III                              2                               2
  STAGE IIIA                            38                              47
  STAGE IIIB                            25                              37
  STAGE IIIC                            13                              28
  STAGE IV                              15                              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 50(22Q13.31) MUTATED     5  34  76  39
  DEL PEAK 50(22Q13.31) WILD-TYPE  17  56 119  80
D86V4, multiclass
    clus
vv   DEL PEAK 50(22Q13.31) MUTATED DEL PEAK 50(22Q13.31) WILD-TYPE
  T1                             5                              17
  T2                            34                              56
  T3                            76                             119
  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 50(22Q13.31) MUTATED   41 37 39 34
  DEL PEAK 50(22Q13.31) WILD-TYPE 88 81 45 55
D86V5, multiclass
    clus
vv   DEL PEAK 50(22Q13.31) MUTATED DEL PEAK 50(22Q13.31) WILD-TYPE
  N0                            41                              88
  N1                            37                              81
  N2                            39                              45
  N3                            34                              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"
D86V6, binary
                                 cls
clus                                0   1
  DEL PEAK 50(22Q13.31) MUTATED   145   7
  DEL PEAK 50(22Q13.31) WILD-TYPE 242  23
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 50(22Q13.31) MUTATED    145    7
  DEL PEAK 50(22Q13.31) WILD-TYPE  242   23
   clus
vv  DEL PEAK 50(22Q13.31) MUTATED DEL PEAK 50(22Q13.31) WILD-TYPE
  0                           145                             242
  1                             7                              23
[1] 2 2
[1] FALSE
D86V7, binary
                                 cls
clus                                0   1
  DEL PEAK 50(22Q13.31) MUTATED    52 106
  DEL PEAK 50(22Q13.31) WILD-TYPE 106 172
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 50(22Q13.31) MUTATED     52  106
  DEL PEAK 50(22Q13.31) WILD-TYPE  106  172
        clus
vv       DEL PEAK 50(22Q13.31) MUTATED DEL PEAK 50(22Q13.31) WILD-TYPE
  FEMALE                            52                             106
  MALE                             106                             172
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 50(22Q13.31) MUTATED                                      18
  DEL PEAK 50(22Q13.31) WILD-TYPE                                    53
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 50(22Q13.31) MUTATED                                                       56
  DEL PEAK 50(22Q13.31) WILD-TYPE                                                    106
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 50(22Q13.31) MUTATED                                                                  27
  DEL PEAK 50(22Q13.31) WILD-TYPE                                                                54
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 50(22Q13.31) MUTATED                                                 40
  DEL PEAK 50(22Q13.31) WILD-TYPE                                               38
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 50(22Q13.31) MUTATED                                                          9
  DEL PEAK 50(22Q13.31) WILD-TYPE                                                       12
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 50(22Q13.31) MUTATED                                                           2
  DEL PEAK 50(22Q13.31) WILD-TYPE                                                         6
                                 vv
clus                              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 50(22Q13.31) MUTATED                                          6
  DEL PEAK 50(22Q13.31) WILD-TYPE                                        7
D86V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 50(22Q13.31) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        18
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       56
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            27
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             40
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      6
                                                                   clus
vv                                                                  DEL PEAK 50(22Q13.31) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          53
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        106
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              54
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                        7
[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"
D86V9, binary
                                 cls
clus                                0   1
  DEL PEAK 50(22Q13.31) MUTATED     4 154
  DEL PEAK 50(22Q13.31) WILD-TYPE   2 276
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 50(22Q13.31) MUTATED      4  154
  DEL PEAK 50(22Q13.31) WILD-TYPE    2  276
     clus
vv    DEL PEAK 50(22Q13.31) MUTATED DEL PEAK 50(22Q13.31) WILD-TYPE
  NO                              4                               2
  YES                           154                             276
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 50(22Q13.31) MUTATED   122   8   9   8
  DEL PEAK 50(22Q13.31) WILD-TYPE 225  10  10  17
D86V10, multiclass
    clus
vv   DEL PEAK 50(22Q13.31) MUTATED DEL PEAK 50(22Q13.31) WILD-TYPE
  R0                           122                             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"
D86V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 50(22Q13.31) MUTATED      31                         3
  DEL PEAK 50(22Q13.31) WILD-TYPE    57                         8
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 50(22Q13.31) MUTATED                                           1
  DEL PEAK 50(22Q13.31) WILD-TYPE                                         0
                                 vv
clus                              WHITE
  DEL PEAK 50(22Q13.31) MUTATED      99
  DEL PEAK 50(22Q13.31) WILD-TYPE   175
D86V12, multiclass
                                           clus
vv                                          DEL PEAK 50(22Q13.31) MUTATED
  ASIAN                                                                31
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                99
                                           clus
vv                                          DEL PEAK 50(22Q13.31) WILD-TYPE
  ASIAN                                                                  57
  BLACK OR AFRICAN AMERICAN                                               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               0
  WHITE                                                                 175
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V13, binary
                                 cls
clus                                0   1
  DEL PEAK 50(22Q13.31) MUTATED     1 108
  DEL PEAK 50(22Q13.31) WILD-TYPE   3 205
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 50(22Q13.31) MUTATED      1  108
  DEL PEAK 50(22Q13.31) WILD-TYPE    3  205
                        clus
vv                       DEL PEAK 50(22Q13.31) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           108
                        clus
vv                       DEL PEAK 50(22Q13.31) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             205
[1] 2 2
[1] FALSE

Clustering(87) Variable = DEL PEAK 51(XP22.2) MUTATION ANALYSIS
D87V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 51(XP22.2) MUTATED    51  28
  DEL PEAK 51(XP22.2) WILD-TYPE 203 122
  DEL PEAK 51(XP22.2) MUTATED DEL PEAK 51(XP22.2) WILD-TYPE 
                           79                           325 
  DEL PEAK 51(XP22.2) MUTATED DEL PEAK 51(XP22.2) WILD-TYPE 
                           28                           122 
$`DEL PEAK 51(XP22.2) MUTATED`
TCGA-B7-A5TN TCGA-BR-4191 TCGA-BR-6458 TCGA-BR-7716 TCGA-BR-8059 TCGA-BR-8289 
        9.44        18.35        19.33        28.01        14.43         2.66 
TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8369 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8590 
        7.40        13.08        14.04         9.21        20.22         9.34 
TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4J6 
       15.81         9.86        10.68        13.87        22.26         0.66 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-8524 
       20.65         1.15        13.64         3.25         0.30         0.07 
TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MH 
        0.10         0.13         0.13         9.34        11.31        12.20 
TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-5718 
       54.08        14.01        47.05        19.07        21.99        36.00 
TCGA-CG-5725 TCGA-CG-5734 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       15.02         7.99        11.93        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A6EX TCGA-D7-A6EZ 
       15.98        12.79        12.33        18.21        11.31         9.76 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-FP-8211 TCGA-FP-A4BF 
        2.96        15.65         7.40         0.62        13.58         5.52 
TCGA-HU-A4G3 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GU TCGA-HU-A4H5 TCGA-IN-7806 
        5.59        22.75        25.81         6.25        12.30        21.21 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RP TCGA-R5-A7O7 
        3.45         3.39        18.38         5.19         6.44        45.67 
TCGA-RD-A8N6 TCGA-VQ-A8P3 TCGA-VQ-A8PC TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A8PU 
        8.94        32.48        46.26         1.87        13.35        27.35 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A928 TCGA-VQ-A94U TCGA-VQ-AA68 
        9.73        52.24         9.04         5.72        22.09        40.08 
TCGA-VQ-AA6A 
       32.94 

$`DEL PEAK 51(XP22.2) WILD-TYPE`
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-4267 TCGA-BR-4279 
        6.97         4.64         7.43        30.90         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-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        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       32.94        12.82         9.21        24.76        35.24        23.93 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       15.42        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       12.26         9.60        20.55         8.05         0.56        12.95 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       16.31         2.20        15.58         6.18        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 
       22.19        17.52         0.95        26.33         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8591 
        5.39        25.18         1.12        12.79        15.81        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8686 
        6.28         7.53         0.49        11.54        16.44        15.68 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
        8.22        12.56         7.53         6.08         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        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 
       12.82        19.36        13.51         0.46        20.42        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8525 
        5.13         2.83        13.15        13.18         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI 
        0.10         3.42        12.43        11.61         6.58         0.10 
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-4455 TCGA-CG-4462 
        7.99         8.05         4.01        29.98        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
        9.01        18.97         7.07        12.00        22.98        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-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       21.07        12.36        12.66        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6818 TCGA-D7-6820 
       18.54        18.61        17.85        13.35        10.55        11.31 
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        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A747 TCGA-D7-A748 
       14.76        13.71        11.24        11.44         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         7.99        16.24        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-A8CX TCGA-HF-A5NB TCGA-HJ-7597 
       59.54         5.03         0.56         0.23        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        1.51         5.92        14.27        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 
       12.10        10.62         0.76        24.30        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       24.20         3.25        11.77        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        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       19.36        23.84         9.67         8.88         8.81        27.42 
TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS 
       18.81         5.36        13.08         1.41         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51         5.56         1.81         7.82        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        60.56        20.15        37.64         3.72        19.73 
TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
        9.86        18.21         8.52        61.25         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-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-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        5.46        13.25        13.02        18.48        35.24        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       34.45        27.88         7.73        28.96        34.29        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-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       23.41        15.65        26.24        64.57        14.33        65.16 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       36.69        11.70        11.93        61.22        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A923 
       22.68         1.71        36.16         7.36         9.50         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P 
       55.43         4.54         6.58        64.18        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        29.98        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        21.11        12.43        10.62 
TCGA-ZQ-A9CR 
        0.79 

  DEL PEAK 51(XP22.2) MUTATED DEL PEAK 51(XP22.2) WILD-TYPE 
                         0.07                          0.00 
  DEL PEAK 51(XP22.2) MUTATED DEL PEAK 51(XP22.2) WILD-TYPE 
                        54.08                        122.30 
  DEL PEAK 51(XP22.2) MUTATED DEL PEAK 51(XP22.2) WILD-TYPE 
                        12.33                         12.89 
[1] "0.1 - 54.1 (12.3)"  "0.0 - 122.3 (12.9)"
[1] "hr=" "1"  
D87V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 51(XP22.2) MUTATED         1        1        6        8         6
  DEL PEAK 51(XP22.2) WILD-TYPE       2       13       35       23        32
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 51(XP22.2) MUTATED          13         2         21          5
  DEL PEAK 51(XP22.2) WILD-TYPE        42         2         64         57
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 51(XP22.2) MUTATED            8        9
  DEL PEAK 51(XP22.2) WILD-TYPE         33       37
D87V3, multiclass
            clus
vv           DEL PEAK 51(XP22.2) MUTATED DEL PEAK 51(XP22.2) WILD-TYPE
  STAGE I                              1                             2
  STAGE IA                             1                            13
  STAGE IB                             6                            35
  STAGE II                             8                            23
  STAGE IIA                            6                            32
  STAGE IIB                           13                            42
  STAGE III                            2                             2
  STAGE IIIA                          21                            64
  STAGE IIIB                           5                            57
  STAGE IIIC                           8                            33
  STAGE IV                             9                            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(XP22.2) MUTATED     3  19  36  23
  DEL PEAK 51(XP22.2) WILD-TYPE  19  71 159  96
D87V4, multiclass
    clus
vv   DEL PEAK 51(XP22.2) MUTATED DEL PEAK 51(XP22.2) WILD-TYPE
  T1                           3                            19
  T2                          19                            71
  T3                          36                           159
  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
  DEL PEAK 51(XP22.2) MUTATED    20  26  18  16
  DEL PEAK 51(XP22.2) WILD-TYPE 109  92  66  73
D87V5, multiclass
    clus
vv   DEL PEAK 51(XP22.2) MUTATED DEL PEAK 51(XP22.2) WILD-TYPE
  N0                          20                           109
  N1                          26                            92
  N2                          18                            66
  N3                          16                            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"
D87V6, binary
                               cls
clus                              0   1
  DEL PEAK 51(XP22.2) MUTATED    75   6
  DEL PEAK 51(XP22.2) WILD-TYPE 312  24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XP22.2) MUTATED     75    6
  DEL PEAK 51(XP22.2) WILD-TYPE  312   24
   clus
vv  DEL PEAK 51(XP22.2) MUTATED DEL PEAK 51(XP22.2) WILD-TYPE
  0                          75                           312
  1                           6                            24
[1] 2 2
[1] FALSE
D87V7, binary
                               cls
clus                              0   1
  DEL PEAK 51(XP22.2) MUTATED    25  57
  DEL PEAK 51(XP22.2) WILD-TYPE 133 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XP22.2) MUTATED     25   57
  DEL PEAK 51(XP22.2) WILD-TYPE  133  221
        clus
vv       DEL PEAK 51(XP22.2) MUTATED DEL PEAK 51(XP22.2) WILD-TYPE
  FEMALE                          25                           133
  MALE                            57                           221
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 51(XP22.2) MUTATED                                       9
  DEL PEAK 51(XP22.2) WILD-TYPE                                    62
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 51(XP22.2) MUTATED                                                       29
  DEL PEAK 51(XP22.2) WILD-TYPE                                                    133
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 51(XP22.2) MUTATED                                                                  14
  DEL PEAK 51(XP22.2) WILD-TYPE                                                                67
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 51(XP22.2) MUTATED                                                 21
  DEL PEAK 51(XP22.2) WILD-TYPE                                               57
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 51(XP22.2) MUTATED                                                          2
  DEL PEAK 51(XP22.2) WILD-TYPE                                                       19
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 51(XP22.2) MUTATED                                                           3
  DEL PEAK 51(XP22.2) WILD-TYPE                                                         5
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 51(XP22.2) MUTATED                                          4
  DEL PEAK 51(XP22.2) WILD-TYPE                                        9
D87V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 51(XP22.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     29
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    4
                                                                   clus
vv                                                                  DEL PEAK 51(XP22.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            67
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             57
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      9
[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"
D87V9, binary
                               cls
clus                              0   1
  DEL PEAK 51(XP22.2) MUTATED     1  81
  DEL PEAK 51(XP22.2) WILD-TYPE   5 349
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XP22.2) MUTATED      1   81
  DEL PEAK 51(XP22.2) WILD-TYPE    5  349
     clus
vv    DEL PEAK 51(XP22.2) MUTATED DEL PEAK 51(XP22.2) WILD-TYPE
  NO                            1                             5
  YES                          81                           349
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 51(XP22.2) MUTATED    67   3   3   2
  DEL PEAK 51(XP22.2) WILD-TYPE 280  15  16  23
D87V10, multiclass
    clus
vv   DEL PEAK 51(XP22.2) MUTATED DEL PEAK 51(XP22.2) WILD-TYPE
  R0                          67                           280
  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"
D87V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 51(XP22.2) MUTATED      17                         0
  DEL PEAK 51(XP22.2) WILD-TYPE    71                        11
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 51(XP22.2) MUTATED                                           0    56
  DEL PEAK 51(XP22.2) WILD-TYPE                                         1   218
D87V12, multiclass
                                           clus
vv                                          DEL PEAK 51(XP22.2) MUTATED
  ASIAN                                                              17
  BLACK OR AFRICAN AMERICAN                                           0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              56
                                           clus
vv                                          DEL PEAK 51(XP22.2) WILD-TYPE
  ASIAN                                                                71
  BLACK OR AFRICAN AMERICAN                                            11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V13, binary
                               cls
clus                              0   1
  DEL PEAK 51(XP22.2) MUTATED     1  61
  DEL PEAK 51(XP22.2) WILD-TYPE   3 252
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XP22.2) MUTATED      1   61
  DEL PEAK 51(XP22.2) WILD-TYPE    3  252
                        clus
vv                       DEL PEAK 51(XP22.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          61
                        clus
vv                       DEL PEAK 51(XP22.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           252
[1] 2 2
[1] FALSE

Clustering(88) Variable = DEL PEAK 52(XP21.1) MUTATION ANALYSIS
D88V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 52(XP21.1) MUTATED    42  27
  DEL PEAK 52(XP21.1) WILD-TYPE 212 123
  DEL PEAK 52(XP21.1) MUTATED DEL PEAK 52(XP21.1) WILD-TYPE 
                           69                           335 
  DEL PEAK 52(XP21.1) MUTATED DEL PEAK 52(XP21.1) WILD-TYPE 
                           27                           123 
$`DEL PEAK 52(XP21.1) MUTATED`
TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4191 TCGA-BR-6458 TCGA-BR-8059 TCGA-BR-8291 
       19.56         9.44        18.35        19.33        14.43        16.31 
TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8683 TCGA-BR-A44U 
        7.40        13.08        17.52        14.04         9.86        13.87 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4J6 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI 
        7.53        22.26         0.66        20.65         1.15        13.64 
TCGA-CD-8524 TCGA-CD-8533 TCGA-CD-A489 TCGA-CD-A4MH TCGA-CG-4437 TCGA-CG-4438 
        0.07         0.13        11.31        12.20         8.05        54.08 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4469 TCGA-CG-5725 
       29.98        47.05        19.07        21.99         7.07        15.02 
TCGA-CG-5734 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 
        7.99        11.93        19.13        13.35        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F2 
       12.79        12.33        18.21        11.31         9.76        15.65 
TCGA-D7-A74A TCGA-EQ-5647 TCGA-FP-8211 TCGA-FP-A4BF TCGA-HU-A4GD TCGA-HU-A4H5 
        7.40         0.62        13.58         5.52        22.75        12.30 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RP TCGA-KB-A93H 
        3.45         3.39        18.38         5.19         6.44        37.64 
TCGA-R5-A7O7 TCGA-RD-A8N6 TCGA-VQ-A8PC TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A8PY 
       45.67         8.94        46.26        13.35        27.35        14.33 
TCGA-VQ-A91N TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 
       18.74        52.24         9.04        22.09        18.41        40.08 
TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6J 
       32.94        17.13        21.11 

$`DEL PEAK 52(XP21.1) WILD-TYPE`
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-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.64         7.43        30.90         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        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       12.82         9.21        24.76        35.24        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       12.26         9.60        20.55         8.05         0.56        12.95 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.66         2.20        15.58         6.18        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
       22.19         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 
       19.17        14.79         0.26        15.85         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        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       15.81        16.44        15.68         8.22        10.68        12.56 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08         1.48        13.41        13.51        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        12.82        19.36        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        0.46        20.42        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 
       13.15        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         0.10         3.42         9.34        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 
       15.95         1.02         7.99         4.01        14.01        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97        12.00        22.98        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-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6520 
       69.04        21.07        12.36        12.66        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6818 
       18.54        18.61        17.85        17.19        10.26        10.55 
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        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6F0 
       13.78        14.76        13.71        11.24        11.44         2.96 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
        8.38         4.34         7.13         7.99        16.24        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-A8CX 
       22.29        17.06        59.54         5.03         0.56         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       18.08        26.47         1.51         5.92        14.27        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
        5.59        12.30        11.84        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 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84         9.67         8.88         8.81        27.42        21.21 
TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS 
       18.81         5.36        13.08         1.41         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51         5.56         1.81         7.82        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        5.56        60.56        20.15         3.72        19.73         9.86 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        61.25         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        35.24        21.73        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       27.88        32.48         7.73        28.96        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        26.24        64.57        65.16 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S 
       36.69        11.70        11.93        61.22        20.81        22.68 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A923 
        1.71        36.16         7.36         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        64.18        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        29.98        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        12.43        10.62         0.79 

  DEL PEAK 52(XP21.1) MUTATED DEL PEAK 52(XP21.1) WILD-TYPE 
                         0.07                          0.00 
  DEL PEAK 52(XP21.1) MUTATED DEL PEAK 52(XP21.1) WILD-TYPE 
                        54.08                        122.30 
  DEL PEAK 52(XP21.1) MUTATED DEL PEAK 52(XP21.1) WILD-TYPE 
                        14.04                         12.59 
[1] "0.1 - 54.1 (14.0)"  "0.0 - 122.3 (12.6)"
[1] "hr=" "1"  
D88V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 52(XP21.1) MUTATED         1        1        5        5         5
  DEL PEAK 52(XP21.1) WILD-TYPE       2       13       36       26        33
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 52(XP21.1) MUTATED          10         2         20          7
  DEL PEAK 52(XP21.1) WILD-TYPE        45         2         65         55
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 52(XP21.1) MUTATED            6        7
  DEL PEAK 52(XP21.1) WILD-TYPE         35       39
D88V3, multiclass
            clus
vv           DEL PEAK 52(XP21.1) MUTATED DEL PEAK 52(XP21.1) WILD-TYPE
  STAGE I                              1                             2
  STAGE IA                             1                            13
  STAGE IB                             5                            36
  STAGE II                             5                            26
  STAGE IIA                            5                            33
  STAGE IIB                           10                            45
  STAGE III                            2                             2
  STAGE IIIA                          20                            65
  STAGE IIIB                           7                            55
  STAGE IIIC                           6                            35
  STAGE IV                             7                            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 52(XP21.1) MUTATED     3  16  30  21
  DEL PEAK 52(XP21.1) WILD-TYPE  19  74 165  98
D88V4, multiclass
    clus
vv   DEL PEAK 52(XP21.1) MUTATED DEL PEAK 52(XP21.1) WILD-TYPE
  T1                           3                            19
  T2                          16                            74
  T3                          30                           165
  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 52(XP21.1) MUTATED    17  21  17  14
  DEL PEAK 52(XP21.1) WILD-TYPE 112  97  67  75
D88V5, multiclass
    clus
vv   DEL PEAK 52(XP21.1) MUTATED DEL PEAK 52(XP21.1) WILD-TYPE
  N0                          17                           112
  N1                          21                            97
  N2                          17                            67
  N3                          14                            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"
D88V6, binary
                               cls
clus                              0   1
  DEL PEAK 52(XP21.1) MUTATED    66   4
  DEL PEAK 52(XP21.1) WILD-TYPE 321  26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 52(XP21.1) MUTATED     66    4
  DEL PEAK 52(XP21.1) WILD-TYPE  321   26
   clus
vv  DEL PEAK 52(XP21.1) MUTATED DEL PEAK 52(XP21.1) WILD-TYPE
  0                          66                           321
  1                           4                            26
[1] 2 2
[1] FALSE
D88V7, binary
                               cls
clus                              0   1
  DEL PEAK 52(XP21.1) MUTATED    22  49
  DEL PEAK 52(XP21.1) WILD-TYPE 136 229
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 52(XP21.1) MUTATED     22   49
  DEL PEAK 52(XP21.1) WILD-TYPE  136  229
        clus
vv       DEL PEAK 52(XP21.1) MUTATED DEL PEAK 52(XP21.1) WILD-TYPE
  FEMALE                          22                           136
  MALE                            49                           229
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 52(XP21.1) MUTATED                                       9
  DEL PEAK 52(XP21.1) WILD-TYPE                                    62
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 52(XP21.1) MUTATED                                                       22
  DEL PEAK 52(XP21.1) WILD-TYPE                                                    140
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 52(XP21.1) MUTATED                                                                  14
  DEL PEAK 52(XP21.1) WILD-TYPE                                                                67
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 52(XP21.1) MUTATED                                                 20
  DEL PEAK 52(XP21.1) WILD-TYPE                                               58
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 52(XP21.1) MUTATED                                                          2
  DEL PEAK 52(XP21.1) WILD-TYPE                                                       19
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 52(XP21.1) MUTATED                                                           1
  DEL PEAK 52(XP21.1) WILD-TYPE                                                         7
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 52(XP21.1) MUTATED                                          3
  DEL PEAK 52(XP21.1) WILD-TYPE                                       10
D88V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 52(XP21.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     22
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    3
                                                                   clus
vv                                                                  DEL PEAK 52(XP21.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      140
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            67
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             58
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     10
[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"
D88V9, binary
                               cls
clus                              0   1
  DEL PEAK 52(XP21.1) MUTATED     1  70
  DEL PEAK 52(XP21.1) WILD-TYPE   5 360
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 52(XP21.1) MUTATED      1   70
  DEL PEAK 52(XP21.1) WILD-TYPE    5  360
     clus
vv    DEL PEAK 52(XP21.1) MUTATED DEL PEAK 52(XP21.1) WILD-TYPE
  NO                            1                             5
  YES                          70                           360
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 52(XP21.1) MUTATED    56   5   2   2
  DEL PEAK 52(XP21.1) WILD-TYPE 291  13  17  23
D88V10, multiclass
    clus
vv   DEL PEAK 52(XP21.1) MUTATED DEL PEAK 52(XP21.1) WILD-TYPE
  R0                          56                           291
  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"
D88V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 52(XP21.1) MUTATED      10                         1
  DEL PEAK 52(XP21.1) WILD-TYPE    78                        10
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 52(XP21.1) MUTATED                                           0    48
  DEL PEAK 52(XP21.1) WILD-TYPE                                         1   226
D88V12, multiclass
                                           clus
vv                                          DEL PEAK 52(XP21.1) MUTATED
  ASIAN                                                              10
  BLACK OR AFRICAN AMERICAN                                           1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              48
                                           clus
vv                                          DEL PEAK 52(XP21.1) WILD-TYPE
  ASIAN                                                                78
  BLACK OR AFRICAN AMERICAN                                            10
  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"
D88V13, binary
                               cls
clus                              0   1
  DEL PEAK 52(XP21.1) MUTATED     1  47
  DEL PEAK 52(XP21.1) WILD-TYPE   3 266
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 52(XP21.1) MUTATED      1   47
  DEL PEAK 52(XP21.1) WILD-TYPE    3  266
                        clus
vv                       DEL PEAK 52(XP21.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          47
                        clus
vv                       DEL PEAK 52(XP21.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           266
[1] 2 2
[1] FALSE

Clustering(89) Variable = DEL PEAK 53(XQ21.33) MUTATION ANALYSIS
D89V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 53(XQ21.33) MUTATED    35  17
  DEL PEAK 53(XQ21.33) WILD-TYPE 219 133
  DEL PEAK 53(XQ21.33) MUTATED DEL PEAK 53(XQ21.33) WILD-TYPE 
                            52                            352 
  DEL PEAK 53(XQ21.33) MUTATED DEL PEAK 53(XQ21.33) WILD-TYPE 
                            17                            133 
$`DEL PEAK 53(XQ21.33) MUTATED`
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-7197 TCGA-BR-7716 TCGA-BR-8058 
       11.70        19.56         9.44         9.21        28.01        17.49 
TCGA-BR-8291 TCGA-BR-8361 TCGA-BR-8365 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-A44U 
       16.31        19.50        17.52        11.54        15.81        13.87 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J8 TCGA-CD-5800 TCGA-CD-8527 
        7.53        22.26         1.48        13.51        13.15         0.07 
TCGA-CD-8529 TCGA-CD-A489 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4443 
        0.13        11.31        20.02         3.02         7.99        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-5725 TCGA-D7-6519 TCGA-D7-6528 
       47.05        19.07         7.07        15.02        20.55        15.22 
TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A74A TCGA-EQ-8122 
       12.33        18.21        11.31         9.76         7.40         7.99 
TCGA-FP-8211 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-A6RI TCGA-IN-A6RR 
       13.58        12.30        27.42        21.21        18.38         6.74 
TCGA-VQ-A8DT TCGA-VQ-A8E0 TCGA-VQ-A8P5 TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A91Q 
       48.79        18.48         7.73        13.35        27.35        20.81 
TCGA-VQ-A91X TCGA-VQ-A94U TCGA-VQ-AA6A TCGA-VQ-AA6D 
        9.50        22.09        32.94        17.13 

$`DEL PEAK 53(XQ21.33) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       26.70        11.01         9.47         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        7.43        18.35        30.90         6.18         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-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        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82        24.76        35.24        23.93        15.42 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       18.15        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        14.43        11.44         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        20.55         8.05         0.56        12.95         2.66 
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-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        19.17        14.79         0.26        15.85         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 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        6.08        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 
       14.17         0.53        12.82         0.66        19.36         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        2.83         3.25        13.18         0.30         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.07         0.10         0.16         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A 
        0.13         0.13         0.10         3.42         9.34        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 
       11.61         6.58        12.20         0.10        12.62        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         8.05        54.08         4.01        14.01 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 
       12.03        21.99         0.00         9.01        18.97        12.00 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        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-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
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        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.66        11.93        19.13        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        17.19        10.26        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       10.55        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 
       15.16        13.78        14.76        13.71        11.24        11.44 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 
        2.96        15.65         8.38         4.34         7.13         0.62 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
       16.24        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-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        0.56         5.52         0.23        18.08        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        5.92        14.27        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
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-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
        0.26         2.10        12.95        19.36        23.84         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ 
        8.88         8.81         3.45        18.81         3.39         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR 
        5.19        13.08         1.41         6.44        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        5.56         1.81         7.82        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
       60.56        20.15        37.64         3.72        19.73         9.86 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        61.25         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-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        5.46        13.25        13.02        35.24        21.73        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       27.88        32.48        28.96        34.29        46.26        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-A8PY 
        9.27        23.41        15.65        26.24        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       65.16        36.69        11.70        11.93        61.22        18.74 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z 
       22.68         1.71        36.16         7.36         9.73        52.24 
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 
       64.18        21.04         2.66        42.54        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       40.08        28.41        29.98        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11        12.43        10.62         0.79 

  DEL PEAK 53(XQ21.33) MUTATED DEL PEAK 53(XQ21.33) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 53(XQ21.33) MUTATED DEL PEAK 53(XQ21.33) WILD-TYPE 
                         48.79                         122.30 
  DEL PEAK 53(XQ21.33) MUTATED DEL PEAK 53(XQ21.33) WILD-TYPE 
                        14.445                         12.710 
[1] "0.1 - 48.8 (14.4)"  "0.0 - 122.3 (12.7)"
[1] "hr=" "1.2"
D89V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 53(XQ21.33) MUTATED         1        1        7        5         3
  DEL PEAK 53(XQ21.33) WILD-TYPE       2       13       34       26        35
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 53(XQ21.33) MUTATED           7         0         13          7
  DEL PEAK 53(XQ21.33) WILD-TYPE        48         4         72         55
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 53(XQ21.33) MUTATED            4        6
  DEL PEAK 53(XQ21.33) WILD-TYPE         37       40
D89V3, multiclass
            clus
vv           DEL PEAK 53(XQ21.33) MUTATED DEL PEAK 53(XQ21.33) WILD-TYPE
  STAGE I                               1                              2
  STAGE IA                              1                             13
  STAGE IB                              7                             34
  STAGE II                              5                             26
  STAGE IIA                             3                             35
  STAGE IIB                             7                             48
  STAGE III                             0                              4
  STAGE IIIA                           13                             72
  STAGE IIIB                            7                             55
  STAGE IIIC                            4                             37
  STAGE IV                              6                             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 53(XQ21.33) MUTATED     2  13  26  14
  DEL PEAK 53(XQ21.33) WILD-TYPE  20  77 169 105
D89V4, multiclass
    clus
vv   DEL PEAK 53(XQ21.33) MUTATED DEL PEAK 53(XQ21.33) WILD-TYPE
  T1                            2                             20
  T2                           13                             77
  T3                           26                            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 53(XQ21.33) MUTATED    17  15  12   9
  DEL PEAK 53(XQ21.33) WILD-TYPE 112 103  72  80
D89V5, multiclass
    clus
vv   DEL PEAK 53(XQ21.33) MUTATED DEL PEAK 53(XQ21.33) WILD-TYPE
  N0                           17                            112
  N1                           15                            103
  N2                           12                             72
  N3                            9                             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"
D89V6, binary
                                cls
clus                               0   1
  DEL PEAK 53(XQ21.33) MUTATED    50   3
  DEL PEAK 53(XQ21.33) WILD-TYPE 337  27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 53(XQ21.33) MUTATED     50    3
  DEL PEAK 53(XQ21.33) WILD-TYPE  337   27
   clus
vv  DEL PEAK 53(XQ21.33) MUTATED DEL PEAK 53(XQ21.33) WILD-TYPE
  0                           50                            337
  1                            3                             27
[1] 2 2
[1] FALSE
D89V7, binary
                                cls
clus                               0   1
  DEL PEAK 53(XQ21.33) MUTATED    16  39
  DEL PEAK 53(XQ21.33) WILD-TYPE 142 239
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 53(XQ21.33) MUTATED     16   39
  DEL PEAK 53(XQ21.33) WILD-TYPE  142  239
        clus
vv       DEL PEAK 53(XQ21.33) MUTATED DEL PEAK 53(XQ21.33) WILD-TYPE
  FEMALE                           16                            142
  MALE                             39                            239
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 53(XQ21.33) MUTATED                                       8
  DEL PEAK 53(XQ21.33) WILD-TYPE                                    63
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 53(XQ21.33) MUTATED                                                       18
  DEL PEAK 53(XQ21.33) WILD-TYPE                                                    144
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 53(XQ21.33) MUTATED                                                                  12
  DEL PEAK 53(XQ21.33) WILD-TYPE                                                                69
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 53(XQ21.33) MUTATED                                                 11
  DEL PEAK 53(XQ21.33) WILD-TYPE                                               67
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 53(XQ21.33) MUTATED                                                          3
  DEL PEAK 53(XQ21.33) WILD-TYPE                                                       18
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 53(XQ21.33) MUTATED                                                           2
  DEL PEAK 53(XQ21.33) WILD-TYPE                                                         6
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 53(XQ21.33) MUTATED                                          1
  DEL PEAK 53(XQ21.33) WILD-TYPE                                       12
D89V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 53(XQ21.33) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      18
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           12
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     1
                                                                   clus
vv                                                                  DEL PEAK 53(XQ21.33) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       144
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             69
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              67
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      12
[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"
D89V9, binary
                                cls
clus                               0   1
  DEL PEAK 53(XQ21.33) MUTATED     1  54
  DEL PEAK 53(XQ21.33) WILD-TYPE   5 376
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 53(XQ21.33) MUTATED      1   54
  DEL PEAK 53(XQ21.33) WILD-TYPE    5  376
     clus
vv    DEL PEAK 53(XQ21.33) MUTATED DEL PEAK 53(XQ21.33) WILD-TYPE
  NO                             1                              5
  YES                           54                            376
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 53(XQ21.33) MUTATED    46   3   1   1
  DEL PEAK 53(XQ21.33) WILD-TYPE 301  15  18  24
D89V10, multiclass
    clus
vv   DEL PEAK 53(XQ21.33) MUTATED DEL PEAK 53(XQ21.33) WILD-TYPE
  R0                           46                            301
  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"
D89V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 53(XQ21.33) MUTATED       9                         1
  DEL PEAK 53(XQ21.33) WILD-TYPE    79                        10
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 53(XQ21.33) MUTATED                                           0
  DEL PEAK 53(XQ21.33) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 53(XQ21.33) MUTATED      33
  DEL PEAK 53(XQ21.33) WILD-TYPE   241
D89V12, multiclass
                                           clus
vv                                          DEL PEAK 53(XQ21.33) MUTATED
  ASIAN                                                                9
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               33
                                           clus
vv                                          DEL PEAK 53(XQ21.33) WILD-TYPE
  ASIAN                                                                 79
  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"
D89V13, binary
                                cls
clus                               0   1
  DEL PEAK 53(XQ21.33) MUTATED     0  36
  DEL PEAK 53(XQ21.33) WILD-TYPE   4 277
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 53(XQ21.33) MUTATED      0   36
  DEL PEAK 53(XQ21.33) WILD-TYPE    4  277
                        clus
vv                       DEL PEAK 53(XQ21.33) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           36
                        clus
vv                       DEL PEAK 53(XQ21.33) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            277
[1] 2 2
[1] FALSE
