[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-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/11541908/STAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/STAD-TP/11549120/transformed.cor.cli.txt"

nPatients in clinical file=397, in cluster file=441, common to both=395
[1]  89 395
[1] "AMP PEAK  1(1P36.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                            56                            339 
  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                            56                            339 
[1] "AMP PEAK  2(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          144                           251 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          144                           251 
[1] "AMP PEAK  3(1Q42.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                          133                           262 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                          133                           262 
[1] "AMP PEAK  4(3Q26.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                          144                           251 
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                          144                           251 
[1] "AMP PEAK  5(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                           116                            279 
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                           116                            279 
[1] "AMP PEAK  6(5P13.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE 
                          112                           283 
  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE 
                          112                           283 
[1] "AMP PEAK  7(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE 
                          109                           286 
  AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE 
                          109                           286 
[1] "AMP PEAK  8(6Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE 
                         81                         314 
  AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE 
                         81                         314 
[1] "AMP PEAK  9(6Q21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE 
                         73                         322 
  AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE 
                         73                         322 
[1] "AMP PEAK 10(7P22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                          205                           190 
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                          205                           190 
[1] "AMP PEAK 11(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                          191                           204 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                          191                           204 
[1] "AMP PEAK 12(7Q21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                          180                           215 
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                          180                           215 
[1] "AMP PEAK 13(7Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE 
                          176                           219 
  AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE 
                          176                           219 
[1] "AMP PEAK 14(8P23.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE 
                          160                           235 
  AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE 
                          160                           235 
[1] "AMP PEAK 15(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                           273                            122 
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                           273                            122 
[1] "AMP PEAK 16(9P24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE 
                           57                           338 
  AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE 
                           57                           338 
[1] "AMP PEAK 17(9P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE 
                           75                           320 
  AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE 
                           75                           320 
[1] "AMP PEAK 18(9Q34.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE 
                          104                           291 
  AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE 
                          104                           291 
[1] "AMP PEAK 19(10P11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE 
                            107                             288 
  AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE 
                            107                             288 
[1] "AMP PEAK 20(10Q22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE 
                            80                            315 
  AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE 
                            80                            315 
[1] "AMP PEAK 21(10Q26.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE 
                             79                             316 
  AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE 
                             79                             316 
[1] "AMP PEAK 22(11P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE 
                          77                          318 
  AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE 
                          77                          318 
[1] "AMP PEAK 23(11P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE 
                            80                            315 
  AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE 
                            80                            315 
[1] "AMP PEAK 24(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE 
                           103                            292 
  AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE 
                           103                            292 
[1] "AMP PEAK 25(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE 
                           114                            281 
  AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE 
                           114                            281 
[1] "AMP PEAK 26(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE 
                          98                          297 
  AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE 
                          98                          297 
[1] "AMP PEAK 27(13Q12.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE 
                           154                            241 
  AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE 
                           154                            241 
[1] "AMP PEAK 28(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE 
                           159                            236 
  AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE 
                           159                            236 
[1] "AMP PEAK 29(15Q26.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(15Q26.1) MUTATED AMP PEAK 29(15Q26.1) WILD-TYPE 
                            99                            296 
  AMP PEAK 29(15Q26.1) MUTATED AMP PEAK 29(15Q26.1) WILD-TYPE 
                            99                            296 
[1] "AMP PEAK 30(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE 
                         128                          267 
  AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE 
                         128                          267 
[1] "AMP PEAK 31(18Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 31(18Q11.2) MUTATED AMP PEAK 31(18Q11.2) WILD-TYPE 
                           124                            271 
  AMP PEAK 31(18Q11.2) MUTATED AMP PEAK 31(18Q11.2) WILD-TYPE 
                           124                            271 
[1] "AMP PEAK 32(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 32(19P13.2) MUTATED AMP PEAK 32(19P13.2) WILD-TYPE 
                            42                            353 
  AMP PEAK 32(19P13.2) MUTATED AMP PEAK 32(19P13.2) WILD-TYPE 
                            42                            353 
[1] "AMP PEAK 33(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE 
                         116                          279 
  AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE 
                         116                          279 
[1] "AMP PEAK 34(19Q13.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE 
                             96                             299 
  AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE 
                             96                             299 
[1] "AMP PEAK 35(20Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE 
                           261                            134 
  AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE 
                           261                            134 
[1] "AMP PEAK 36(XQ27.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE 
                           77                           318 
  AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE 
                           77                           318 
[1] "DEL PEAK  1(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           116                            279 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           116                            279 
[1] "DEL PEAK  2(1P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           82                           313 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           82                           313 
[1] "DEL PEAK  3(1Q44) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         28                         367 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         28                         367 
[1] "DEL PEAK  4(1Q44) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE 
                         24                         371 
  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE 
                         24                         371 
[1] "DEL PEAK  5(2Q32.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE 
                           57                           338 
  DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE 
                           57                           338 
[1] "DEL PEAK  6(2Q33.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(2Q33.3) MUTATED DEL PEAK  6(2Q33.3) WILD-TYPE 
                           46                           349 
  DEL PEAK  6(2Q33.3) MUTATED DEL PEAK  6(2Q33.3) WILD-TYPE 
                           46                           349 
[1] "DEL PEAK  7(2Q37.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(2Q37.2) MUTATED DEL PEAK  7(2Q37.2) WILD-TYPE 
                           62                           333 
  DEL PEAK  7(2Q37.2) MUTATED DEL PEAK  7(2Q37.2) WILD-TYPE 
                           62                           333 
[1] "DEL PEAK  8(3P26.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3P26.1) MUTATED DEL PEAK  8(3P26.1) WILD-TYPE 
                          121                           274 
  DEL PEAK  8(3P26.1) MUTATED DEL PEAK  8(3P26.1) WILD-TYPE 
                          121                           274 
[1] "DEL PEAK  9(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                          136                           259 
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                          136                           259 
[1] "DEL PEAK 10(3Q26.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                            41                            354 
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                            41                            354 
[1] "DEL PEAK 11(4P16.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE 
                          151                           244 
  DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE 
                          151                           244 
[1] "DEL PEAK 12(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                          173                           222 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                          173                           222 
[1] "DEL PEAK 13(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                          173                           222 
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                          173                           222 
[1] "DEL PEAK 14(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                          147                           248 
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                          147                           248 
[1] "DEL PEAK 15(5Q23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE 
                          133                           262 
  DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE 
                          133                           262 
[1] "DEL PEAK 16(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                          101                           294 
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                          101                           294 
[1] "DEL PEAK 17(6Q14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE 
                           76                           319 
  DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE 
                           76                           319 
[1] "DEL PEAK 18(6Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE 
                           67                           328 
  DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE 
                           67                           328 
[1] "DEL PEAK 19(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                         89                         306 
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                         89                         306 
[1] "DEL PEAK 20(7Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                           61                           334 
  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                           61                           334 
[1] "DEL PEAK 21(7Q36.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                           83                           312 
  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                           83                           312 
[1] "DEL PEAK 22(8P23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(8P23.3) MUTATED DEL PEAK 22(8P23.3) WILD-TYPE 
                          106                           289 
  DEL PEAK 22(8P23.3) MUTATED DEL PEAK 22(8P23.3) WILD-TYPE 
                          106                           289 
[1] "DEL PEAK 23(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                        165                         230 
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                        165                         230 
[1] "DEL PEAK 24(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                          165                           230 
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                          165                           230 
[1] "DEL PEAK 25(9Q21.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                            96                            299 
  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                            96                            299 
[1] "DEL PEAK 26(10P12.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(10P12.31) MUTATED DEL PEAK 26(10P12.31) WILD-TYPE 
                             57                             338 
  DEL PEAK 26(10P12.31) MUTATED DEL PEAK 26(10P12.31) WILD-TYPE 
                             57                             338 
[1] "DEL PEAK 27(10Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE 
                            66                            329 
  DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE 
                            66                            329 
[1] "DEL PEAK 28(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                             97                             298 
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                             97                             298 
[1] "DEL PEAK 29(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                            87                            308 
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                            87                            308 
[1] "DEL PEAK 30(11Q23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE 
                            85                            310 
  DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE 
                            85                            310 
[1] "DEL PEAK 31(12P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE 
                            66                            329 
  DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE 
                            66                            329 
[1] "DEL PEAK 32(12Q12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE 
                          51                          344 
  DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE 
                          51                          344 
[1] "DEL PEAK 33(13Q12.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                             57                             338 
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                             57                             338 
[1] "DEL PEAK 34(14Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                           120                            275 
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                           120                            275 
[1] "DEL PEAK 35(14Q32.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                            119                             276 
  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                            119                             276 
[1] "DEL PEAK 36(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                           108                            287 
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                           108                            287 
[1] "DEL PEAK 37(15Q15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE 
                           112                            283 
  DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE 
                           112                            283 
[1] "DEL PEAK 38(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                            85                            310 
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                            85                            310 
[1] "DEL PEAK 39(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                           161                            234 
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                           161                            234 
[1] "DEL PEAK 40(17P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(17P13.3) MUTATED DEL PEAK 40(17P13.3) WILD-TYPE 
                           151                            244 
  DEL PEAK 40(17P13.3) MUTATED DEL PEAK 40(17P13.3) WILD-TYPE 
                           151                            244 
[1] "DEL PEAK 41(17P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(17P12) MUTATED DEL PEAK 41(17P12) WILD-TYPE 
                         157                          238 
  DEL PEAK 41(17P12) MUTATED DEL PEAK 41(17P12) WILD-TYPE 
                         157                          238 
[1] "DEL PEAK 42(17Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(17Q24.3) MUTATED DEL PEAK 42(17Q24.3) WILD-TYPE 
                            70                            325 
  DEL PEAK 42(17Q24.3) MUTATED DEL PEAK 42(17Q24.3) WILD-TYPE 
                            70                            325 
[1] "DEL PEAK 43(18Q12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(18Q12.2) MUTATED DEL PEAK 43(18Q12.2) WILD-TYPE 
                           155                            240 
  DEL PEAK 43(18Q12.2) MUTATED DEL PEAK 43(18Q12.2) WILD-TYPE 
                           155                            240 
[1] "DEL PEAK 44(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(18Q21.2) MUTATED DEL PEAK 44(18Q21.2) WILD-TYPE 
                           177                            218 
  DEL PEAK 44(18Q21.2) MUTATED DEL PEAK 44(18Q21.2) WILD-TYPE 
                           177                            218 
[1] "DEL PEAK 45(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE 
                           137                            258 
  DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE 
                           137                            258 
[1] "DEL PEAK 46(19Q13.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 46(19Q13.11) MUTATED DEL PEAK 46(19Q13.11) WILD-TYPE 
                             64                             331 
  DEL PEAK 46(19Q13.11) MUTATED DEL PEAK 46(19Q13.11) WILD-TYPE 
                             64                             331 
[1] "DEL PEAK 47(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                            34                            361 
  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                            34                            361 
[1] "DEL PEAK 48(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE 
                           158                            237 
  DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE 
                           158                            237 
[1] "DEL PEAK 49(21Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 49(21Q22.3) MUTATED DEL PEAK 49(21Q22.3) WILD-TYPE 
                           163                            232 
  DEL PEAK 49(21Q22.3) MUTATED DEL PEAK 49(21Q22.3) WILD-TYPE 
                           163                            232 
[1] "DEL PEAK 50(22Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 50(22Q13.31) MUTATED DEL PEAK 50(22Q13.31) WILD-TYPE 
                            141                             254 
  DEL PEAK 50(22Q13.31) MUTATED DEL PEAK 50(22Q13.31) WILD-TYPE 
                            141                             254 
[1] "DEL PEAK 51(XP22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 51(XP22.2) MUTATED DEL PEAK 51(XP22.2) WILD-TYPE 
                           77                           318 
  DEL PEAK 51(XP22.2) MUTATED DEL PEAK 51(XP22.2) WILD-TYPE 
                           77                           318 
[1] "DEL PEAK 52(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 52(XP21.1) MUTATED DEL PEAK 52(XP21.1) WILD-TYPE 
                           62                           333 
  DEL PEAK 52(XP21.1) MUTATED DEL PEAK 52(XP21.1) WILD-TYPE 
                           62                           333 
[1] "DEL PEAK 53(XQ21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 53(XQ21.33) MUTATED DEL PEAK 53(XQ21.33) WILD-TYPE 
                            48                            347 
  DEL PEAK 53(XQ21.33) MUTATED DEL PEAK 53(XQ21.33) WILD-TYPE 
                            48                            347 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "RADIATIONTHERAPY"                      
[14] "HISTOLOGICALTYPE"                      
[15] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "COMPLETENESS.OF.RESECTION"             
[17] "NUMBER.OF.LYMPH.NODES"                 
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 395 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
         171          356           NA           NA           NA           NA 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-4292 TCGA-BR-4294 TCGA-BR-4357 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4361 TCGA-BR-4362 TCGA-BR-4363 TCGA-BR-4366 TCGA-BR-4367 TCGA-BR-4368 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4369 TCGA-BR-4370 TCGA-BR-4371 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6454 
          NA           NA           NA         1055          485           NA 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
         399          308          416          213         1190           25 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
          19          997          421          402          491           38 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
         273          642          940          949         1002          390 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
         280          753         1072          728          469          852 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
          21            5          564          378           29           21 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
         388          569          532           25           40           21 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
         373           15          625           22            8          394 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
           8          496           47           45          225          188 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
         593           11           NA          675           90           29 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
         418          131          427          101           11          583 
TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
         450           21            8          482          113          164 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
          22          280          615           34          389          481 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
          65          409            6          229           15          351 
TCGA-BR-8679 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
          NA          481          500           18          477           19 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
         325          382           35           20           92          677 
TCGA-BR-A4CR TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
          NA           28          408          411          392           24 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
          NA          431           16          390           20          589 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
         411           14          628          621           35          415 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
         352          156           86           99          400          401 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
           9            2           NA            2            2            2 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
           2            3            4            5            3            3 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
           4           NA            4            3          193            4 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
           4            4            4            2            3            3 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
           3           NA           92          822          485           NA 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4442 
         243          245         1645           NA           NA           NA 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
         912         1431          580          366           NA           NA 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4475 
          NA          577           NA          365           NA          699 
TCGA-CG-4476 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
          NA          942           NA           NA           31           31 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
          NA          183           30         3196           NA           NA 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
          NA         2405         1980          122         1674           NA 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
          NA          376          385          363          582          625 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
         573          564          566          543          181          523 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
         126          463          486          389          321          344 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
         375          752          511          593          523            7 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
         212          643          636          434          500          180 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
         461          419          449          417          342          344 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A 
          NA          297           90          476           NA          225 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 
          NA           19          237          494          200          440 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
          NA          647          247           12          594           92 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
         678          519           NA           NA          413           17 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-7131 TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
          47            7           NA           NA           NA           NA 
TCGA-HF-7136 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
          NA          550           NA           46           NA          434 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
         383          431          347          368          323           23 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
         739          170          374          360          736           99 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
         692          785          358          650          912          273 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
          NA          198          190          310            8           64 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
         394          589          538          374          294          270 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
         268          834          645           NA          572           NA 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
         559          163          158          398           NA          196 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 
          NA          209          169           55           77          169 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS 
        1842          879           NA          600          131           NA 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
          NA           NA           NA         3720         1153         1236 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
        3519         3540         2171           NA           NA         1083 
TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
          NA          176           NA         1148           NA           NA 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
          NA          946           NA          680          723           NA 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK 
         580         1023           NA           NA           NA           NA 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU 
          NA           NA           NA           NA          587          717 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
        1964           NA         1800          873           NA          264 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
        1498           NA           NA          224          261           NA 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        1346          262           NA           NA           NA           NA 
TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        1219          912          642          128           NA 
Variable 1:'AGE':	nDistinctValues=53,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=114,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=230,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=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:'DCCUPLOADDAY':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
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=33,	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=TRUE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=27,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "NEOPLASM.DISEASESTAGE"                 
 [3] "PATHOLOGY.T.STAGE"                     
 [4] "PATHOLOGY.N.STAGE"                     
 [5] "PATHOLOGY.M.STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL.TYPE"                     
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "COMPLETENESS.OF.RESECTION"             
[10] "NUMBER.OF.LYMPH.NODES"                 
[11] "RACE"                                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 395 columns, 1 survival variables, and 11 non-survival variables.
AGE, nv=53, 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 
 21  87 173 104 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 21  87 173 104 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
 21  87 173 104 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 21  87 173 104 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
122 107  75  79 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
122 107  75  79 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
122 107  75  79 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
122 107  75  79 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
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=33, binary=FALSE, numeric=TRUE
RACE, nv=4, 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    33  19
  AMP PEAK  1(1P36.22) WILD-TYPE 209 103
  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                            52                            312 
  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                            19                            103 
$`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         0.95        12.95         0.26         0.72 
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 
        0.13         0.10        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 
        1.02        55.04        18.54         4.14        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-RD-A7BT 
        1.41         6.44         6.74         1.81         2.53         8.61 
TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-VQ-A8DU TCGA-VQ-A8E2 TCGA-VQ-A8PK 
       16.67        37.91       115.69         5.46        31.10        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PX TCGA-VQ-A91U TCGA-VQ-A925 
        1.87        64.57         1.71         4.54 

$`AMP PEAK  1(1P36.22) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
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-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.12        10.13        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        0.62        32.78        13.84        13.22        16.14         1.25 
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-7715 TCGA-BR-7716 TCGA-BR-7717 
       24.76        35.24        23.93        15.42        28.01         0.69 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
        0.16        18.54        12.43         0.69        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       17.49         0.82         1.32         0.69        12.26         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
       20.55         0.72         0.26        16.31         1.55         1.48 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        19.50         0.36         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
        2.96         0.95        13.74         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 
        0.36        19.17        14.79         0.69         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 
        3.72         5.39         9.21        20.22         1.12        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        2.14        13.45         0.20         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         0.59        15.68         0.62        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       12.56         1.15         0.66         3.02         0.92        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       13.51        12.89         0.79        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-5800 TCGA-CD-5801 
       13.64        11.57         5.13         2.83        13.15        13.18 
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-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-A48C TCGA-CD-A4MG 
        0.10         6.35         0.13         0.13         0.13         0.07 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10         0.10        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-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-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-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-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-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        20.55        18.84        18.61        17.85         5.95 
TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       17.19        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         0.23         6.97 
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-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 
       14.76        13.71        11.31        11.44         9.76        15.65 
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         7.79        16.24 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        6.58        14.47        72.23        21.27         8.12         0.39 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        3.02        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        0.56         1.55         0.23         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-A4GQ TCGA-HU-A4GT 
       22.75        25.81        21.37        29.98         0.10         6.51 
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        17.69 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-8462 TCGA-IN-8663 
       12.30         9.67         8.88         8.81        18.81         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NT TCGA-KB-A6F5 
        5.36         5.19        13.08         6.87         5.56         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS 
       60.56        28.90         3.72        19.73         4.31        11.05 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
        4.67       122.30        40.64       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        16.87         5.79         0.92        37.74 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       13.25        13.02        21.73        22.36        23.77         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PO 
       19.07        33.63        46.26        16.31         2.70         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       23.41        15.65        19.30        23.57        14.33        59.18 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91W 
       28.70        11.70         8.68        49.25        20.81         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 
        8.58         9.73        44.25         8.61        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        5.72        40.08        29.98        21.11         4.21         0.79 

  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                          0.10                           0.07 
  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 
                        10.225                         11.700 
[1] "0.1 - 115.7 (10.2)" "0.1 - 122.3 (11.7)"
[1] "hr=" "1.1"
D1V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  1(1P36.22) MUTATED         0        4        5        7         3
  AMP PEAK  1(1P36.22) WILD-TYPE       2        9       34       24        33
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  1(1P36.22) MUTATED           7         1         11          7
  AMP PEAK  1(1P36.22) WILD-TYPE        42         2         66         48
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK  1(1P36.22) MUTATED            5        4
  AMP PEAK  1(1P36.22) WILD-TYPE         32       33
D1V3, multiclass
            clus
vv           AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              4                              9
  STAGE IB                              5                             34
  STAGE II                              7                             24
  STAGE IIA                             3                             33
  STAGE IIB                             7                             42
  STAGE III                             1                              2
  STAGE IIIA                           11                             66
  STAGE IIIB                            7                             48
  STAGE IIIC                            5                             32
  STAGE IV                              4                             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  1(1P36.22) MUTATED     6  13  27   9
  AMP PEAK  1(1P36.22) WILD-TYPE  15  74 146  95
D1V4, multiclass
    clus
vv   AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  T1                            6                             15
  T2                           13                             74
  T3                           27                            146
  T4                            9                             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
  AMP PEAK  1(1P36.22) MUTATED    15  17  10  13
  AMP PEAK  1(1P36.22) WILD-TYPE 107  90  65  66
D1V5, multiclass
    clus
vv   AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  N0                           15                            107
  N1                           17                             90
  N2                           10                             65
  N3                           13                             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"
                                vv
clus                              M0  M1  MX
  AMP PEAK  1(1P36.22) MUTATED    51   2   3
  AMP PEAK  1(1P36.22) WILD-TYPE 302  22  15
D1V6, multiclass
    clus
vv   AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  M0                           51                            302
  M1                            2                             22
  MX                            3                             15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.22) MUTATED    12  44
  AMP PEAK  1(1P36.22) WILD-TYPE 139 200
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.22) MUTATED     12   44
  AMP PEAK  1(1P36.22) WILD-TYPE  139  200
        clus
vv       AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  FEMALE                           12                            139
  MALE                             44                            200
[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                                    56
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  1(1P36.22) MUTATED                                                       22
  AMP PEAK  1(1P36.22) WILD-TYPE                                                    135
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  1(1P36.22) MUTATED                                                                  11
  AMP PEAK  1(1P36.22) WILD-TYPE                                                                58
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  1(1P36.22) MUTATED                                                  7
  AMP PEAK  1(1P36.22) WILD-TYPE                                               57
                                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                                        7
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)                           11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             7
  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                                                         56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       135
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             58
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              57
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      7
  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"
D1V9, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.22) MUTATED     0  56
  AMP PEAK  1(1P36.22) WILD-TYPE   6 333
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.22) MUTATED      0   56
  AMP PEAK  1(1P36.22) WILD-TYPE    6  333
     clus
vv    AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  NO                             0                              6
  YES                           56                            333
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  1(1P36.22) MUTATED    44   2   2   3
  AMP PEAK  1(1P36.22) WILD-TYPE 274  14  16  22
D1V10, multiclass
    clus
vv   AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  R0                           44                            274
  R1                            2                             14
  R2                            2                             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"
D1V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  1(1P36.22) MUTATED      12                         0
  AMP PEAK  1(1P36.22) WILD-TYPE    76                         6
                                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      34
  AMP PEAK  1(1P36.22) WILD-TYPE   209
D1V12, multiclass
                                           clus
vv                                          AMP PEAK  1(1P36.22) MUTATED
  ASIAN                                                               12
  BLACK OR AFRICAN AMERICAN                                            0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               34
                                           clus
vv                                          AMP PEAK  1(1P36.22) WILD-TYPE
  ASIAN                                                                 76
  BLACK OR AFRICAN AMERICAN                                              6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = AMP PEAK  2(1Q21.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  2(1Q21.3) MUTATED    86  42
  AMP PEAK  2(1Q21.3) WILD-TYPE 156  80
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          128                           236 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           42                            80 
$`AMP PEAK  2(1Q21.3) MUTATED`
TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6705 TCGA-BR-7197 TCGA-BR-7717 
        6.61        10.13         7.00        13.84         9.21         0.69 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 
       18.54         0.95         1.32        12.95         0.26         1.55 
TCGA-BR-8360 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8484 
        6.18        14.04        14.79         0.26         5.39         0.72 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8680 TCGA-BR-8687 
        9.21        20.22         1.12        12.79        15.81         0.62 
TCGA-BR-A4J1 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.72        12.82        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 
       13.64        13.15         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A 
        0.16         0.13         0.13         6.35         0.13         0.13 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4444 
        0.13         0.07         0.10         7.99        54.08        47.05 
TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5718 
       21.99        18.97         7.07        12.00        22.98         1.02 
TCGA-CG-5724 TCGA-CG-5730 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6526 
       12.03         4.01        11.93        20.55        18.54        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
        4.14        15.22        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6EX 
       24.72        19.50        14.27        16.44        11.24        11.31 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 
        2.96        15.65         0.62         7.79        16.24        72.23 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-A5NB 
        0.39         3.02        13.58         0.56         1.55        18.08 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-A4GC TCGA-HU-A4GD 
       26.47         5.92        14.27        12.59         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4H2 
       25.81        11.77         8.98         6.51         6.25        12.95 
TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO 
       12.30        27.42         3.45        18.38         5.19         1.41 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU TCGA-KB-A6F7 TCGA-RD-A7BT TCGA-RD-A7C1 
        6.44         6.74         1.81        60.56         8.61        16.67 
TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
      122.30       115.69         8.94        37.74         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PX 
       13.02        31.10        21.73         2.70        17.85        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91Y 
       14.33        59.18        28.70        20.81         1.71         9.73 
TCGA-VQ-A925 TCGA-VQ-AA68 
        4.54        40.08 

$`AMP PEAK  2(1Q21.3) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
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-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.12        13.68        39.12         0.82         0.62        32.78 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       13.22        16.14         1.25         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-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 
       15.42        28.01         0.16        12.43         0.69        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49         0.82         0.69        12.26         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 
       20.55         0.72         0.26        16.31         1.48         7.40 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       19.50         0.36         0.26        22.19         2.96         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 
       13.74         4.31         3.32         0.36        19.17         0.69 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       15.85         3.72        15.81         2.14        13.45         0.20 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         0.59        15.68 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56         1.15         0.66         3.02        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        0.92        13.41        13.51        12.89         0.79        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-BR-A4QM 
        0.53         0.66        19.36         0.46        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-8527 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A4MI 
        0.07         0.10         0.10         0.10         0.13         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        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-4455 
        8.05         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        9.01        30.97         6.97         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        15.02        28.96        79.07        65.10 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 
       55.04        21.07         7.99        12.36        12.66        19.13 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-8572 
       18.84        18.61        17.85         5.95        15.98        16.80 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YV 
       17.19         0.23         6.97        21.14        20.91         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-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 
        4.34         7.40         7.13         6.58        14.47        21.27 
TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        8.12        19.53        22.29        17.06        59.54         5.03 
TCGA-FP-A8CX TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        0.23         1.51        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-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
       21.37        29.98         0.10        10.19         0.26         2.10 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       19.36        17.69         9.67         8.88         8.81        21.21 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NT 
       18.81         3.39         5.36        13.08         6.87         5.56 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        2.53         5.56        28.90         3.72        19.73         4.31 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
       11.05         4.67        37.91        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8P2 
       57.44        35.61        16.87         5.79         0.92        22.36 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       23.77         7.73        19.07        33.63        46.26        16.31 
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        19.30        23.57 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z 
       11.70         8.68        49.25         7.36         8.58        44.25 
TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6B TCGA-VQ-AA6J 
        8.61        55.43         6.58         5.72        29.98        21.11 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        4.21         0.79 

  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                         0.07                          0.07 
  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 
                        11.31                         11.70 
[1] "0.1 - 122.3 (11.3)" "0.1 - 116.4 (11.7)"
[1] "hr=" "1"  
D2V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  2(1Q21.3) MUTATED         1        6       16        9        14
  AMP PEAK  2(1Q21.3) WILD-TYPE       1        7       23       22        22
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  2(1Q21.3) MUTATED          17         1         28         19
  AMP PEAK  2(1Q21.3) WILD-TYPE        32         2         49         36
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK  2(1Q21.3) MUTATED           10       16
  AMP PEAK  2(1Q21.3) WILD-TYPE         27       21
D2V3, multiclass
            clus
vv           AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             6                             7
  STAGE IB                            16                            23
  STAGE II                             9                            22
  STAGE IIA                           14                            22
  STAGE IIB                           17                            32
  STAGE III                            1                             2
  STAGE IIIA                          28                            49
  STAGE IIIB                          19                            36
  STAGE IIIC                          10                            27
  STAGE IV                            16                            21
[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  33  69  29
  AMP PEAK  2(1Q21.3) WILD-TYPE  11  54 104  75
D2V4, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  T1                          10                            11
  T2                          33                            54
  T3                          69                           104
  T4                          29                            75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  2(1Q21.3) MUTATED   47 35 24 31
  AMP PEAK  2(1Q21.3) WILD-TYPE 75 72 51 48
D2V5, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  N0                          47                            75
  N1                          35                            72
  N2                          24                            51
  N3                          31                            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"
                               vv
clus                             M0  M1  MX
  AMP PEAK  2(1Q21.3) MUTATED   125  10   9
  AMP PEAK  2(1Q21.3) WILD-TYPE 228  14   9
D2V6, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  M0                         125                           228
  M1                          10                            14
  MX                           9                             9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED    54  90
  AMP PEAK  2(1Q21.3) WILD-TYPE  97 154
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     54   90
  AMP PEAK  2(1Q21.3) WILD-TYPE   97  154
        clus
vv       AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  FEMALE                          54                            97
  MALE                            90                           154
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  2(1Q21.3) MUTATED                                      15
  AMP PEAK  2(1Q21.3) WILD-TYPE                                    50
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  2(1Q21.3) MUTATED                                                       58
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                     99
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  2(1Q21.3) MUTATED                                                                  27
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                                42
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  2(1Q21.3) MUTATED                                                 28
  AMP PEAK  2(1Q21.3) WILD-TYPE                                               36
                               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                                          4
  AMP PEAK  2(1Q21.3) WILD-TYPE                                        5
D2V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  2(1Q21.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     58
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          27
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           28
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    4
                                                                   clus
vv                                                                  AMP PEAK  2(1Q21.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       99
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            42
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     15
  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"
D2V9, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED     5 139
  AMP PEAK  2(1Q21.3) WILD-TYPE   1 250
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED      5  139
  AMP PEAK  2(1Q21.3) WILD-TYPE    1  250
     clus
vv    AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  NO                            5                             1
  YES                         139                           250
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  2(1Q21.3) MUTATED   108   9   9   9
  AMP PEAK  2(1Q21.3) WILD-TYPE 210   7   9  16
D2V10, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  R0                         108                           210
  R1                           9                             7
  R2                           9                             9
  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                         3
  AMP PEAK  2(1Q21.3) WILD-TYPE    53                         3
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  2(1Q21.3) MUTATED                                           1    84
  AMP PEAK  2(1Q21.3) WILD-TYPE                                         0   159
D2V12, multiclass
                                           clus
vv                                          AMP PEAK  2(1Q21.3) MUTATED
  ASIAN                                                              35
  BLACK OR AFRICAN AMERICAN                                           3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              84
                                           clus
vv                                          AMP PEAK  2(1Q21.3) WILD-TYPE
  ASIAN                                                                53
  BLACK OR AFRICAN AMERICAN                                             3
  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"

Clustering(3) Variable = AMP PEAK  3(1Q42.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  3(1Q42.3) MUTATED    81  40
  AMP PEAK  3(1Q42.3) WILD-TYPE 161  82
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                          121                           243 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                           40                            82 
$`AMP PEAK  3(1Q42.3) MUTATED`
TCGA-BR-4183 TCGA-BR-4267 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-7197 
        6.61         6.18         7.00         0.62        13.84         9.21 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-8059 TCGA-BR-8060 
       15.42        28.01         0.69        18.54         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8297 
        0.69         0.49        12.95         0.26         1.55         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8369 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8484 
        6.18        19.50        14.04         0.26         5.39         0.72 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8680 TCGA-BR-8687 
        9.21        20.22         1.12        12.79        15.81         0.62 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.66        22.26         0.72        12.82        13.51         0.46 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-CD-5800 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8528 
       20.42         1.15        13.15         0.07         0.07         0.10 
TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48C TCGA-CD-A4MG 
        0.16         0.13         6.35         0.13         0.13         0.07 
TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4466 
        0.10         7.99        54.08        19.07        21.99        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5719 TCGA-CG-5730 TCGA-D7-5578 TCGA-D7-5579 
        7.07        12.00         1.02         4.01        12.66        11.93 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 
       18.84        18.54        17.19         4.14        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-A4YU TCGA-D7-A6EX 
       11.31        12.33        24.72        19.50        16.44        11.31 
TCGA-D7-A6F0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7735 
        2.96         0.62         7.79        16.24        72.23         0.39 
TCGA-FP-7916 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 
        3.02         0.56         1.55        18.08        26.47         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4GC TCGA-HU-A4GD 
       14.27        12.59        14.17         0.76         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4H2 TCGA-HU-A4HD 
       25.81        11.77         0.10         6.51        12.95        27.42 
TCGA-IN-7808 TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-KB-A6F7 
        3.45         5.19        13.08         1.41         6.44        60.56 
TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
      122.30       115.69        35.61        37.74         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PY 
       13.02        31.10         7.73         2.70        17.85        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91Q TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       59.18        28.70        20.81         9.73        44.25         8.61 
TCGA-VQ-A925 
        4.54 

$`AMP PEAK  3(1Q42.3) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         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        13.12 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6706 
       10.13        13.68        39.12         0.82        32.78        13.22 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       16.14         1.25         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-7722 
       32.94        12.82        24.76        35.24        23.93         0.16 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         0.95         0.69        12.76        18.71        17.49 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8296 
       12.26        20.55         0.72         0.26        16.31         1.48 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        0.36         0.26        22.19         2.96         0.95        13.74 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 
        4.31         3.32         0.36        19.17        14.79         0.69 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       15.85         3.72        15.81         2.14        13.45         0.20 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         0.59        15.68 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       10.68        12.56         1.15         3.02         0.92        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       13.51        12.89         0.79        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       19.36        20.65        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8526 TCGA-CD-8527 
        3.25        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A489 
        0.13         0.10         0.10         0.13         0.10         0.13 
TCGA-CD-A48A TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.13         0.10         0.10        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       15.95         1.02         8.05         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
       47.05        12.03         9.01        22.98        30.97         6.97 
TCGA-CG-5718 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-5732 TCGA-CG-5733 
       15.02        28.96        79.07        65.10        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 
        7.99        12.36        19.13        20.55        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 
        5.95        15.22        15.98        16.80        17.19         0.23 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX 
        6.97        21.14        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-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6177 TCGA-F1-6874 
       15.65         4.34         7.40         7.13         6.58        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       21.27         8.12        19.53        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A8CX TCGA-HU-8238 TCGA-HU-8602 TCGA-HU-8604 
        5.03        13.58         0.23         1.51        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-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       21.37        29.98         8.98         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        17.69        12.30         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-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 
        6.74         6.87         5.56         1.81         2.53         5.56 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT 
       28.90         3.72        19.73         4.31        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
        4.67        16.67        37.91        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8E3 
       57.44         8.94        16.87         5.79         0.92        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       22.36        23.77        19.07        33.63        46.26        16.31 
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        19.30        23.57 
TCGA-VQ-A8PX TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91W 
       64.57        11.70         8.68        49.25         1.71         7.36 
TCGA-VQ-A91X TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B 
        8.58        55.43         6.58         5.72        40.08        29.98 
TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11         4.21         0.79 

  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                         0.07                          0.07 
  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 
                         9.73                         12.03 
[1] "0.1 - 122.3 (9.7)"  "0.1 - 116.4 (12.0)"
[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        6       12       10        13
  AMP PEAK  3(1Q42.3) WILD-TYPE       1        7       27       21        23
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  3(1Q42.3) MUTATED          12         2         26         19
  AMP PEAK  3(1Q42.3) WILD-TYPE        37         1         51         36
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK  3(1Q42.3) MUTATED           12       14
  AMP PEAK  3(1Q42.3) WILD-TYPE         25       23
D3V3, multiclass
            clus
vv           AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             6                             7
  STAGE IB                            12                            27
  STAGE II                            10                            21
  STAGE IIA                           13                            23
  STAGE IIB                           12                            37
  STAGE III                            2                             1
  STAGE IIIA                          26                            51
  STAGE IIIB                          19                            36
  STAGE IIIC                          12                            25
  STAGE IV                            14                            23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  3(1Q42.3) MUTATED     9  25  61  35
  AMP PEAK  3(1Q42.3) WILD-TYPE  12  62 112  69
D3V4, multiclass
    clus
vv   AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  T1                           9                            12
  T2                          25                            62
  T3                          61                           112
  T4                          35                            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  3(1Q42.3) MUTATED   43 31 26 27
  AMP PEAK  3(1Q42.3) WILD-TYPE 79 76 49 52
D3V5, multiclass
    clus
vv   AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  N0                          43                            79
  N1                          31                            76
  N2                          26                            49
  N3                          27                            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"
                               vv
clus                             M0  M1  MX
  AMP PEAK  3(1Q42.3) MUTATED   116   9   8
  AMP PEAK  3(1Q42.3) WILD-TYPE 237  15  10
D3V6, multiclass
    clus
vv   AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  M0                         116                           237
  M1                           9                            15
  MX                           8                            10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q42.3) MUTATED    49  84
  AMP PEAK  3(1Q42.3) WILD-TYPE 102 160
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED     49   84
  AMP PEAK  3(1Q42.3) WILD-TYPE  102  160
        clus
vv       AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  FEMALE                          49                           102
  MALE                            84                           160
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  3(1Q42.3) MUTATED                                      11
  AMP PEAK  3(1Q42.3) WILD-TYPE                                    54
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  3(1Q42.3) MUTATED                                                       52
  AMP PEAK  3(1Q42.3) WILD-TYPE                                                    105
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  3(1Q42.3) MUTATED                                                                  23
  AMP PEAK  3(1Q42.3) WILD-TYPE                                                                46
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  3(1Q42.3) MUTATED                                                 32
  AMP PEAK  3(1Q42.3) WILD-TYPE                                               32
                               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                                          4
  AMP PEAK  3(1Q42.3) WILD-TYPE                                        5
D3V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  3(1Q42.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      11
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     52
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          23
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    4
                                                                   clus
vv                                                                  AMP PEAK  3(1Q42.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        54
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      105
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            46
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     5
  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"
D3V9, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q42.3) MUTATED     3 130
  AMP PEAK  3(1Q42.3) WILD-TYPE   3 259
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED      3  130
  AMP PEAK  3(1Q42.3) WILD-TYPE    3  259
     clus
vv    AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  NO                            3                             3
  YES                         130                           259
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  3(1Q42.3) MUTATED   103   6   7   9
  AMP PEAK  3(1Q42.3) WILD-TYPE 215  10  11  16
D3V10, multiclass
    clus
vv   AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  R0                         103                           215
  R1                           6                            10
  R2                           7                            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"
D3V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  3(1Q42.3) MUTATED      33                         3
  AMP PEAK  3(1Q42.3) WILD-TYPE    55                         3
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  3(1Q42.3) MUTATED                                           0    80
  AMP PEAK  3(1Q42.3) WILD-TYPE                                         1   163
D3V12, multiclass
                                           clus
vv                                          AMP PEAK  3(1Q42.3) MUTATED
  ASIAN                                                              33
  BLACK OR AFRICAN AMERICAN                                           3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              80
                                           clus
vv                                          AMP PEAK  3(1Q42.3) WILD-TYPE
  ASIAN                                                                55
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               163
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = AMP PEAK  4(3Q26.2) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(3Q26.2) MUTATED    88  44
  AMP PEAK  4(3Q26.2) WILD-TYPE 154  78
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                          132                           232 
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                           44                            78 
$`AMP PEAK  4(3Q26.2) MUTATED`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6452 
        5.62        11.70         6.61        18.35         6.18        34.68 
TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-6706 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-7196 
       10.13         0.62        13.22        21.11        30.90        12.82 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 
        0.16        18.54         0.95        12.76         0.82         1.32 
TCGA-BR-8284 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8361 TCGA-BR-8367 
        0.72         0.26         1.55         1.48        19.50        13.74 
TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8676 
       14.79         0.72        12.79        15.81         2.14         7.53 
TCGA-BR-8687 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4J4 TCGA-BR-A4J7 TCGA-BR-A4PD 
        0.62        22.26        13.41         0.53        19.36        20.65 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       20.42        13.64         3.25        13.18         0.30         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8533 
        0.07         0.07         0.07         0.10         0.16         0.13 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4305 
        0.13         0.13         0.13         0.10         3.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4472 TCGA-CG-4477 
        7.99         8.05        47.05        12.03        12.00        30.97 
TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6815 
        1.02        12.03        15.02        18.54         4.14        15.98 
TCGA-D7-8570 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6EZ 
       24.72        20.91        16.44        14.76        11.24         9.76 
TCGA-D7-A6F0 TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 
        2.96         0.62        16.24        21.27         0.39         3.02 
TCGA-FP-7998 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8243 
       22.29        13.58         0.56         0.23        26.47         5.92 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
        8.98         2.10        12.95        19.36        17.69         9.67 
TCGA-HU-A4HD TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A7NT 
       27.42         5.19        13.08         1.41         6.44         5.56 
TCGA-IN-A7NU TCGA-KB-A6F7 TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-VQ-A8DL 
        1.81        60.56        16.67       115.69        35.61         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P5 
       37.74         5.46        13.02        31.10        21.73         7.73 
TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PP TCGA-VQ-A8PU TCGA-VQ-A8PX 
       16.31         2.70        17.85        23.41        23.57        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       59.18         8.68        20.81         9.73        44.25         8.61 
TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZQ-A9CR 
        4.54         5.72        40.08        29.98        21.11         0.79 

$`AMP PEAK  4(3Q26.2) WILD-TYPE`
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-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.12        13.68         7.00        39.12         0.82 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6803 
       32.78        13.84        16.14         1.25         8.98        31.20 
TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       32.94         9.21        24.76        35.24        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 
       28.01         0.69        12.43         0.69        18.71        17.49 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 
        0.69        12.26         0.49        20.55         0.26        12.95 
TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
       16.31         7.40         6.18         0.36         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        2.96         0.95         4.31        14.04         3.32         0.36 
TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17         0.69         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         0.20         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         0.59        15.68        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IV 
       12.56         1.15         0.66         3.02         0.92        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         0.79         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         6.35         0.13         0.07         0.10         0.10 
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         1.02         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        55.04 
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         5.95        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         0.23         6.97        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-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6177 
       15.65         4.34         7.40         7.13         7.79         6.58 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8209 
       14.47        72.23         8.12        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         1.55        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-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A5UG 
        6.74         6.87         2.53         5.56        28.90         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV 
       19.73         4.31        11.05         8.61         4.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       37.91        40.64       116.38        71.38        57.44         8.94 
TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DV TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       16.87         5.79        13.25        22.36        23.77        19.07 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       33.63        46.26         1.87         9.27        15.65        19.30 
TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91W 
       14.33        28.70        11.70        49.25         1.71         7.36 
TCGA-VQ-A91X TCGA-VQ-A924 TCGA-VQ-A927 TCGA-ZA-A8F6 
        8.58        55.43         6.58         4.21 

  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                         0.07                          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 
                       11.885                        11.490 
[1] "0.1 - 115.7 (11.9)" "0.1 - 122.3 (11.5)"
[1] "hr=" "1"  
D4V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  4(3Q26.2) MUTATED         0        5       13       12        10
  AMP PEAK  4(3Q26.2) WILD-TYPE       2        8       26       19        26
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  4(3Q26.2) MUTATED          18         1         28         18
  AMP PEAK  4(3Q26.2) WILD-TYPE        31         2         49         37
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK  4(3Q26.2) MUTATED           19       15
  AMP PEAK  4(3Q26.2) WILD-TYPE         18       22
D4V3, multiclass
            clus
vv           AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             5                             8
  STAGE IB                            13                            26
  STAGE II                            12                            19
  STAGE IIA                           10                            26
  STAGE IIB                           18                            31
  STAGE III                            1                             2
  STAGE IIIA                          28                            49
  STAGE IIIB                          18                            37
  STAGE IIIC                          19                            18
  STAGE IV                            15                            22
[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     8  29  57  46
  AMP PEAK  4(3Q26.2) WILD-TYPE  13  58 116  58
D4V4, multiclass
    clus
vv   AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  T1                           8                            13
  T2                          29                            58
  T3                          57                           116
  T4                          46                            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"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  4(3Q26.2) MUTATED   40 41 27 32
  AMP PEAK  4(3Q26.2) WILD-TYPE 82 66 48 47
D4V5, multiclass
    clus
vv   AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  N0                          40                            82
  N1                          41                            66
  N2                          27                            48
  N3                          32                            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                             M0  M1  MX
  AMP PEAK  4(3Q26.2) MUTATED   124   9  11
  AMP PEAK  4(3Q26.2) WILD-TYPE 229  15   7
D4V6, multiclass
    clus
vv   AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  M0                         124                           229
  M1                           9                            15
  MX                          11                             7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                               cls
clus                              0   1
  AMP PEAK  4(3Q26.2) MUTATED    57  87
  AMP PEAK  4(3Q26.2) WILD-TYPE  94 157
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(3Q26.2) MUTATED     57   87
  AMP PEAK  4(3Q26.2) WILD-TYPE   94  157
        clus
vv       AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  FEMALE                          57                            94
  MALE                            87                           157
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  4(3Q26.2) MUTATED                                      19
  AMP PEAK  4(3Q26.2) WILD-TYPE                                    46
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  4(3Q26.2) MUTATED                                                       61
  AMP PEAK  4(3Q26.2) WILD-TYPE                                                     96
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  4(3Q26.2) MUTATED                                                                  25
  AMP PEAK  4(3Q26.2) WILD-TYPE                                                                44
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  4(3Q26.2) MUTATED                                                 26
  AMP PEAK  4(3Q26.2) WILD-TYPE                                               38
                               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                                          4
  AMP PEAK  4(3Q26.2) WILD-TYPE                                        5
D4V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  4(3Q26.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      19
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     61
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          25
  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                                                    4
                                                                   clus
vv                                                                  AMP PEAK  4(3Q26.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       96
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            44
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     5
  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"
D4V9, binary
                               cls
clus                              0   1
  AMP PEAK  4(3Q26.2) MUTATED     2 142
  AMP PEAK  4(3Q26.2) WILD-TYPE   4 247
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(3Q26.2) MUTATED      2  142
  AMP PEAK  4(3Q26.2) WILD-TYPE    4  247
     clus
vv    AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  NO                            2                             4
  YES                         142                           247
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  4(3Q26.2) MUTATED   114   5   8   9
  AMP PEAK  4(3Q26.2) WILD-TYPE 204  11  10  16
D4V10, multiclass
    clus
vv   AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  R0                         114                           204
  R1                           5                            11
  R2                           8                            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"
D4V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  4(3Q26.2) MUTATED      36                         3
  AMP PEAK  4(3Q26.2) WILD-TYPE    52                         3
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  4(3Q26.2) MUTATED                                           0    83
  AMP PEAK  4(3Q26.2) WILD-TYPE                                         1   160
D4V12, multiclass
                                           clus
vv                                          AMP PEAK  4(3Q26.2) MUTATED
  ASIAN                                                              36
  BLACK OR AFRICAN AMERICAN                                           3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              83
                                           clus
vv                                          AMP PEAK  4(3Q26.2) WILD-TYPE
  ASIAN                                                                52
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               160
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = AMP PEAK  5(5P15.33) MUTATION ANALYSIS
D5V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  5(5P15.33) MUTATED    70  38
  AMP PEAK  5(5P15.33) WILD-TYPE 172  84
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                           108                            256 
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                            38                             84 
$`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         0.69 
TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        0.95         1.32         0.69         0.72        12.95         0.26 
TCGA-BR-8296 TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8373 TCGA-BR-8485 
        1.48         0.26         2.96        13.74        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         0.62        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 
        6.35         0.13         0.13         0.10         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         1.02         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         4.14 
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         6.97        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         7.79        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-A8CX TCGA-HU-8238 TCGA-HU-8245 
        0.39        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-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8N5 
        6.74         5.56         5.56         8.61       122.30        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        8.94        35.61         5.46        13.25        13.02        31.10 
TCGA-VQ-A8E3 TCGA-VQ-A8PK TCGA-VQ-A91A TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Z 
       21.73        17.85        28.70         1.71         8.58        44.25 
TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-AA68 TCGA-VQ-AA6J TCGA-ZQ-A9CR 
        8.61         4.54         6.58        40.08        21.11         0.79 

$`AMP PEAK  5(5P15.33) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.61         6.97         7.43        18.35 
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-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.12        10.13        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        0.62        32.78        13.84        13.22        16.14         1.25 
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-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 
       24.76        23.93         0.16        18.54        12.43         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 
       12.76        18.71        17.49         0.82        12.26         0.49 
TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       20.55         0.26        16.31         1.55         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8369 
       19.50         0.36        22.19         0.95         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 
        3.32         0.36        19.17         0.69         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         0.72         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        2.14        13.45         0.20         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         0.59        15.68        10.68        12.56         1.15 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        0.66         3.02        22.26         0.92        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         0.79         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-5802 TCGA-CD-5803 
       11.57         5.13         2.83         3.25         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.07         0.07         0.16         0.10         0.10 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.10         0.13         0.13         0.07         0.10         0.10 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         1.02         8.05 
TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4477 
        4.01        29.98        19.07        21.99         9.01        30.97 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 
        6.97         1.02         0.99         6.02       105.07        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-6519 
       79.07        65.10        55.04        21.07         7.99        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         5.95        15.98 
TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.79        12.33        16.80        19.50        17.19         0.23 
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-A748 TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 
        4.34         7.13        16.24         6.58        14.47        21.27 
TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        8.12         3.02        22.29        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 
        0.56         1.55        18.08        26.47         5.92        14.27 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 
       11.41        12.10        10.62         0.76         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       11.84        24.20        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        17.69 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 
        9.67         8.88         8.81        21.21        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RS 
       18.38         5.36        13.08         1.41         6.44         6.87 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        1.81         2.53        60.56        28.90         3.72        19.73 
TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 
        4.31        11.05         4.67        16.67        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL 
      115.69       116.38        71.38        16.87         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.74        22.36        23.77         7.73        19.07        33.63 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       46.26        16.31         2.70         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        19.30        23.57        64.57        14.33        59.18 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91W TCGA-VQ-A91Y 
       11.70         8.68        49.25        20.81         7.36         9.73 
TCGA-VQ-A924 TCGA-VQ-A928 TCGA-VQ-AA6B TCGA-ZA-A8F6 
       55.43         5.72        29.98         4.21 

  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                          0.07                           0.07 
  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 
                         10.93                          11.97 
[1] "0.1 - 122.3 (10.9)" "0.1 - 116.4 (12.0)"
[1] "hr=" "1.2"
D5V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  5(5P15.33) MUTATED         0        3       11       10        11
  AMP PEAK  5(5P15.33) WILD-TYPE       2       10       28       21        25
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  5(5P15.33) MUTATED          12         1         28         13
  AMP PEAK  5(5P15.33) WILD-TYPE        37         2         49         42
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK  5(5P15.33) MUTATED            9       13
  AMP PEAK  5(5P15.33) WILD-TYPE         28       24
D5V3, multiclass
            clus
vv           AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              3                             10
  STAGE IB                             11                             28
  STAGE II                             10                             21
  STAGE IIA                            11                             25
  STAGE IIB                            12                             37
  STAGE III                             1                              2
  STAGE IIIA                           28                             49
  STAGE IIIB                           13                             42
  STAGE IIIC                            9                             28
  STAGE IV                             13                             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  5(5P15.33) MUTATED     2  28  60  23
  AMP PEAK  5(5P15.33) WILD-TYPE  19  59 113  81
D5V4, multiclass
    clus
vv   AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  T1                            2                             19
  T2                           28                             59
  T3                           60                            113
  T4                           23                             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
  AMP PEAK  5(5P15.33) MUTATED   33 32 24 23
  AMP PEAK  5(5P15.33) WILD-TYPE 89 75 51 56
D5V5, multiclass
    clus
vv   AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  N0                           33                             89
  N1                           32                             75
  N2                           24                             51
  N3                           23                             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"
                                vv
clus                              M0  M1  MX
  AMP PEAK  5(5P15.33) MUTATED   102   8   6
  AMP PEAK  5(5P15.33) WILD-TYPE 251  16  12
D5V6, multiclass
    clus
vv   AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  M0                          102                            251
  M1                            8                             16
  MX                            6                             12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                                cls
clus                               0   1
  AMP PEAK  5(5P15.33) MUTATED    40  76
  AMP PEAK  5(5P15.33) WILD-TYPE 111 168
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(5P15.33) MUTATED     40   76
  AMP PEAK  5(5P15.33) WILD-TYPE  111  168
        clus
vv       AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  FEMALE                           40                            111
  MALE                             76                            168
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  5(5P15.33) MUTATED                                      11
  AMP PEAK  5(5P15.33) WILD-TYPE                                    54
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  5(5P15.33) MUTATED                                                       40
  AMP PEAK  5(5P15.33) WILD-TYPE                                                    117
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  5(5P15.33) MUTATED                                                                  26
  AMP PEAK  5(5P15.33) WILD-TYPE                                                                43
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  5(5P15.33) MUTATED                                                 23
  AMP PEAK  5(5P15.33) WILD-TYPE                                               41
                                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                                          2
  AMP PEAK  5(5P15.33) WILD-TYPE                                        7
D5V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  5(5P15.33) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       11
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      40
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           26
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            23
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
                                                                   clus
vv                                                                  AMP PEAK  5(5P15.33) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         54
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       117
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             43
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              41
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      13
  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"
D5V9, binary
                                cls
clus                               0   1
  AMP PEAK  5(5P15.33) MUTATED     2 114
  AMP PEAK  5(5P15.33) WILD-TYPE   4 275
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(5P15.33) MUTATED      2  114
  AMP PEAK  5(5P15.33) WILD-TYPE    4  275
     clus
vv    AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  NO                             2                              4
  YES                          114                            275
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  5(5P15.33) MUTATED    93   5   7   5
  AMP PEAK  5(5P15.33) WILD-TYPE 225  11  11  20
D5V10, multiclass
    clus
vv   AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  R0                           93                            225
  R1                            5                             11
  R2                            7                             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"
D5V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  5(5P15.33) MUTATED      27                         4
  AMP PEAK  5(5P15.33) WILD-TYPE    61                         2
                                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      67
  AMP PEAK  5(5P15.33) WILD-TYPE   176
D5V12, multiclass
                                           clus
vv                                          AMP PEAK  5(5P15.33) MUTATED
  ASIAN                                                               27
  BLACK OR AFRICAN AMERICAN                                            4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               67
                                           clus
vv                                          AMP PEAK  5(5P15.33) WILD-TYPE
  ASIAN                                                                 61
  BLACK OR AFRICAN AMERICAN                                              2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                176
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = AMP PEAK  6(5P13.1) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  6(5P13.1) MUTATED    67  36
  AMP PEAK  6(5P13.1) WILD-TYPE 175  86
  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE 
                          103                           261 
  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE 
                           36                            86 
$`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         7.00         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 
        0.69         0.95        18.71         1.32         0.69         0.72 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8367 
       12.95         0.26         1.48         0.26         2.96        13.74 
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         0.62 
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         6.35         0.13         0.13         0.10 
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         1.02         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         4.14 
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         6.97        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         7.79        72.23         0.39 
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-A7NT 
        2.10        12.30        27.42         3.45         5.19         5.56 
TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DU 
        1.81         5.56        57.44         8.94        35.61         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8PK TCGA-VQ-A91A TCGA-VQ-A91X 
       13.25        13.02        21.73        17.85        28.70         8.58 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A927 TCGA-VQ-AA68 TCGA-VQ-AA6J 
        9.73        44.25         8.61         6.58        40.08        21.11 
TCGA-ZQ-A9CR 
        0.79 

$`AMP PEAK  6(5P13.1) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.61         6.97         7.43        18.35 
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-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.12        10.13        13.68        39.12         0.82         0.62 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        13.84        13.22        16.14         1.25         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-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 
       23.93         0.16        18.54        12.43         0.69        12.76 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 
       17.49         0.82        12.26         0.49        20.55         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       16.31         1.55         7.40         6.18        19.50         0.36 
TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       22.19         0.95         4.31         3.32         0.36        19.17 
TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
        0.69         0.26        15.85         3.72         5.39         0.72 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         2.14        13.45         0.20 
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         0.59        15.68 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS 
       10.68        12.56         1.15         0.66         3.02         0.92 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         0.79         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-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-8526 TCGA-CD-8527 TCGA-CD-8529 
       13.15         0.30         0.07         0.07         0.07         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A487 
        0.16         0.10         0.10         0.13         0.10         0.13 
TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        0.13         0.07         0.10         0.10        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 
       27.02        15.95         1.02         8.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 
       29.98        19.07         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-D7-5577 TCGA-D7-6519 TCGA-D7-6520 
       55.04        21.07         7.99        12.36        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 
       18.54        18.61        17.85         5.95        17.19        15.98 
TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.79        12.33        16.80        19.50        17.19         0.23 
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-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 
        4.34         7.40         7.13        16.24         6.58        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
       21.27         8.12         3.02        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56         1.55        18.08        26.47         5.92 
TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 
       14.27        11.41        10.62         0.76         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       11.84        24.20        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.25        10.19         0.26        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 
       17.69         9.67         8.88         8.81        21.21        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
        3.39        18.38         5.36        13.08         1.41         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG 
        6.74         6.87         2.53        60.56        28.90         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
       19.73         4.31        11.05         8.61         4.67        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8E2 TCGA-VQ-A8P2 
       16.87         5.79         0.92        37.74        31.10        22.36 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       23.77         7.73        19.07        33.63        46.26        16.31 
TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
        2.70         1.87         9.27        23.41        15.65        19.30 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E 
       23.57        64.57        14.33        59.18        11.70         8.68 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A924 TCGA-VQ-A925 
       49.25        20.81         1.71         7.36        55.43         4.54 
TCGA-VQ-A928 TCGA-VQ-AA6B TCGA-ZA-A8F6 
        5.72        29.98         4.21 

  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE 
                         0.07                          0.07 
  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 
                        11.31                         11.70 
[1] "0.1 - 72.2 (11.3)"  "0.1 - 122.3 (11.7)"
[1] "hr=" "1.1"
D6V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  6(5P13.1) MUTATED         0        3       11        9        12
  AMP PEAK  6(5P13.1) WILD-TYPE       2       10       28       22        24
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  6(5P13.1) MUTATED          12         1         24         11
  AMP PEAK  6(5P13.1) WILD-TYPE        37         2         53         44
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK  6(5P13.1) MUTATED           12       12
  AMP PEAK  6(5P13.1) WILD-TYPE         25       25
D6V3, multiclass
            clus
vv           AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             3                            10
  STAGE IB                            11                            28
  STAGE II                             9                            22
  STAGE IIA                           12                            24
  STAGE IIB                           12                            37
  STAGE III                            1                             2
  STAGE IIIA                          24                            53
  STAGE IIIB                          11                            44
  STAGE IIIC                          12                            25
  STAGE IV                            12                            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  6(5P13.1) MUTATED     2  26  54  27
  AMP PEAK  6(5P13.1) WILD-TYPE  19  61 119  77
D6V4, multiclass
    clus
vv   AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  T1                           2                            19
  T2                          26                            61
  T3                          54                           119
  T4                          27                            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  6(5P13.1) MUTATED   32 33 18 25
  AMP PEAK  6(5P13.1) WILD-TYPE 90 74 57 54
D6V5, multiclass
    clus
vv   AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  N0                          32                            90
  N1                          33                            74
  N2                          18                            57
  N3                          25                            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"
                               vv
clus                             M0  M1  MX
  AMP PEAK  6(5P13.1) MUTATED    98   8   6
  AMP PEAK  6(5P13.1) WILD-TYPE 255  16  12
D6V6, multiclass
    clus
vv   AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  M0                          98                           255
  M1                           8                            16
  MX                           6                            12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                               cls
clus                              0   1
  AMP PEAK  6(5P13.1) MUTATED    41  71
  AMP PEAK  6(5P13.1) WILD-TYPE 110 173
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(5P13.1) MUTATED     41   71
  AMP PEAK  6(5P13.1) WILD-TYPE  110  173
        clus
vv       AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  FEMALE                          41                           110
  MALE                            71                           173
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  6(5P13.1) MUTATED                                      11
  AMP PEAK  6(5P13.1) WILD-TYPE                                    54
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  6(5P13.1) MUTATED                                                       42
  AMP PEAK  6(5P13.1) WILD-TYPE                                                    115
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  6(5P13.1) MUTATED                                                                  24
  AMP PEAK  6(5P13.1) WILD-TYPE                                                                45
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  6(5P13.1) MUTATED                                                 20
  AMP PEAK  6(5P13.1) WILD-TYPE                                               44
                               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                                          2
  AMP PEAK  6(5P13.1) WILD-TYPE                                        7
D6V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  6(5P13.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      11
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     42
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          24
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    2
                                                                   clus
vv                                                                  AMP PEAK  6(5P13.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        54
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      115
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            45
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             44
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     13
  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"
D6V9, binary
                               cls
clus                              0   1
  AMP PEAK  6(5P13.1) MUTATED     2 110
  AMP PEAK  6(5P13.1) WILD-TYPE   4 279
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(5P13.1) MUTATED      2  110
  AMP PEAK  6(5P13.1) WILD-TYPE    4  279
     clus
vv    AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  NO                            2                             4
  YES                         110                           279
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  6(5P13.1) MUTATED    89   5   7   5
  AMP PEAK  6(5P13.1) WILD-TYPE 229  11  11  20
D6V10, multiclass
    clus
vv   AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  R0                          89                           229
  R1                           5                            11
  R2                           7                            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"
D6V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  6(5P13.1) MUTATED      23                         4
  AMP PEAK  6(5P13.1) WILD-TYPE    65                         2
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  6(5P13.1) MUTATED                                           0    67
  AMP PEAK  6(5P13.1) WILD-TYPE                                         1   176
D6V12, multiclass
                                           clus
vv                                          AMP PEAK  6(5P13.1) MUTATED
  ASIAN                                                              23
  BLACK OR AFRICAN AMERICAN                                           4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              67
                                           clus
vv                                          AMP PEAK  6(5P13.1) WILD-TYPE
  ASIAN                                                                65
  BLACK OR AFRICAN AMERICAN                                             2
  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"

Clustering(7) Variable = AMP PEAK  7(6P21.1) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  7(6P21.1) MUTATED    62  35
  AMP PEAK  7(6P21.1) WILD-TYPE 180  87
  AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE 
                           97                           267 
  AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE 
                           35                            87 
$`AMP PEAK  7(6P21.1) MUTATED`
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6457 
        6.61         6.97        18.35         6.18        10.13        13.68 
TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 
        7.00         0.62         9.21        35.24        15.42         0.69 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8369 
       18.54         0.95         1.32        12.95         0.26        14.04 
TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8683 
       14.79         0.72         9.21        20.22        11.54         0.59 
TCGA-BR-8686 TCGA-BR-A4CQ TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-5799 
       15.68        22.26        20.65        20.42        13.64         3.25 
TCGA-CD-5803 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48C TCGA-CG-4436 
        0.07         0.13         6.35         0.13         0.13         7.99 
TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5718 
       54.08        19.07        12.03        18.97        30.97         1.02 
TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-6518 TCGA-D7-6527 TCGA-D7-6528 
       79.07         4.01        55.04        19.13         4.14        15.22 
TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8576 TCGA-D7-A4YT 
       15.98        10.55        11.31        12.33         6.97        14.27 
TCGA-D7-A4YU TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-8122 TCGA-FP-7735 TCGA-FP-7829 
       16.44         2.96        15.65         7.79         0.39        19.53 
TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-A4GF 
       17.06         0.56         1.55         5.92        14.17        25.81 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL 
       17.69        12.30         9.67         3.39        18.38         5.19 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IP-7968 
       13.08         1.41         6.74         6.87         5.56         2.53 
TCGA-KB-A93H TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-VQ-A8DU 
       28.90         8.61       122.30        37.91       115.69         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PU 
       13.02        31.10         7.73         2.70        17.85        23.57 
TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-AA68 TCGA-VQ-AA6B 
        1.71         8.58         8.61         4.54        40.08        29.98 
TCGA-ZQ-A9CR 
        0.79 

$`AMP PEAK  7(6P21.1) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4279 
        5.62        11.70         4.64         7.43        30.90         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6563 TCGA-BR-6564 
        6.61        34.68        15.95        13.12        39.12         0.82 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        13.84        13.22        16.14         1.25         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-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 
       23.93        28.01         0.16        12.43         0.69        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49         0.82         0.69        12.26         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
       20.55         0.72         0.26        16.31         1.55         1.48 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        19.50         0.36         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
        2.96         0.95        13.74         4.31         3.32         0.36 
TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17         0.69         0.26        15.85         3.72         5.39 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         2.14        13.45         0.20 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8687 TCGA-BR-8690 
        7.53         0.49        15.81        16.44         0.62        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       12.56         1.15         0.66         3.02         0.92        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         0.79         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF 
       12.82         0.66        19.36        13.51         0.46         1.15 
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-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A489 
        0.16         0.10         0.10         0.13         0.10         0.13 
TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
        0.13         0.07         0.10         0.10         0.10        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-4460 TCGA-CG-4465 TCGA-CG-4469 
       14.01        29.98        47.05        21.99         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-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 
       21.07         7.99        12.36        12.66        11.93        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85         5.95        17.19 
TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.79        24.72        16.80        19.50        17.19         0.23 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       21.14        20.91         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-A748 
       13.71        11.24        11.31        11.44         9.76         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 
        7.40         7.13         0.62        16.24         6.58        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
       72.23        21.27         8.12         3.02        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-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-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       19.36         8.88         8.81        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RP TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 
       18.81         5.36         6.44         1.81         5.56        60.56 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
        3.72        19.73         4.31        11.05         4.67        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-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E3 
       16.87         5.79         0.92        37.74        13.25        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       22.36        23.77        19.07        33.63        46.26        16.31 
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        19.30        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        59.18        28.70        11.70         8.68        49.25 
TCGA-VQ-A91Q TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A924 TCGA-VQ-A927 
       20.81         7.36         9.73        44.25        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-AA6J TCGA-ZA-A8F6 
        5.72        21.11         4.21 

  AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE 
                         0.07                          0.07 
  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 
                        10.55                         11.77 
[1] "0.1 - 122.3 (10.6)" "0.1 - 116.4 (11.8)"
[1] "hr=" "1.1"
D7V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  7(6P21.1) MUTATED         1        3       15       10         8
  AMP PEAK  7(6P21.1) WILD-TYPE       1       10       24       21        28
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  7(6P21.1) MUTATED          15         0         23         13
  AMP PEAK  7(6P21.1) WILD-TYPE        34         3         54         42
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK  7(6P21.1) MUTATED            6       10
  AMP PEAK  7(6P21.1) WILD-TYPE         31       27
D7V3, multiclass
            clus
vv           AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             3                            10
  STAGE IB                            15                            24
  STAGE II                            10                            21
  STAGE IIA                            8                            28
  STAGE IIB                           15                            34
  STAGE III                            0                             3
  STAGE IIIA                          23                            54
  STAGE IIIB                          13                            42
  STAGE IIIC                           6                            31
  STAGE IV                            10                            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  7(6P21.1) MUTATED     6  30  48  20
  AMP PEAK  7(6P21.1) WILD-TYPE  15  57 125  84
D7V4, multiclass
    clus
vv   AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE
  T1                           6                            15
  T2                          30                            57
  T3                          48                           125
  T4                          20                            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
  AMP PEAK  7(6P21.1) MUTATED   34 34 21 18
  AMP PEAK  7(6P21.1) WILD-TYPE 88 73 54 61
D7V5, multiclass
    clus
vv   AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE
  N0                          34                            88
  N1                          34                            73
  N2                          21                            54
  N3                          18                            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                             M0  M1  MX
  AMP PEAK  7(6P21.1) MUTATED    97   4   8
  AMP PEAK  7(6P21.1) WILD-TYPE 256  20  10
D7V6, multiclass
    clus
vv   AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE
  M0                          97                           256
  M1                           4                            20
  MX                           8                            10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                               cls
clus                              0   1
  AMP PEAK  7(6P21.1) MUTATED    38  71
  AMP PEAK  7(6P21.1) WILD-TYPE 113 173
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(6P21.1) MUTATED     38   71
  AMP PEAK  7(6P21.1) WILD-TYPE  113  173
        clus
vv       AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE
  FEMALE                          38                           113
  MALE                            71                           173
[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                                    61
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  7(6P21.1) MUTATED                                                       50
  AMP PEAK  7(6P21.1) WILD-TYPE                                                    107
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  7(6P21.1) MUTATED                                                                  24
  AMP PEAK  7(6P21.1) WILD-TYPE                                                                45
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  7(6P21.1) MUTATED                                                 24
  AMP PEAK  7(6P21.1) WILD-TYPE                                               40
                               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                                        7
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)                          24
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           24
  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                                                        61
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      107
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            45
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             40
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     18
  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"
D7V9, binary
                               cls
clus                              0   1
  AMP PEAK  7(6P21.1) MUTATED     3 106
  AMP PEAK  7(6P21.1) WILD-TYPE   3 283
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(6P21.1) MUTATED      3  106
  AMP PEAK  7(6P21.1) WILD-TYPE    3  283
     clus
vv    AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE
  NO                            3                             3
  YES                         106                           283
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  7(6P21.1) MUTATED    84   4   5  10
  AMP PEAK  7(6P21.1) WILD-TYPE 234  12  13  15
D7V10, multiclass
    clus
vv   AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE
  R0                          84                           234
  R1                           4                            12
  R2                           5                            13
  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                         2
  AMP PEAK  7(6P21.1) WILD-TYPE    70                         4
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  7(6P21.1) MUTATED                                           1    73
  AMP PEAK  7(6P21.1) WILD-TYPE                                         0   170
D7V12, multiclass
                                           clus
vv                                          AMP PEAK  7(6P21.1) MUTATED
  ASIAN                                                              18
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              73
                                           clus
vv                                          AMP PEAK  7(6P21.1) WILD-TYPE
  ASIAN                                                                70
  BLACK OR AFRICAN AMERICAN                                             4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               170
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = AMP PEAK  8(6Q12) MUTATION ANALYSIS
D8V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  8(6Q12) MUTATED    43  28
  AMP PEAK  8(6Q12) WILD-TYPE 199  94
  AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE 
                         71                         293 
  AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE 
                         28                          94 
$`AMP PEAK  8(6Q12) MUTATED`
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-7197 
        6.61         6.97         6.18        10.13         7.00         9.21 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7723 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8289 
       35.24        15.42        18.54         1.32        12.95         0.26 
TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8686 
       14.04        14.79         0.72         9.21        11.54        15.68 
TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-5799 
        0.72        13.51        20.65        20.42        13.64         3.25 
TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CG-4436 TCGA-CG-4438 
        0.13         6.35         0.13         0.13         7.99        54.08 
TCGA-CG-4440 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5730 TCGA-D7-6526 
        4.01        18.97        30.97         1.02         4.01        17.19 
TCGA-D7-6527 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8576 TCGA-D7-A4YT 
        4.14        10.55        11.31        12.33         6.97        14.27 
TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-A4BF TCGA-HU-A4GF 
        2.96         7.79         0.39        19.53         1.55        25.81 
TCGA-HU-A4GT TCGA-HU-A4H6 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO 
        6.51         9.67         3.39        18.38         5.19         1.41 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A663 TCGA-RD-A7BT TCGA-RD-A8MW TCGA-RD-A8N1 
       60.56        28.90         4.31         8.61        37.91       115.69 
TCGA-RD-A8N6 TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8P5 TCGA-VQ-A8PJ TCGA-VQ-A8PK 
        8.94        13.25        13.02         7.73         2.70        17.85 
TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-AA68 TCGA-VQ-AA6B 
        1.71         8.58         8.61        40.08        29.98 

$`AMP PEAK  8(6Q12) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        5.62        11.70         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        13.12        13.68 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12         0.82         0.62        32.78        13.84        13.22 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       16.14         1.25         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         0.69 
TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
        0.16        12.43         0.95         0.69        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49         0.82         0.69        12.26         0.49        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.72         0.26        16.31         1.55         1.48         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        19.50         0.36         0.26        22.19         2.96 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        13.74         4.31         3.32         0.36        19.17 
TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8486 
        0.69         0.26        15.85         3.72         5.39        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         2.14        13.45         0.20 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 
        7.53         0.49        15.81        16.44         0.59         0.62 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56         1.15         0.66         3.02        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        0.92        13.41        13.51        12.89         0.79        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PF 
        0.53        12.82         0.66        19.36         0.46         1.15 
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-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-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-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.13         0.13         0.07         0.10         0.10         0.10 
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-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
       14.01        29.98        47.05        19.07        12.03        21.99 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 
        9.01         7.07        12.00        22.98         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        55.04        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-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 
       18.54        18.61        17.85         5.95        15.22        15.98 
TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.79        24.72        16.80        19.50        17.19         0.23 
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-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-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO 
       15.65         4.34         7.40         7.13         0.62        16.24 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7916 
        6.58        14.47        72.23        21.27         8.12         3.02 
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-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-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-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-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       17.69        12.30         8.88         8.81        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
        3.45        18.81         5.36        13.08         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-MX-A5UG 
        6.87         5.56         1.81         2.53         5.56         3.72 
TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 
       19.73        11.05         4.67        16.67       122.30        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB 
      116.38        71.38        57.44        35.61        16.87         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 
        0.92        37.74         5.46        31.10        21.73        22.36 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PM 
       23.77        19.07        33.63        46.26        16.31         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        19.30        23.57        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        59.18        28.70        11.70         8.68        49.25 
TCGA-VQ-A91Q TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A924 TCGA-VQ-A925 
       20.81         7.36         9.73        44.25        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        6.58         5.72        21.11         4.21         0.79 

  AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE 
                       0.13                        0.07 
  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 
                       9.21                       12.03 
[1] "0.1 - 115.7 (9.2)"  "0.1 - 122.3 (12.0)"
[1] "hr=" "1.3"
D8V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  8(6Q12) MUTATED         1        1       12        6         8
  AMP PEAK  8(6Q12) WILD-TYPE       1       12       27       25        28
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  8(6Q12) MUTATED          10         0         16         10
  AMP PEAK  8(6Q12) WILD-TYPE        39         3         61         45
                             vv
clus                          STAGE IIIC STAGE IV
  AMP PEAK  8(6Q12) MUTATED            4       10
  AMP PEAK  8(6Q12) WILD-TYPE         33       27
D8V3, multiclass
            clus
vv           AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE
  STAGE I                            1                           1
  STAGE IA                           1                          12
  STAGE IB                          12                          27
  STAGE II                           6                          25
  STAGE IIA                          8                          28
  STAGE IIB                         10                          39
  STAGE III                          0                           3
  STAGE IIIA                        16                          61
  STAGE IIIB                        10                          45
  STAGE IIIC                         4                          33
  STAGE IV                          10                          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  8(6Q12) MUTATED     4  20  39  16
  AMP PEAK  8(6Q12) WILD-TYPE  17  67 134  88
D8V4, multiclass
    clus
vv   AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE
  T1                         4                          17
  T2                        20                          67
  T3                        39                         134
  T4                        16                          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  8(6Q12) MUTATED   27 24 13 15
  AMP PEAK  8(6Q12) WILD-TYPE 95 83 62 64
D8V5, multiclass
    clus
vv   AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE
  N0                        27                          95
  N1                        24                          83
  N2                        13                          62
  N3                        15                          64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1  MX
  AMP PEAK  8(6Q12) MUTATED    71   6   4
  AMP PEAK  8(6Q12) WILD-TYPE 282  18  14
D8V6, multiclass
    clus
vv   AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE
  M0                        71                         282
  M1                         6                          18
  MX                         4                          14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                             cls
clus                            0   1
  AMP PEAK  8(6Q12) MUTATED    32  49
  AMP PEAK  8(6Q12) WILD-TYPE 119 195
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(6Q12) MUTATED     32   49
  AMP PEAK  8(6Q12) WILD-TYPE  119  195
        clus
vv       AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE
  FEMALE                        32                         119
  MALE                          49                         195
[1] 2 2
[1] FALSE
                             vv
clus                          STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  8(6Q12) MUTATED                                       4
  AMP PEAK  8(6Q12) WILD-TYPE                                    61
                             vv
clus                          STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  8(6Q12) MUTATED                                                       36
  AMP PEAK  8(6Q12) WILD-TYPE                                                    121
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  8(6Q12) MUTATED                                                                  24
  AMP PEAK  8(6Q12) WILD-TYPE                                                                45
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  8(6Q12) MUTATED                                                 13
  AMP PEAK  8(6Q12) WILD-TYPE                                               51
                             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                                        7
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)                        24
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                         13
  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                                                      61
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    121
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          45
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           51
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   7
  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"
D8V9, binary
                             cls
clus                            0   1
  AMP PEAK  8(6Q12) MUTATED     2  79
  AMP PEAK  8(6Q12) WILD-TYPE   4 310
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(6Q12) MUTATED      2   79
  AMP PEAK  8(6Q12) WILD-TYPE    4  310
     clus
vv    AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE
  NO                          2                           4
  YES                        79                         310
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  8(6Q12) MUTATED    60   3   5   8
  AMP PEAK  8(6Q12) WILD-TYPE 258  13  13  17
D8V10, multiclass
    clus
vv   AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE
  R0                        60                         258
  R1                         3                          13
  R2                         5                          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"
D8V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  8(6Q12) MUTATED      14                         2
  AMP PEAK  8(6Q12) WILD-TYPE    74                         4
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  8(6Q12) MUTATED                                           1    51
  AMP PEAK  8(6Q12) WILD-TYPE                                         0   192
D8V12, multiclass
                                           clus
vv                                          AMP PEAK  8(6Q12) MUTATED
  ASIAN                                                            14
  BLACK OR AFRICAN AMERICAN                                         2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         1
  WHITE                                                            51
                                           clus
vv                                          AMP PEAK  8(6Q12) WILD-TYPE
  ASIAN                                                              74
  BLACK OR AFRICAN AMERICAN                                           4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             192
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = AMP PEAK  9(6Q21) MUTATION ANALYSIS
D9V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  9(6Q21) MUTATED    39  28
  AMP PEAK  9(6Q21) WILD-TYPE 203  94
  AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE 
                         67                         297 
  AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE 
                         28                          94 
$`AMP PEAK  9(6Q21) MUTATED`
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-6456 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 
        6.61         6.97        10.13         9.21        35.24        15.42 
TCGA-BR-7717 TCGA-BR-8060 TCGA-BR-8289 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8484 
        0.69         1.32         0.26        14.04        14.79         0.72 
TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
        9.21        11.54        15.68         0.66        22.26         0.92 
TCGA-BR-A4J1 TCGA-BR-A4J7 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8528 TCGA-CD-A487 
        0.72        19.36         3.25        13.15         0.10         0.13 
TCGA-CD-A48A TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 
        0.13         3.02         7.99        54.08         4.01        47.05 
TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5724 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6528 
       18.97        30.97        12.03        18.54         4.14        15.22 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-A4YT TCGA-EQ-8122 TCGA-EQ-A4SO 
       10.55        11.31        12.33        14.27         7.79        16.24 
TCGA-FP-A4BF TCGA-HU-A4GH TCGA-HU-A4GT TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-IN-7808 
        1.55        11.77         6.51        12.95         9.67         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-MX-A663 TCGA-RD-A7BT 
       18.81         3.39         1.81         5.56         4.31         8.61 
TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       16.67        37.91         8.94         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A922 
       31.10         2.70        17.85         1.71         8.58         8.61 
TCGA-VQ-AA6J 
       21.11 

$`AMP PEAK  9(6Q21) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        5.62        11.70         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        13.12 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68         7.00        39.12         0.82         0.62        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       13.84        13.22        16.14         1.25         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-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       28.01         0.16        18.54        12.43         0.95         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        17.49         0.82         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 
        0.49        20.55         0.72         0.26        12.95        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        1.55         1.48         7.40         6.18        19.50         0.36 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19         2.96         0.95        13.74         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 
        3.32         0.36        19.17         0.69         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        3.72         5.39        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 
        2.14        13.45         0.20         7.53         0.49        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       16.44         0.59         0.62        10.68        12.56         1.15 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        3.02        13.41        13.51        12.89         0.79        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
        0.53        12.82         0.66        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
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-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.07         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG 
        0.13         0.10         6.35         0.13         0.13         0.07 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 
        0.10         0.10         0.10        20.02        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-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 
       21.99         9.01         7.07        12.00        22.98         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        1.02         1.02         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-5732 
       15.02        28.96        79.07        65.10         4.01        55.04 
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         5.95        17.19 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       15.98        12.79        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 
        0.23         6.97        21.14        20.91        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       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-A748 TCGA-D7-A74A 
       11.44         9.76         2.96        15.65         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         6.58        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
        8.12         0.39        19.53         3.02        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HF-A5NB 
       59.54         5.03        13.58         0.56         0.23        18.08 
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-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-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 
        0.26         2.10        19.36        17.69        12.30         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        8.81        27.42        21.21        18.38         5.36         5.19 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT 
       13.08         1.41         6.44         6.74         6.87         5.56 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS 
        2.53        60.56        28.90         3.72        19.73        11.05 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
        4.67       122.30        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       57.44        35.61        16.87         5.79         0.92        37.74 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        22.36        23.77         7.73        19.07        33.63 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       46.26        16.31         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       19.30        23.57        64.57        14.33        59.18        28.70 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91W TCGA-VQ-A91Y 
       11.70         8.68        49.25        20.81         7.36         9.73 
TCGA-VQ-A91Z TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 
       44.25        55.43         4.54         6.58         5.72        40.08 
TCGA-VQ-AA6B TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       29.98         4.21         0.79 

  AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE 
                       0.10                        0.07 
  AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE 
                      54.08                      122.30 
  AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE 
                       9.21                       12.03 
[1] "0.1 - 54.1 (9.2)"   "0.1 - 122.3 (12.0)"
[1] "hr=" "1.5"
D9V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  9(6Q21) MUTATED         0        1        8        5         4
  AMP PEAK  9(6Q21) WILD-TYPE       2       12       31       26        32
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  9(6Q21) MUTATED           8         1         20          9
  AMP PEAK  9(6Q21) WILD-TYPE        41         2         57         46
                             vv
clus                          STAGE IIIC STAGE IV
  AMP PEAK  9(6Q21) MUTATED            4       11
  AMP PEAK  9(6Q21) WILD-TYPE         33       26
D9V3, multiclass
            clus
vv           AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE
  STAGE I                            0                           2
  STAGE IA                           1                          12
  STAGE IB                           8                          31
  STAGE II                           5                          26
  STAGE IIA                          4                          32
  STAGE IIB                          8                          41
  STAGE III                          1                           2
  STAGE IIIA                        20                          57
  STAGE IIIB                         9                          46
  STAGE IIIC                         4                          33
  STAGE IV                          11                          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  9(6Q21) MUTATED     1  19  30  21
  AMP PEAK  9(6Q21) WILD-TYPE  20  68 143  83
D9V4, multiclass
    clus
vv   AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE
  T1                         1                          20
  T2                        19                          68
  T3                        30                         143
  T4                        21                          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  9(6Q21) MUTATED    17  23  16  15
  AMP PEAK  9(6Q21) WILD-TYPE 105  84  59  64
D9V5, multiclass
    clus
vv   AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE
  N0                        17                         105
  N1                        23                          84
  N2                        16                          59
  N3                        15                          64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1  MX
  AMP PEAK  9(6Q21) MUTATED    63   7   3
  AMP PEAK  9(6Q21) WILD-TYPE 290  17  15
D9V6, multiclass
    clus
vv   AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE
  M0                        63                         290
  M1                         7                          17
  MX                         3                          15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                             cls
clus                            0   1
  AMP PEAK  9(6Q21) MUTATED    24  49
  AMP PEAK  9(6Q21) WILD-TYPE 127 195
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q21) MUTATED     24   49
  AMP PEAK  9(6Q21) WILD-TYPE  127  195
        clus
vv       AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE
  FEMALE                        24                         127
  MALE                          49                         195
[1] 2 2
[1] FALSE
                             vv
clus                          STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  9(6Q21) MUTATED                                       7
  AMP PEAK  9(6Q21) WILD-TYPE                                    58
                             vv
clus                          STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  9(6Q21) MUTATED                                                       28
  AMP PEAK  9(6Q21) WILD-TYPE                                                    129
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  9(6Q21) MUTATED                                                                  19
  AMP PEAK  9(6Q21) WILD-TYPE                                                                50
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  9(6Q21) MUTATED                                                 14
  AMP PEAK  9(6Q21) WILD-TYPE                                               50
                             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                                        7
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)                        19
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                         14
  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                                                      58
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          50
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           50
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   20
  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"
D9V9, binary
                             cls
clus                            0   1
  AMP PEAK  9(6Q21) MUTATED     2  71
  AMP PEAK  9(6Q21) WILD-TYPE   4 318
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q21) MUTATED      2   71
  AMP PEAK  9(6Q21) WILD-TYPE    4  318
     clus
vv    AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE
  NO                          2                           4
  YES                        71                         318
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  9(6Q21) MUTATED    54   2   6   6
  AMP PEAK  9(6Q21) WILD-TYPE 264  14  12  19
D9V10, multiclass
    clus
vv   AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE
  R0                        54                         264
  R1                         2                          14
  R2                         6                          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"
D9V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  9(6Q21) MUTATED      15                         2
  AMP PEAK  9(6Q21) WILD-TYPE    73                         4
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  9(6Q21) MUTATED                                           1    43
  AMP PEAK  9(6Q21) WILD-TYPE                                         0   200
D9V12, multiclass
                                           clus
vv                                          AMP PEAK  9(6Q21) MUTATED
  ASIAN                                                            15
  BLACK OR AFRICAN AMERICAN                                         2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         1
  WHITE                                                            43
                                           clus
vv                                          AMP PEAK  9(6Q21) WILD-TYPE
  ASIAN                                                              73
  BLACK OR AFRICAN AMERICAN                                           4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             200
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = AMP PEAK 10(7P22.1) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(7P22.1) MUTATED   125  63
  AMP PEAK 10(7P22.1) WILD-TYPE 117  59
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                          188                           176 
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                           63                            59 
$`AMP PEAK 10(7P22.1) MUTATED`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-6456 
       11.70         6.61         6.97         4.64        18.35        10.13 
TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6801 
        7.00         0.62        32.78        13.84        13.22        21.11 
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         0.69 
TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.95        12.76        18.71         0.82         1.32         0.69 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.72         0.26        12.95         1.55         1.48         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8370 
        6.18        19.50         0.36        22.19         0.95         3.32 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
       14.79         0.26         5.39         9.21        20.22         1.12 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 
       16.44         0.59         0.62        10.68         1.15         0.66 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J7 
       22.26         0.92        12.89         0.72         0.53        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5801 
       13.51        20.42         1.15        13.64         3.25        13.18 
TCGA-CD-8524 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-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        6.35         0.13         0.13         0.13         0.07         0.10 
TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       20.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
        4.01        21.99        18.97         7.07        12.00        22.98 
TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5733 
        1.02        12.03        28.96        79.07         4.01        21.07 
TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
        7.99        12.66        11.93        19.13        18.84        18.54 
TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       17.19        15.22        15.98        10.55        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         0.23         6.97        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 
       14.27        16.44        15.16        11.31         2.96        15.65 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
        6.58        14.47        72.23         0.39        19.53         3.02 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 
       22.29        17.06         0.56         1.55         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        17.69        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-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A663 
        6.87         1.81         5.56        60.56        28.90         4.31 
TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-SW-A7EB 
        8.61       122.30       115.69        57.44         8.94         5.79 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       37.74         5.46        13.25        13.02        31.10        21.73 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PU TCGA-VQ-A8PY 
       33.63        46.26         2.70        17.85        23.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A91U 
       59.18        28.70        11.70         8.68        20.81         1.71 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A925 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J 
        7.36         8.58         4.54        40.08        29.98        21.11 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        4.21         0.79 

$`AMP PEAK 10(7P22.1) WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        5.62         7.43        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        13.12        13.68        39.12         0.82 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       16.14         1.25         8.98        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 
       12.82        23.93         0.16        18.54        12.43         0.69 
TCGA-BR-8058 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8289 TCGA-BR-8291 
       17.49        12.26         0.49        20.55         0.26        16.31 
TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 
        0.26         2.96        13.74         4.31        14.04         0.36 
TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8588 
       19.17         0.69        15.85         3.72         0.72        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         2.14        13.45         0.20         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU 
       11.54        15.81        15.68        12.56         3.02        13.41 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 
       13.51         0.79        14.17        12.82         0.66         0.46 
TCGA-BR-A4PD TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5802 
       20.65        11.57         5.13         2.83        13.15         0.30 
TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8531 
        0.07         0.07         0.07         0.07         0.13         0.10 
TCGA-CD-8532 TCGA-CD-A487 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4306 
        0.10         0.13         0.10         0.10         3.02         1.02 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 
       14.01        29.98        47.05        19.07        12.03         9.01 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       30.97         6.97         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-6519 
      105.07        15.02        65.10        55.04        12.36        20.55 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-8572 
       18.61        17.85         5.95         4.14        12.79        16.80 
TCGA-D7-8573 TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       19.50         5.92        13.78        14.76        13.71        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       11.44         9.76         4.34         7.40         7.13         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-8209 TCGA-FP-8210 
        7.79        16.24        21.27         8.12        59.54         5.03 
TCGA-FP-8211 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 
       13.58        18.08         1.51         5.92        14.27        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 
       12.10        10.62         0.76        24.30         5.59        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H3 
       24.20        21.37        29.98         6.51         0.26        19.36 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR 
        8.88         8.81        21.21         5.36        13.08         6.74 
TCGA-IN-A7NT TCGA-IP-7968 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW 
        5.56         2.53         3.72        19.73        11.05         4.67 
TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 
       16.67        37.91        40.64       116.38        71.38        35.61 
TCGA-RD-A8NB TCGA-VQ-A8DL TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       16.87         0.92        22.36        23.77         7.73        19.07 
TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       16.31         1.87         9.27        23.41        15.65        19.30 
TCGA-VQ-A8PX TCGA-VQ-A91K TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 
       64.57        49.25         9.73        44.25         8.61        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 
        6.58         5.72 

  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                         0.07                          0.07 
  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 
                       11.505                        11.705 
[1] "0.1 - 122.3 (11.5)" "0.1 - 116.4 (11.7)"
[1] "hr=" "1"  
D10V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 10(7P22.1) MUTATED         2        8       20       15        19
  AMP PEAK 10(7P22.1) WILD-TYPE       0        5       19       16        17
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 10(7P22.1) MUTATED          24         2         43         27
  AMP PEAK 10(7P22.1) WILD-TYPE        25         1         34         28
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 10(7P22.1) MUTATED           22       14
  AMP PEAK 10(7P22.1) WILD-TYPE         15       23
D10V3, multiclass
            clus
vv           AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  STAGE I                              2                             0
  STAGE IA                             8                             5
  STAGE IB                            20                            19
  STAGE II                            15                            16
  STAGE IIA                           19                            17
  STAGE IIB                           24                            25
  STAGE III                            2                             1
  STAGE IIIA                          43                            34
  STAGE IIIB                          27                            28
  STAGE IIIC                          22                            15
  STAGE IV                            14                            23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  AMP PEAK 10(7P22.1) MUTATED   12 42 95 49
  AMP PEAK 10(7P22.1) WILD-TYPE  9 45 78 55
D10V4, multiclass
    clus
vv   AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  T1                          12                             9
  T2                          42                            45
  T3                          95                            78
  T4                          49                            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"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK 10(7P22.1) MUTATED   64 49 47 38
  AMP PEAK 10(7P22.1) WILD-TYPE 58 58 28 41
D10V5, multiclass
    clus
vv   AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  N0                          64                            58
  N1                          49                            58
  N2                          47                            28
  N3                          38                            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                             M0  M1  MX
  AMP PEAK 10(7P22.1) MUTATED   184   8  13
  AMP PEAK 10(7P22.1) WILD-TYPE 169  16   5
D10V6, multiclass
    clus
vv   AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  M0                         184                           169
  M1                           8                            16
  MX                          13                             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P22.1) MUTATED    67 138
  AMP PEAK 10(7P22.1) WILD-TYPE  84 106
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P22.1) MUTATED     67  138
  AMP PEAK 10(7P22.1) WILD-TYPE   84  106
        clus
vv       AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  FEMALE                          67                            84
  MALE                           138                           106
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 10(7P22.1) MUTATED                                      23
  AMP PEAK 10(7P22.1) WILD-TYPE                                    42
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 10(7P22.1) MUTATED                                                       81
  AMP PEAK 10(7P22.1) WILD-TYPE                                                     76
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 10(7P22.1) MUTATED                                                                  45
  AMP PEAK 10(7P22.1) WILD-TYPE                                                                24
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 10(7P22.1) MUTATED                                                 35
  AMP PEAK 10(7P22.1) WILD-TYPE                                               29
                               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                                          6
  AMP PEAK 10(7P22.1) WILD-TYPE                                        3
D10V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 10(7P22.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      23
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     81
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          45
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    6
                                                                   clus
vv                                                                  AMP PEAK 10(7P22.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        42
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       76
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            24
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             29
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      3
[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     3 202
  AMP PEAK 10(7P22.1) WILD-TYPE   3 187
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P22.1) MUTATED      3  202
  AMP PEAK 10(7P22.1) WILD-TYPE    3  187
     clus
vv    AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  NO                            3                             3
  YES                         202                           187
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 10(7P22.1) MUTATED   168   7   9  12
  AMP PEAK 10(7P22.1) WILD-TYPE 150   9   9  13
D10V10, multiclass
    clus
vv   AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  R0                         168                           150
  R1                           7                             9
  R2                           9                             9
  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                         5
  AMP PEAK 10(7P22.1) WILD-TYPE    43                         1
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 10(7P22.1) MUTATED                                           1   125
  AMP PEAK 10(7P22.1) WILD-TYPE                                         0   118
D10V12, multiclass
                                           clus
vv                                          AMP PEAK 10(7P22.1) MUTATED
  ASIAN                                                              45
  BLACK OR AFRICAN AMERICAN                                           5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             125
                                           clus
vv                                          AMP PEAK 10(7P22.1) WILD-TYPE
  ASIAN                                                                43
  BLACK OR AFRICAN AMERICAN                                             1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               118
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = AMP PEAK 11(7P11.2) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 11(7P11.2) MUTATED   109  66
  AMP PEAK 11(7P11.2) WILD-TYPE 133  56
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                          175                           189 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                           66                            56 
$`AMP PEAK 11(7P11.2) MUTATED`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-6456 
       11.70         6.61         6.97         4.64        18.35        10.13 
TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6801 
        7.00         0.62        32.78        13.84        13.22        21.11 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7901 
        9.21        24.76        35.24        15.42         0.69         0.95 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8284 TCGA-BR-8285 
       12.76        18.71         0.82         0.69         0.72         0.26 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8365 TCGA-BR-8366 
        1.55         1.48         7.40         0.36         2.96         0.95 
TCGA-BR-8370 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-8487 
        3.32        14.79         0.26         5.39        20.22         1.12 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4CQ 
       16.44         0.59         0.62        10.68         1.15        22.26 
TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J7 
        0.92        12.89         0.72        14.17         0.53        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-8526 
       13.51        20.42        13.64         3.25        13.18         0.07 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.10         0.16         0.13         0.13         0.10         6.35 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 
        0.13         0.07         0.10        20.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
        7.99         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-5733 
       22.98         1.02        12.03        28.96        79.07        21.07 
TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
        7.99        12.66        11.93        19.13        18.84        18.54 
TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       17.19        15.22        15.98        11.31        12.33        24.72 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU 
       17.19         0.23         6.97        21.14        20.91        16.44 
TCGA-D7-A4YX TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-F1-6177 TCGA-F1-6874 
       15.16        11.31         2.96        15.65         6.58        14.47 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 
       72.23         0.39        19.53         3.02        17.06         0.56 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-A4G2 
        1.55         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        17.69 
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-A7NU TCGA-KB-A6F5 
        1.41         6.44         6.74         6.87         1.81         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A663 TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV 
       60.56        28.90         4.31         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        37.74         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PB TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       13.02        31.10        21.73        33.63         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
        1.87        23.57        14.33        59.18        28.70        11.70 
TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z 
        8.68        20.81         1.71         7.36         8.58        44.25 
TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 
        8.61         4.54        40.08        29.98        21.11         4.21 
TCGA-ZQ-A9CR 
        0.79 

$`AMP PEAK 11(7P11.2) WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        5.62         7.43        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        13.12        13.68        39.12         0.82 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       16.14         1.25         8.98        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       12.82        23.93        28.01         0.16        18.54        12.43 
TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
        0.69        17.49         1.32        12.26         0.49        20.55 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       12.95         0.26        16.31         6.18        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 
       22.19        13.74         4.31        14.04         0.36        19.17 
TCGA-BR-8380 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8588 
        0.69        15.85         3.72         0.72         9.21        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         2.14        13.45         0.20         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 
       11.54        15.81        15.68        12.56         0.66         3.02 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 
       13.41        13.51         0.79        12.82         0.66         0.46 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 
       20.65         1.15        11.57         5.13         2.83        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8529 
        0.30         0.07         0.07         0.07         0.07         0.13 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MI 
        0.10         0.10         0.13         0.13         0.13         0.10 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 
        0.10         3.02         1.02         8.05        54.08        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4477 
       29.98        47.05        19.07        12.03         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-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-6519 
       15.02        65.10         4.01        55.04        12.36        20.55 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 
       18.61        17.85         5.95         4.14        12.79        10.55 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 
       16.80        19.50        14.27         5.92        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74A 
       13.71        11.24        11.44         9.76         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.79        16.24        21.27         8.12 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-A5NB TCGA-HU-8238 
       22.29        59.54         5.03        13.58        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-A4GD TCGA-HU-A4GJ TCGA-HU-A4GN 
        5.59        11.84        24.20        22.75        21.37        29.98 
TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
        6.51         0.26        12.30         9.67         8.88         8.81 
TCGA-IN-7806 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A7NT TCGA-IP-7968 TCGA-MX-A5UG 
       21.21         5.36        13.08         5.56         2.53         3.72 
TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 
       19.73        11.05         4.67        37.91        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8P2 
       71.38        35.61        16.87         5.79         0.92        22.36 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PO 
       23.77         7.73        19.07        46.26        16.31         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A91K TCGA-VQ-A91Y 
       23.41        15.65        19.30        64.57        49.25         9.73 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
       55.43         6.58         5.72 

  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                         0.07                          0.07 
  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 
                        11.70                         11.57 
[1] "0.1 - 122.3 (11.7)" "0.1 - 116.4 (11.6)"
[1] "hr=" "1.3"
D11V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 11(7P11.2) MUTATED         2        8       20       12        16
  AMP PEAK 11(7P11.2) WILD-TYPE       0        5       19       19        20
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 11(7P11.2) MUTATED          23         2         40         26
  AMP PEAK 11(7P11.2) WILD-TYPE        26         1         37         29
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 11(7P11.2) MUTATED           20       14
  AMP PEAK 11(7P11.2) WILD-TYPE         17       23
D11V3, multiclass
            clus
vv           AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  STAGE I                              2                             0
  STAGE IA                             8                             5
  STAGE IB                            20                            19
  STAGE II                            12                            19
  STAGE IIA                           16                            20
  STAGE IIB                           23                            26
  STAGE III                            2                             1
  STAGE IIIA                          40                            37
  STAGE IIIB                          26                            29
  STAGE IIIC                          20                            17
  STAGE IV                            14                            23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  AMP PEAK 11(7P11.2) MUTATED   12 37 88 47
  AMP PEAK 11(7P11.2) WILD-TYPE  9 50 85 57
D11V4, multiclass
    clus
vv   AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  T1                          12                             9
  T2                          37                            50
  T3                          88                            85
  T4                          47                            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"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK 11(7P11.2) MUTATED   60 48 40 37
  AMP PEAK 11(7P11.2) WILD-TYPE 62 59 35 42
D11V5, multiclass
    clus
vv   AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  N0                          60                            62
  N1                          48                            59
  N2                          40                            35
  N3                          37                            42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  AMP PEAK 11(7P11.2) MUTATED   173   7  11
  AMP PEAK 11(7P11.2) WILD-TYPE 180  17   7
D11V6, multiclass
    clus
vv   AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  M0                         173                           180
  M1                           7                            17
  MX                          11                             7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                               cls
clus                              0   1
  AMP PEAK 11(7P11.2) MUTATED    63 128
  AMP PEAK 11(7P11.2) WILD-TYPE  88 116
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED     63  128
  AMP PEAK 11(7P11.2) WILD-TYPE   88  116
        clus
vv       AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  FEMALE                          63                            88
  MALE                           128                           116
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 11(7P11.2) MUTATED                                      23
  AMP PEAK 11(7P11.2) WILD-TYPE                                    42
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 11(7P11.2) MUTATED                                                       75
  AMP PEAK 11(7P11.2) WILD-TYPE                                                     82
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 11(7P11.2) MUTATED                                                                  41
  AMP PEAK 11(7P11.2) WILD-TYPE                                                                28
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 11(7P11.2) MUTATED                                                 34
  AMP PEAK 11(7P11.2) WILD-TYPE                                               30
                               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                                          6
  AMP PEAK 11(7P11.2) WILD-TYPE                                        3
D11V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 11(7P11.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      23
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     75
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          41
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    6
                                                                   clus
vv                                                                  AMP PEAK 11(7P11.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        42
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       82
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            28
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             30
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      3
[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     2 189
  AMP PEAK 11(7P11.2) WILD-TYPE   4 200
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED      2  189
  AMP PEAK 11(7P11.2) WILD-TYPE    4  200
     clus
vv    AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  NO                            2                             4
  YES                         189                           200
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 11(7P11.2) MUTATED   158   7   8  11
  AMP PEAK 11(7P11.2) WILD-TYPE 160   9  10  14
D11V10, multiclass
    clus
vv   AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  R0                         158                           160
  R1                           7                             9
  R2                           8                            10
  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                         5
  AMP PEAK 11(7P11.2) WILD-TYPE    46                         1
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 11(7P11.2) MUTATED                                           1   116
  AMP PEAK 11(7P11.2) WILD-TYPE                                         0   127
D11V12, multiclass
                                           clus
vv                                          AMP PEAK 11(7P11.2) MUTATED
  ASIAN                                                              42
  BLACK OR AFRICAN AMERICAN                                           5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             116
                                           clus
vv                                          AMP PEAK 11(7P11.2) WILD-TYPE
  ASIAN                                                                46
  BLACK OR AFRICAN AMERICAN                                             1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = AMP PEAK 12(7Q21.2) MUTATION ANALYSIS
D12V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 12(7Q21.2) MUTATED   105  59
  AMP PEAK 12(7Q21.2) WILD-TYPE 137  63
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                          164                           200 
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                           59                            63 
$`AMP PEAK 12(7Q21.2) MUTATED`
TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6458 
       11.70         6.97         4.64        18.35        10.13         7.00 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6801 
        0.82         0.62        32.78        13.84        13.22        21.11 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7958 TCGA-BR-7959 
        9.21        24.76        35.24        15.42        12.76        18.71 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8295 TCGA-BR-8296 
        0.82         1.32         0.72         0.26         1.55         1.48 
TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8370 TCGA-BR-8373 
        7.40         0.36         2.96         0.95         3.32        14.79 
TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8682 
        0.26         5.39         0.72        20.22         1.12        16.44 
TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.59        10.68         1.15        12.89         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-CD-5799 
        0.53        13.51        20.65        20.42         1.15         3.25 
TCGA-CD-5801 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8533 
       13.18         0.07         0.10         0.13         0.16         0.13 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        0.13         0.10         6.35         0.13         0.13         0.07 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
        0.10        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 
       54.08         4.01        14.01        12.03        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
       12.00        22.98         1.02        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         5.95        17.19         4.14        15.22        15.98 
TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 
       12.79        24.72        19.50        17.19         6.97        21.14 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 
       20.91        16.44        15.16        11.24        11.31         2.96 
TCGA-D7-A6F2 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
       15.65         6.58        14.47        72.23         0.39        19.53 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8243 
       22.29        17.06         0.56         0.23        26.47         5.92 
TCGA-HU-8249 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GQ 
       14.17        24.30        12.30        25.81         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-IN-7808 
        6.25        10.19         2.10        12.95        19.36         3.45 
TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU 
        3.39         5.19         1.41         6.44         5.56         1.81 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A663 TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW 
        5.56        60.56         4.31         8.61       122.30        37.91 
TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E2 
      115.69        57.44         8.94        37.74        13.25        31.10 
TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PB TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       21.73         7.73        33.63         2.70        17.85         1.87 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91Q 
       14.33        59.18        28.70        11.70         8.68        20.81 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A925 TCGA-VQ-AA6B TCGA-VQ-AA6J 
        1.71         7.36         8.58         4.54        29.98        21.11 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        4.21         0.79 

$`AMP PEAK 12(7Q21.2) WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        5.62         6.61         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        13.12        13.68        39.12 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       16.14         1.25         8.98        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       12.82        23.93        28.01         0.69         0.16        18.54 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 
       12.43         0.95         0.69        17.49         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8360 
        0.49        20.55        12.95         0.26        16.31         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       19.50         0.26        22.19        13.74         4.31        14.04 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8485 
        0.36        19.17         0.69        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         2.14        13.45         0.20         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         0.62        12.56 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        0.66         3.02        22.26         0.92        13.41        13.51 
TCGA-BR-A4IZ TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QI 
        0.79        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         0.13 
TCGA-CD-A489 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4443 
        0.13         0.10         0.10         1.02         8.05        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 
       47.05        19.07        21.99         9.01        30.97         6.97 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5728 
        1.02         0.99         6.02         0.99       105.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6522 
        4.01        55.04         7.99        12.36        20.55        18.61 
TCGA-D7-6524 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8575 
       17.85        10.55        11.31        12.33        16.80         0.23 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY 
       14.27         5.92        13.78        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         7.79 
TCGA-EQ-A4SO TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8209 TCGA-FP-8210 
       16.24        21.27         8.12         3.02        59.54         5.03 
TCGA-FP-8211 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
       13.58         1.55        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-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-A4GT TCGA-HU-A4GY TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        6.51         0.26        17.69        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-IP-7968 TCGA-KB-A93H TCGA-MX-A5UG 
       13.08         6.74         6.87         2.53        28.90         3.72 
TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N0 TCGA-RD-A8N2 
       19.73        11.05         4.67        16.67        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU 
       71.38        35.61        16.87         5.79         0.92         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PC TCGA-VQ-A8PD 
       13.02        22.36        23.77        19.07        46.26        16.31 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX 
        9.27        23.41        15.65        19.30        23.57        64.57 
TCGA-VQ-A91K TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 
       49.25         9.73        44.25         8.61        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-AA68 
        5.72        40.08 

  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                         0.07                          0.07 
  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 
                       11.275                        11.805 
[1] "0.1 - 122.3 (11.3)" "0.1 - 116.4 (11.8)"
[1] "hr=" "1.2"
D12V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 12(7Q21.2) MUTATED         2        6       18       15        18
  AMP PEAK 12(7Q21.2) WILD-TYPE       0        7       21       16        18
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 12(7Q21.2) MUTATED          20         2         34         26
  AMP PEAK 12(7Q21.2) WILD-TYPE        29         1         43         29
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 12(7Q21.2) MUTATED           17       13
  AMP PEAK 12(7Q21.2) WILD-TYPE         20       24
D12V3, multiclass
            clus
vv           AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  STAGE I                              2                             0
  STAGE IA                             6                             7
  STAGE IB                            18                            21
  STAGE II                            15                            16
  STAGE IIA                           18                            18
  STAGE IIB                           20                            29
  STAGE III                            2                             1
  STAGE IIIA                          34                            43
  STAGE IIIB                          26                            29
  STAGE IIIC                          17                            20
  STAGE IV                            13                            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 12(7Q21.2) MUTATED    9 41 82 41
  AMP PEAK 12(7Q21.2) WILD-TYPE 12 46 91 63
D12V4, multiclass
    clus
vv   AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  T1                           9                            12
  T2                          41                            46
  T3                          82                            91
  T4                          41                            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 12(7Q21.2) MUTATED   60 38 41 35
  AMP PEAK 12(7Q21.2) WILD-TYPE 62 69 34 44
D12V5, multiclass
    clus
vv   AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  N0                          60                            62
  N1                          38                            69
  N2                          41                            34
  N3                          35                            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"
                               vv
clus                             M0  M1  MX
  AMP PEAK 12(7Q21.2) MUTATED   161   7  12
  AMP PEAK 12(7Q21.2) WILD-TYPE 192  17   6
D12V6, multiclass
    clus
vv   AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  M0                         161                           192
  M1                           7                            17
  MX                          12                             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                               cls
clus                              0   1
  AMP PEAK 12(7Q21.2) MUTATED    59 121
  AMP PEAK 12(7Q21.2) WILD-TYPE  92 123
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7Q21.2) MUTATED     59  121
  AMP PEAK 12(7Q21.2) WILD-TYPE   92  123
        clus
vv       AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  FEMALE                          59                            92
  MALE                           121                           123
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 12(7Q21.2) MUTATED                                      23
  AMP PEAK 12(7Q21.2) WILD-TYPE                                    42
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 12(7Q21.2) MUTATED                                                       73
  AMP PEAK 12(7Q21.2) WILD-TYPE                                                     84
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 12(7Q21.2) MUTATED                                                                  42
  AMP PEAK 12(7Q21.2) WILD-TYPE                                                                27
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 12(7Q21.2) MUTATED                                                 24
  AMP PEAK 12(7Q21.2) WILD-TYPE                                               40
                               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                                          4
  AMP PEAK 12(7Q21.2) WILD-TYPE                                        5
D12V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 12(7Q21.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      23
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     73
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          42
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           24
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    4
                                                                   clus
vv                                                                  AMP PEAK 12(7Q21.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        42
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       84
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            27
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             40
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     13
  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"
D12V9, binary
                               cls
clus                              0   1
  AMP PEAK 12(7Q21.2) MUTATED     2 178
  AMP PEAK 12(7Q21.2) WILD-TYPE   4 211
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7Q21.2) MUTATED      2  178
  AMP PEAK 12(7Q21.2) WILD-TYPE    4  211
     clus
vv    AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  NO                            2                             4
  YES                         178                           211
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 12(7Q21.2) MUTATED   151   4   7  11
  AMP PEAK 12(7Q21.2) WILD-TYPE 167  12  11  14
D12V10, multiclass
    clus
vv   AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  R0                         151                           167
  R1                           4                            12
  R2                           7                            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"
D12V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 12(7Q21.2) MUTATED      37                         4
  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   110
  AMP PEAK 12(7Q21.2) WILD-TYPE                                         0   133
D12V12, multiclass
                                           clus
vv                                          AMP PEAK 12(7Q21.2) MUTATED
  ASIAN                                                              37
  BLACK OR AFRICAN AMERICAN                                           4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             110
                                           clus
vv                                          AMP PEAK 12(7Q21.2) WILD-TYPE
  ASIAN                                                                51
  BLACK OR AFRICAN AMERICAN                                             2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               133
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = AMP PEAK 13(7Q22.1) MUTATION ANALYSIS
D13V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 13(7Q22.1) MUTATED   101  58
  AMP PEAK 13(7Q22.1) WILD-TYPE 141  64
  AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE 
                          159                           205 
  AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE 
                           58                            64 
$`AMP PEAK 13(7Q22.1) MUTATED`
TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6564 
       11.70         6.97         4.64        18.35        10.13         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6801 TCGA-BR-7197 
        0.62        32.78        13.84        13.22        21.11         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 
       24.76        35.24        15.42        12.76        18.71         0.82 
TCGA-BR-8060 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8296 
        1.32         0.72         0.26        12.95         1.55         1.48 
TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8370 TCGA-BR-8373 
        7.40         0.36         2.96         0.95         3.32        14.79 
TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8682 TCGA-BR-8683 
        0.26         5.39        20.22         1.12        16.44         0.59 
TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       10.68         1.15        12.89         0.72        14.17         0.53 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51        20.65        20.42         1.15        13.64 
TCGA-CD-5801 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8533 
       13.18         0.07         0.10         0.13         0.16         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        0.10         6.35         0.13         0.13         0.07         0.10 
TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 
       20.02        27.02        15.95         7.99         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 
       29.98        12.03        18.97         7.07        12.00         1.02 
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         5.95        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8573 
        4.14        15.22        15.98        12.79        24.72        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU 
       17.19         0.23         6.97        21.14        20.91        16.44 
TCGA-D7-A4YX TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-F1-6177 TCGA-F1-6874 
       15.16        11.24         2.96        15.65         6.58        14.47 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A8CX 
       72.23         0.39        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-A4GC 
       26.47         5.92        14.17        24.30        12.30         3.25 
TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 
       25.81         8.98         0.10        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-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A663 TCGA-RD-A7BT 
        5.56         1.81         5.56        60.56         4.31         8.61 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-VQ-A8DT TCGA-VQ-A8DV 
      122.30        37.91       115.69        57.44        37.74        13.25 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PB TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       31.10        21.73         7.73        33.63         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        59.18        28.70        11.70         8.68 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A925 TCGA-VQ-AA6B 
       20.81         1.71         7.36         8.58         4.54        29.98 
TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11         4.21         0.79 

$`AMP PEAK 13(7Q22.1) WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        5.62         6.61         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-6458 
        6.61        34.68        15.95        13.12        13.68         7.00 
TCGA-BR-6563 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 
       39.12        16.14         1.25         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         0.69         0.16 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8077 
       18.54        12.43         0.95         0.69        17.49         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8360 
       12.26         0.49        20.55         0.26        16.31         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       19.50         0.26        22.19        13.74         4.31        14.04 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 
        0.36        19.17         0.69        15.85         3.72         0.72 
TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        9.21        12.79        15.81         2.14        13.45         0.20 
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         0.62 
TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       12.56         0.66         3.02        22.26         0.92        13.41 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-BR-A4QL 
       13.51         0.79        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 
        0.13         0.13         0.10         0.10         3.02         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4465 
        8.05        54.08        47.05        19.07        21.99         9.01 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       22.98        30.97         6.97         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
        0.99       105.07        65.10         4.01        55.04         7.99 
TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6818 TCGA-D7-6820 
       12.36        20.55        18.61        17.85        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 
       12.33        16.80        14.27         5.92        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74A 
       13.71        11.31        11.44         9.76         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.79        16.24        21.27         8.12 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF 
       19.53         3.02        59.54         5.03        13.58         1.55 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 
       18.08         1.51        14.27        12.59        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD 
       10.62         0.76         5.59        11.84        24.20        22.75 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       11.77        21.37        29.98         6.51         6.25         0.26 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       17.69        12.30         9.67         8.88         8.81        27.42 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR 
       21.21        18.81        18.38         5.36        13.08         6.74 
TCGA-IN-A6RS TCGA-IP-7968 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS 
        6.87         2.53        28.90         3.72        19.73        11.05 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N6 
        4.67        16.67        40.64       116.38        71.38         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DZ 
       35.61        16.87         5.79         0.92         5.46        13.02 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PO 
       22.36        23.77        19.07        46.26        16.31         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91K 
       23.41        15.65        19.30        23.57        64.57        49.25 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
        9.73        44.25         8.61        55.43         6.58         5.72 
TCGA-VQ-AA68 
       40.08 

  AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE 
                         0.07                          0.07 
  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 
                        11.93                         11.44 
[1] "0.1 - 122.3 (11.9)" "0.1 - 116.4 (11.4)"
[1] "hr=" "1.2"
D13V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 13(7Q22.1) MUTATED         2        7       18       15        19
  AMP PEAK 13(7Q22.1) WILD-TYPE       0        6       21       16        17
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 13(7Q22.1) MUTATED          17         2         32         27
  AMP PEAK 13(7Q22.1) WILD-TYPE        32         1         45         28
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 13(7Q22.1) MUTATED           17       11
  AMP PEAK 13(7Q22.1) WILD-TYPE         20       26
D13V3, multiclass
            clus
vv           AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE
  STAGE I                              2                             0
  STAGE IA                             7                             6
  STAGE IB                            18                            21
  STAGE II                            15                            16
  STAGE IIA                           19                            17
  STAGE IIB                           17                            32
  STAGE III                            2                             1
  STAGE IIIA                          32                            45
  STAGE IIIB                          27                            28
  STAGE IIIC                          17                            20
  STAGE IV                            11                            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 13(7Q22.1) MUTATED   10 39 80 40
  AMP PEAK 13(7Q22.1) WILD-TYPE 11 48 93 64
D13V4, multiclass
    clus
vv   AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE
  T1                          10                            11
  T2                          39                            48
  T3                          80                            93
  T4                          40                            64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK 13(7Q22.1) MUTATED   63 31 40 35
  AMP PEAK 13(7Q22.1) WILD-TYPE 59 76 35 44
D13V5, multiclass
    clus
vv   AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE
  N0                          63                            59
  N1                          31                            76
  N2                          40                            35
  N3                          35                            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"
                               vv
clus                             M0  M1  MX
  AMP PEAK 13(7Q22.1) MUTATED   158   6  12
  AMP PEAK 13(7Q22.1) WILD-TYPE 195  18   6
D13V6, multiclass
    clus
vv   AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE
  M0                         158                           195
  M1                           6                            18
  MX                          12                             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                               cls
clus                              0   1
  AMP PEAK 13(7Q22.1) MUTATED    57 119
  AMP PEAK 13(7Q22.1) WILD-TYPE  94 125
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7Q22.1) MUTATED     57  119
  AMP PEAK 13(7Q22.1) WILD-TYPE   94  125
        clus
vv       AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE
  FEMALE                          57                            94
  MALE                           119                           125
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 13(7Q22.1) MUTATED                                      23
  AMP PEAK 13(7Q22.1) WILD-TYPE                                    42
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 13(7Q22.1) MUTATED                                                       71
  AMP PEAK 13(7Q22.1) WILD-TYPE                                                     86
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 13(7Q22.1) MUTATED                                                                  40
  AMP PEAK 13(7Q22.1) WILD-TYPE                                                                29
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 13(7Q22.1) MUTATED                                                 25
  AMP PEAK 13(7Q22.1) WILD-TYPE                                               39
                               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                                          4
  AMP PEAK 13(7Q22.1) WILD-TYPE                                        5
D13V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 13(7Q22.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      23
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     71
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           25
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    4
                                                                   clus
vv                                                                  AMP PEAK 13(7Q22.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        42
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       86
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            29
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             39
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     13
  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"
D13V9, binary
                               cls
clus                              0   1
  AMP PEAK 13(7Q22.1) MUTATED     2 174
  AMP PEAK 13(7Q22.1) WILD-TYPE   4 215
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7Q22.1) MUTATED      2  174
  AMP PEAK 13(7Q22.1) WILD-TYPE    4  215
     clus
vv    AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE
  NO                            2                             4
  YES                         174                           215
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 13(7Q22.1) MUTATED   148   4   6  12
  AMP PEAK 13(7Q22.1) WILD-TYPE 170  12  12  13
D13V10, multiclass
    clus
vv   AMP PEAK 13(7Q22.1) MUTATED AMP PEAK 13(7Q22.1) WILD-TYPE
  R0                         148                           170
  R1                           4                            12
  R2                           6                            12
  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                         4
  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   109
  AMP PEAK 13(7Q22.1) WILD-TYPE                                         0   134
D13V12, multiclass
                                           clus
vv                                          AMP PEAK 13(7Q22.1) MUTATED
  ASIAN                                                              36
  BLACK OR AFRICAN AMERICAN                                           4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             109
                                           clus
vv                                          AMP PEAK 13(7Q22.1) WILD-TYPE
  ASIAN                                                                52
  BLACK OR AFRICAN AMERICAN                                             2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               134
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = AMP PEAK 14(8P23.1) MUTATION ANALYSIS
D14V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 14(8P23.1) MUTATED   100  42
  AMP PEAK 14(8P23.1) WILD-TYPE 142  80
  AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE 
                          142                           222 
  AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE 
                           42                            80 
$`AMP PEAK 14(8P23.1) MUTATED`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4201 TCGA-BR-6452 
        5.62         6.61         6.97         4.64        30.90        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6705 TCGA-BR-6707 
       15.95        13.12        13.68         7.00        13.84        16.14 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7717 
       30.90        31.20        32.94        35.24        23.93         0.69 
TCGA-BR-7957 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8284 TCGA-BR-8289 TCGA-BR-8297 
        0.69         1.32        12.26         0.72         0.26         7.40 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
        4.31        14.04         3.32        19.17         0.26        15.85 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 
        5.39         0.72        20.22         2.14        13.45         7.53 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J7 
       22.26         0.92        13.41        14.17        12.82        19.36 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-CD-5799 TCGA-CD-5803 TCGA-CD-8524 
        0.46        20.42        11.57         3.25         0.07         0.07 
TCGA-CD-8530 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MJ 
        0.16         0.10         0.13         0.13         0.07         0.10 
TCGA-CG-4305 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4469 
       15.95        14.01        12.03        21.99        18.97         7.07 
TCGA-CG-4472 TCGA-CG-5722 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-5578 
       12.00         0.99        28.96        65.10        21.07        12.66 
TCGA-D7-5579 TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       11.93        17.85         4.14        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX 
       12.33         0.23         6.97        20.91         5.92        15.16 
TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A748 
       14.76        11.24        11.31        11.44         2.96         4.34 
TCGA-F1-A448 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HJ-7597 
       21.27        19.53        17.06         1.55        18.08        26.47 
TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       14.27        11.41        24.30        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GY 
        3.25        25.81        29.98         8.98         0.10         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        17.69        12.30         8.88 
TCGA-HU-A4HB TCGA-IN-A6RL TCGA-IN-A6RS TCGA-IN-A7NT TCGA-KB-A6F7 TCGA-KB-A93H 
        8.81         5.19         6.87         5.56        60.56        28.90 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-RD-A8NB 
       19.73         4.31        16.67       115.69        35.61        16.87 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       37.74         5.46        22.36        19.07        33.63        16.31 
TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX 
        2.70         9.27        23.41        19.30        23.57        64.57 
TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91W TCGA-VQ-A925 
       14.33         8.68        49.25        20.81         7.36         4.54 
TCGA-VQ-A928 TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        5.72        21.11         4.21         0.79 

$`AMP PEAK 14(8P23.1) WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
       11.70         7.43        18.35         6.18         9.57         6.61 
TCGA-BR-6456 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6706 
       10.13        39.12         0.82         0.62        32.78        13.22 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
        1.25         8.98        21.11        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       15.42        28.01         0.16        18.54        12.43         0.95 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 
       12.76        18.71        17.49         0.82         0.69         0.49 
TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
       20.55         0.26        12.95        16.31         1.55         1.48 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        19.50         0.36         0.26        22.19         2.96 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8384 
        0.95        13.74         0.36        14.79         0.69         3.72 
TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8592 TCGA-BR-8677 
        9.21         1.12        12.79        15.81         0.20         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         0.59        15.68         0.62 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IV 
       10.68        12.56         1.15         0.66         3.02        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J8 
       12.89         0.79         0.72         0.53         0.66        13.51 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 
       20.65         1.15        13.64         5.13         2.83        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       13.18         0.30         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 
        0.13         0.10         0.10         0.13         0.13         6.35 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 
        0.13         0.13         0.10         0.10        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4465 TCGA-CG-4475 TCGA-CG-4477 
       29.98        47.05        19.07         9.01        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 
        6.97         1.02         1.02         0.99         6.02       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       12.03        15.02        79.07         4.01        55.04         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-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-8570 TCGA-D7-8572 
        5.95        17.19        15.22        15.98        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YY 
       19.50        17.19        21.14        14.27        16.44        13.78 
TCGA-D7-A6ET TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       13.71         9.76        15.65         7.40         7.13         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
        7.79        16.24         6.58        14.47        72.23         8.12 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        0.39         3.02        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-A7NU TCGA-IP-7968 
       13.08         1.41         6.44         6.74         1.81         2.53 
TCGA-KB-A6F5 TCGA-MX-A5UG TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV 
        5.56         3.72        11.05         8.61         4.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       37.91        40.64       116.38        71.38        57.44         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        5.79         0.92        13.25        13.02        31.10        21.73 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       23.77         7.73        46.26        17.85         1.87        15.65 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y 
       59.18        28.70        11.70         1.71         8.58         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-AA68 TCGA-VQ-AA6B 
       44.25         8.61        55.43         6.58        40.08        29.98 

  AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE 
                         0.07                          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 
                       12.300                         9.945 
[1] "0.1 - 115.7 (12.3)" "0.1 - 122.3 (9.9)" 
[1] "hr=" "1.3"
D14V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 14(8P23.1) MUTATED         1        7       17       13        13
  AMP PEAK 14(8P23.1) WILD-TYPE       1        6       22       18        23
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 14(8P23.1) MUTATED          24         0         31         16
  AMP PEAK 14(8P23.1) WILD-TYPE        25         3         46         39
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 14(8P23.1) MUTATED           14       15
  AMP PEAK 14(8P23.1) WILD-TYPE         23       22
D14V3, multiclass
            clus
vv           AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             7                             6
  STAGE IB                            17                            22
  STAGE II                            13                            18
  STAGE IIA                           13                            23
  STAGE IIB                           24                            25
  STAGE III                            0                             3
  STAGE IIIA                          31                            46
  STAGE IIIB                          16                            39
  STAGE IIIC                          14                            23
  STAGE IV                            15                            22
[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  39  62  42
  AMP PEAK 14(8P23.1) WILD-TYPE  10  48 111  62
D14V4, multiclass
    clus
vv   AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE
  T1                          11                            10
  T2                          39                            48
  T3                          62                           111
  T4                          42                            62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK 14(8P23.1) MUTATED   48 45 28 31
  AMP PEAK 14(8P23.1) WILD-TYPE 74 62 47 48
D14V5, multiclass
    clus
vv   AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE
  N0                          48                            74
  N1                          45                            62
  N2                          28                            47
  N3                          31                            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"
                               vv
clus                             M0  M1  MX
  AMP PEAK 14(8P23.1) MUTATED   146   8   6
  AMP PEAK 14(8P23.1) WILD-TYPE 207  16  12
D14V6, multiclass
    clus
vv   AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE
  M0                         146                           207
  M1                           8                            16
  MX                           6                            12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                               cls
clus                              0   1
  AMP PEAK 14(8P23.1) MUTATED    72  88
  AMP PEAK 14(8P23.1) WILD-TYPE  79 156
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(8P23.1) MUTATED     72   88
  AMP PEAK 14(8P23.1) WILD-TYPE   79  156
        clus
vv       AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE
  FEMALE                          72                            79
  MALE                            88                           156
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 14(8P23.1) MUTATED                                      27
  AMP PEAK 14(8P23.1) WILD-TYPE                                    38
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 14(8P23.1) MUTATED                                                       58
  AMP PEAK 14(8P23.1) WILD-TYPE                                                     99
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 14(8P23.1) MUTATED                                                                  29
  AMP PEAK 14(8P23.1) WILD-TYPE                                                                40
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 14(8P23.1) MUTATED                                                 27
  AMP PEAK 14(8P23.1) WILD-TYPE                                               37
                               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                                          3
  AMP PEAK 14(8P23.1) WILD-TYPE                                        6
D14V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 14(8P23.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      27
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     58
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          29
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           27
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    3
                                                                   clus
vv                                                                  AMP PEAK 14(8P23.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        38
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       99
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     3
  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"
D14V9, binary
                               cls
clus                              0   1
  AMP PEAK 14(8P23.1) MUTATED     4 156
  AMP PEAK 14(8P23.1) WILD-TYPE   2 233
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(8P23.1) MUTATED      4  156
  AMP PEAK 14(8P23.1) WILD-TYPE    2  233
     clus
vv    AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE
  NO                            4                             2
  YES                         156                           233
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 14(8P23.1) MUTATED   125   8   6  14
  AMP PEAK 14(8P23.1) WILD-TYPE 193   8  12  11
D14V10, multiclass
    clus
vv   AMP PEAK 14(8P23.1) MUTATED AMP PEAK 14(8P23.1) WILD-TYPE
  R0                         125                           193
  R1                           8                             8
  R2                           6                            12
  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                         2
  AMP PEAK 14(8P23.1) WILD-TYPE    54                         4
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 14(8P23.1) MUTATED                                           0    99
  AMP PEAK 14(8P23.1) WILD-TYPE                                         1   144
D14V12, multiclass
                                           clus
vv                                          AMP PEAK 14(8P23.1) MUTATED
  ASIAN                                                              34
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              99
                                           clus
vv                                          AMP PEAK 14(8P23.1) WILD-TYPE
  ASIAN                                                                54
  BLACK OR AFRICAN AMERICAN                                             4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  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"

Clustering(15) Variable = AMP PEAK 15(8Q24.21) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 15(8Q24.21) MUTATED   166  84
  AMP PEAK 15(8Q24.21) WILD-TYPE  76  38
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                           250                            114 
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                            84                             38 
$`AMP PEAK 15(8Q24.21) MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        5.62         6.97         4.64        18.35        30.90         6.18 
TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57        34.68        15.95        13.12        10.13        13.68 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6801 TCGA-BR-6802 
        0.62        13.84        16.14         1.25        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       31.20        32.94         9.21        35.24        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       28.01         0.69        18.54         0.95         0.69        12.76 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       18.71         0.82         0.69        12.26         0.49         0.72 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       12.95         0.26         1.55         1.48         7.40         6.18 
TCGA-BR-8362 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8372 
        0.36        13.74         4.31        14.04         3.32        19.17 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 
        0.26        15.85         3.72         5.39         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8682 
       12.79         2.14        13.45         7.53        11.54        16.44 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
        0.62        10.68         1.15         0.66        22.26         0.92 
TCGA-BR-A4IU TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J9 TCGA-BR-A4PE 
       13.41         0.72        14.17        12.82         0.46        20.42 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 
       13.64        11.57        13.15         0.30         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8535 
        0.07         0.07         0.10         0.16         0.13         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        0.10         6.35         0.13         0.13         0.13         0.07 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
        0.10        20.02         3.02        15.95         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-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
       12.03        21.99        18.97         7.07        12.00        22.98 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.97         1.02         0.99        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 
       65.10         4.01        55.04        21.07         7.99        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       11.93        19.13        18.84        17.85         5.95        17.19 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       24.72         6.97        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 
       15.16        14.76        11.24        11.31        11.44         2.96 
TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.65         4.34         7.40         0.62         7.79        16.24 
TCGA-F1-6177 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 
        6.58        72.23        21.27         0.39        19.53        17.06 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 
        0.56         1.55         0.23        18.08        26.47         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G2 
       14.27        12.59        14.17        11.41         0.76        24.30 
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-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 
        0.26         2.10        19.36        17.69        12.30         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
        8.81        27.42         3.45         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         6.87 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
        5.56         1.81         2.53         5.56        60.56        28.90 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7C1 
        3.72        19.73         4.31        11.05         8.61        16.67 
TCGA-RD-A8N1 TCGA-RD-A8N4 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB 
      115.69        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        37.74         5.46        13.25        13.02        31.10 
TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PJ 
       22.36         7.73        19.07        33.63        16.31         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PT TCGA-VQ-A8PU 
       17.85         1.87         9.27        23.41        19.30        23.57 
TCGA-VQ-A8PX TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X 
       64.57        28.70         8.68         1.71         7.36         8.58 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 
       44.25         8.61         4.54         6.58         5.72        40.08 
TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       29.98        21.11         4.21         0.79 

$`AMP PEAK 15(8Q24.21) WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4188 TCGA-BR-4280 TCGA-BR-6458 TCGA-BR-6563 
       11.70         6.61         7.43         6.61         7.00        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6710 TCGA-BR-7196 TCGA-BR-7703 
        0.82        32.78        13.22         8.98        12.82        24.76 
TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8081 TCGA-BR-8285 
        0.16        12.43        17.49         1.32        20.55         0.26 
TCGA-BR-8291 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       16.31        19.50         0.26        22.19         2.96         0.95 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8589 
        0.36        14.79         0.69         0.72         1.12        15.81 
TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-A44T 
        0.20         0.49        15.81         0.59        15.68        12.56 
TCGA-BR-A453 TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J4 TCGA-BR-A4J6 
        3.02        13.51        12.89         0.79         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 
        0.13         0.10         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         4.14        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YY TCGA-D7-A6ET 
       19.50        17.19         0.23        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         8.12         3.02        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-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 
       18.81         4.67       122.30        37.91        40.64       116.38 
TCGA-RD-A8N5 TCGA-VQ-A8E3 TCGA-VQ-A8P3 TCGA-VQ-A8PC TCGA-VQ-A8PQ TCGA-VQ-A8PY 
       57.44        21.73        23.77        46.26        15.65        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91Y TCGA-VQ-A924 
       59.18        11.70        49.25        20.81         9.73        55.43 

  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                          0.07                           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 
                        11.360                         12.395 
[1] "0.1 - 115.7 (11.4)" "0.1 - 122.3 (12.4)"
[1] "hr=" "1.1"
D15V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 15(8Q24.21) MUTATED         2       12       26       22        23
  AMP PEAK 15(8Q24.21) WILD-TYPE       0        1       13        9        13
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 15(8Q24.21) MUTATED          34         2         56         32
  AMP PEAK 15(8Q24.21) WILD-TYPE        15         1         21         23
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 15(8Q24.21) MUTATED           26       24
  AMP PEAK 15(8Q24.21) WILD-TYPE         11       13
D15V3, multiclass
            clus
vv           AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  STAGE I                               2                              0
  STAGE IA                             12                              1
  STAGE IB                             26                             13
  STAGE II                             22                              9
  STAGE IIA                            23                             13
  STAGE IIB                            34                             15
  STAGE III                             2                              1
  STAGE IIIA                           56                             21
  STAGE IIIB                           32                             23
  STAGE IIIC                           26                             11
  STAGE IV                             24                             13
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 15(8Q24.21) MUTATED    20  60 118  66
  AMP PEAK 15(8Q24.21) WILD-TYPE   1  27  55  38
D15V4, multiclass
    clus
vv   AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  T1                           20                              1
  T2                           60                             27
  T3                          118                             55
  T4                           66                             38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 15(8Q24.21) MUTATED   83 76 46 58
  AMP PEAK 15(8Q24.21) WILD-TYPE 39 31 29 21
D15V5, multiclass
    clus
vv   AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  N0                           83                             39
  N1                           76                             31
  N2                           46                             29
  N3                           58                             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"
                                vv
clus                              M0  M1  MX
  AMP PEAK 15(8Q24.21) MUTATED   244  14  15
  AMP PEAK 15(8Q24.21) WILD-TYPE 109  10   3
D15V6, multiclass
    clus
vv   AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  M0                          244                            109
  M1                           14                             10
  MX                           15                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                                cls
clus                               0   1
  AMP PEAK 15(8Q24.21) MUTATED   103 170
  AMP PEAK 15(8Q24.21) WILD-TYPE  48  74
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8Q24.21) MUTATED    103  170
  AMP PEAK 15(8Q24.21) WILD-TYPE   48   74
        clus
vv       AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  FEMALE                          103                             48
  MALE                            170                             74
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 15(8Q24.21) MUTATED                                      36
  AMP PEAK 15(8Q24.21) WILD-TYPE                                    29
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 15(8Q24.21) MUTATED                                                      109
  AMP PEAK 15(8Q24.21) WILD-TYPE                                                     48
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 15(8Q24.21) MUTATED                                                                  53
  AMP PEAK 15(8Q24.21) WILD-TYPE                                                                16
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 15(8Q24.21) MUTATED                                                 45
  AMP PEAK 15(8Q24.21) WILD-TYPE                                               19
                                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                                          6
  AMP PEAK 15(8Q24.21) WILD-TYPE                                        3
D15V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 15(8Q24.21) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       36
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     109
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           53
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            45
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     6
                                                                   clus
vv                                                                  AMP PEAK 15(8Q24.21) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         29
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        48
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             16
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       3
[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     5 268
  AMP PEAK 15(8Q24.21) WILD-TYPE   1 121
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8Q24.21) MUTATED      5  268
  AMP PEAK 15(8Q24.21) WILD-TYPE    1  121
     clus
vv    AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  NO                             5                              1
  YES                          268                            121
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 15(8Q24.21) MUTATED   217  13  12  20
  AMP PEAK 15(8Q24.21) WILD-TYPE 101   3   6   5
D15V10, multiclass
    clus
vv   AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  R0                          217                            101
  R1                           13                              3
  R2                           12                              6
  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                         6
  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     167
  AMP PEAK 15(8Q24.21) WILD-TYPE    76
D15V12, multiclass
                                           clus
vv                                          AMP PEAK 15(8Q24.21) MUTATED
  ASIAN                                                               57
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              167
                                           clus
vv                                          AMP PEAK 15(8Q24.21) WILD-TYPE
  ASIAN                                                                 31
  BLACK OR AFRICAN AMERICAN                                              0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                 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"

Clustering(16) Variable = AMP PEAK 16(9P24.1) MUTATION ANALYSIS
D16V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 16(9P24.1) MUTATED    32  18
  AMP PEAK 16(9P24.1) WILD-TYPE 210 104
  AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE 
                           50                           314 
  AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE 
                           18                           104 
$`AMP PEAK 16(9P24.1) MUTATED`
TCGA-BR-4267 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-7707 TCGA-BR-8059 
        6.18        13.22        16.14         1.25        23.93         0.82 
TCGA-BR-8080 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8588 TCGA-BR-8678 
        0.49         0.26         0.26         1.55        12.79        11.54 
TCGA-BR-A4IY TCGA-BR-A4J4 TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-8535 
       12.89         0.53        13.64         2.83        13.18         0.13 
TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4460 TCGA-CG-4477 
        0.13         0.10         7.99         8.05        21.99        30.97 
TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-A4YT TCGA-D7-A6EY TCGA-EQ-5647 
       15.22        10.55        12.33        14.27        11.44         0.62 
TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8249 
       16.24        72.23        21.27         0.23        18.08        14.17 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GP 
       12.10        10.62         0.76        12.30        22.75         8.98 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-IN-8663 TCGA-KB-A6F7 TCGA-VQ-A8DU 
        2.10        12.95        12.30         3.39        60.56         5.46 
TCGA-VQ-A8PC TCGA-VQ-A8PP 
       46.26        23.41 

$`AMP PEAK 16(9P24.1) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         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-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.12        10.13        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
        0.62        32.78        13.84         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-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01         0.69         0.16        18.54        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 
        0.95         0.69        12.76        18.71        17.49         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8291 
        0.69        12.26        20.55         0.72        12.95        16.31 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
        1.48         7.40         6.18        19.50         0.36         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19         2.96         0.95        13.74         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 
        3.32         0.36        19.17        14.79         0.69         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         0.72         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        15.81         2.14        13.45         0.20         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         0.59        15.68         0.62 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56         1.15         0.66         3.02        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.92        13.41        13.51         0.79         0.72        14.17 
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-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 
       20.42         1.15        11.57         5.13         3.25        13.15 
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-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG 
        0.10         6.35         0.13         0.13         0.13         0.07 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10         0.10        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        1.02        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       19.07        12.03         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         1.02         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        55.04        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-D7-6815 
       18.61        17.85         5.95        17.19         4.14        15.98 
TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       12.79        11.31        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV 
        0.23         6.97        21.14        20.91        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       15.16        13.78        14.76        13.71        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
        9.76         2.96        15.65         4.34         7.40         7.13 
TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.79         6.58        14.47         8.12         0.39        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        3.02        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        0.56         1.55        26.47         1.51         5.92        14.27 
TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 
       12.59        11.41        24.30         5.59        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
        3.25        25.81        11.77        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.51         6.25        10.19         0.26        19.36        17.69 
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-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO 
       18.81        18.38         5.36         5.19        13.08         1.41 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 
        6.44         6.74         6.87         5.56         1.81         2.53 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS 
        5.56        28.90         3.72        19.73         4.31        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         4.67        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-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       16.87         5.79         0.92        37.74        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       31.10        21.73        22.36        23.77         7.73        19.07 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
       33.63        16.31         2.70        17.85         1.87         9.27 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        19.30        23.57        64.57        14.33        59.18 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U 
       28.70        11.70         8.68        49.25        20.81         1.71 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 
        7.36         8.58         9.73        44.25         8.61        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J 
        4.54         6.58         5.72        40.08        29.98        21.11 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        4.21         0.79 

  AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE 
                         0.10                          0.07 
  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 
                       11.820                        11.635 
[1] "0.1 - 72.2 (11.8)"  "0.1 - 122.3 (11.6)"
[1] "hr=" "1.2"
D16V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 16(9P24.1) MUTATED         1        3        9        3         6
  AMP PEAK 16(9P24.1) WILD-TYPE       1       10       30       28        30
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 16(9P24.1) MUTATED           5         1          9          7
  AMP PEAK 16(9P24.1) WILD-TYPE        44         2         68         48
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 16(9P24.1) MUTATED            6        4
  AMP PEAK 16(9P24.1) WILD-TYPE         31       33
D16V3, multiclass
            clus
vv           AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             3                            10
  STAGE IB                             9                            30
  STAGE II                             3                            28
  STAGE IIA                            6                            30
  STAGE IIB                            5                            44
  STAGE III                            1                             2
  STAGE IIIA                           9                            68
  STAGE IIIB                           7                            48
  STAGE IIIC                           6                            31
  STAGE IV                             4                            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 16(9P24.1) MUTATED     5  15  19  17
  AMP PEAK 16(9P24.1) WILD-TYPE  16  72 154  87
D16V4, multiclass
    clus
vv   AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE
  T1                           5                            16
  T2                          15                            72
  T3                          19                           154
  T4                          17                            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
  AMP PEAK 16(9P24.1) MUTATED    21  15   5  14
  AMP PEAK 16(9P24.1) WILD-TYPE 101  92  70  65
D16V5, multiclass
    clus
vv   AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE
  N0                          21                           101
  N1                          15                            92
  N2                           5                            70
  N3                          14                            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                             M0  M1  MX
  AMP PEAK 16(9P24.1) MUTATED    51   3   3
  AMP PEAK 16(9P24.1) WILD-TYPE 302  21  15
D16V6, multiclass
    clus
vv   AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE
  M0                          51                           302
  M1                           3                            21
  MX                           3                            15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                               cls
clus                              0   1
  AMP PEAK 16(9P24.1) MUTATED    22  35
  AMP PEAK 16(9P24.1) WILD-TYPE 129 209
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(9P24.1) MUTATED     22   35
  AMP PEAK 16(9P24.1) WILD-TYPE  129  209
        clus
vv       AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE
  FEMALE                          22                           129
  MALE                            35                           209
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 16(9P24.1) MUTATED                                       4
  AMP PEAK 16(9P24.1) WILD-TYPE                                    61
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 16(9P24.1) MUTATED                                                       24
  AMP PEAK 16(9P24.1) WILD-TYPE                                                    133
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 16(9P24.1) MUTATED                                                                   9
  AMP PEAK 16(9P24.1) WILD-TYPE                                                                60
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 16(9P24.1) MUTATED                                                 11
  AMP PEAK 16(9P24.1) WILD-TYPE                                               53
                               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                                          2
  AMP PEAK 16(9P24.1) WILD-TYPE                                        7
D16V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 16(9P24.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     24
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           9
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    2
                                                                   clus
vv                                                                  AMP PEAK 16(9P24.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        61
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            60
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             53
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     16
  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"
D16V9, binary
                               cls
clus                              0   1
  AMP PEAK 16(9P24.1) MUTATED     3  54
  AMP PEAK 16(9P24.1) WILD-TYPE   3 335
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(9P24.1) MUTATED      3   54
  AMP PEAK 16(9P24.1) WILD-TYPE    3  335
     clus
vv    AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE
  NO                            3                             3
  YES                          54                           335
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 16(9P24.1) MUTATED    44   4   2   4
  AMP PEAK 16(9P24.1) WILD-TYPE 274  12  16  21
D16V10, multiclass
    clus
vv   AMP PEAK 16(9P24.1) MUTATED AMP PEAK 16(9P24.1) WILD-TYPE
  R0                          44                           274
  R1                           4                            12
  R2                           2                            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"
D16V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 16(9P24.1) MUTATED      17                         1
  AMP PEAK 16(9P24.1) WILD-TYPE    71                         5
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 16(9P24.1) MUTATED                                           0    29
  AMP PEAK 16(9P24.1) WILD-TYPE                                         1   214
D16V12, multiclass
                                           clus
vv                                          AMP PEAK 16(9P24.1) MUTATED
  ASIAN                                                              17
  BLACK OR AFRICAN AMERICAN                                           1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              29
                                           clus
vv                                          AMP PEAK 16(9P24.1) WILD-TYPE
  ASIAN                                                                71
  BLACK OR AFRICAN AMERICAN                                             5
  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"

Clustering(17) Variable = AMP PEAK 17(9P13.2) MUTATION ANALYSIS
D17V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 17(9P13.2) MUTATED    47  23
  AMP PEAK 17(9P13.2) WILD-TYPE 195  99
  AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE 
                           70                           294 
  AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE 
                           23                            99 
$`AMP PEAK 17(9P13.2) MUTATED`
TCGA-BR-4183 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7959 
        6.61        16.14         1.25        23.93         0.69        18.71 
TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8486 
        0.49        12.95         0.26        16.31         1.55        20.22 
TCGA-BR-8588 TCGA-BR-8678 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4J4 
       12.79        11.54         1.15         0.66        22.26         0.53 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-8526 TCGA-CD-8535 
       20.42        13.64         2.83        13.18         0.07         0.13 
TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4466 
        0.10         7.99         8.05        47.05        21.99        18.97 
TCGA-CG-4477 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 
       30.97        11.93        17.19         4.14        15.22        10.55 
TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A4YT TCGA-D7-A4Z0 TCGA-D7-A6EX TCGA-D7-A6EY 
       12.33         0.23        14.27        14.76        11.31        11.44 
TCGA-D7-A6F0 TCGA-EQ-5647 TCGA-F1-A448 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8249 
        2.96         0.62        21.27         0.23        18.08        14.17 
TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4H2 TCGA-HU-A4H5 
        0.76        12.30        22.75         8.98        12.95        12.30 
TCGA-HU-A4H6 TCGA-IN-8663 TCGA-KB-A6F7 TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N9 
        9.67         3.39        60.56       122.30       115.69        35.61 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8PC TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PP 
       37.74         5.46        46.26         2.70        17.85        23.41 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Z 
       20.81         1.71         8.58        44.25 

$`AMP PEAK 17(9P13.2) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
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-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.12        10.13        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6710 TCGA-BR-6801 
        0.62        32.78        13.84        13.22         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-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       35.24        15.42        28.01         0.16        18.54        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69        12.76        17.49         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8296 
        0.69        12.26        20.55         0.72         0.26         1.48 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        19.50         0.36         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
        2.96         0.95        13.74         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 
        0.36        19.17        14.79         0.69         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8589 
        3.72         5.39         0.72         9.21         1.12        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        2.14        13.45         0.20         7.53         0.49        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         0.59        15.68         0.62        10.68        12.56 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        3.02         0.92        13.41        13.51        12.89         0.79 
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-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 
        0.46        20.65         1.15        11.57         5.13         3.25 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 
       13.15         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-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         6.35         0.13         0.13         0.13         0.13 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.07         0.10         0.10        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       15.95         1.02        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
       19.07        12.03         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         1.02         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        55.04        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-D7-6525 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 
        5.95        15.98        12.79        11.31        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU 
       19.50        17.19         6.97        21.14        20.91        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EZ 
        5.92        15.16        13.78        13.71        11.24         9.76 
TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.65         4.34         7.40         7.13         7.79        16.24 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        6.58        14.47        72.23         8.12         0.39        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        3.02        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        0.56         1.55        26.47         1.51         5.92        14.27 
TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 
       12.59        11.41        12.10        10.62        24.30         5.59 
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-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
        2.10        19.36        17.69         8.88         8.81        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       21.21         3.45        18.81        18.38         5.36         5.19 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT 
       13.08         1.41         6.44         6.74         6.87         5.56 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        1.81         2.53         5.56        28.90         3.72        19.73 
TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW 
        4.31        11.05         8.61         4.67        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-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        5.79         0.92        13.25        13.02        31.10        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       22.36        23.77         7.73        19.07        33.63        16.31 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX 
        1.87         9.27        15.65        19.30        23.57        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        59.18        28.70        11.70         8.68        49.25 
TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
        7.36         9.73         8.61        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        5.72        40.08        29.98        21.11         4.21         0.79 

  AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE 
                         0.07                          0.07 
  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 
                       12.315                        11.275 
[1] "0.1 - 122.3 (12.3)" "0.1 - 116.4 (11.3)"
[1] "hr=" "1.1"
D17V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 17(9P13.2) MUTATED         1        3       12        6         4
  AMP PEAK 17(9P13.2) WILD-TYPE       1       10       27       25        32
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 17(9P13.2) MUTATED           6         0         19         12
  AMP PEAK 17(9P13.2) WILD-TYPE        43         3         58         43
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 17(9P13.2) MUTATED            3        7
  AMP PEAK 17(9P13.2) WILD-TYPE         34       30
D17V3, multiclass
            clus
vv           AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             3                            10
  STAGE IB                            12                            27
  STAGE II                             6                            25
  STAGE IIA                            4                            32
  STAGE IIB                            6                            43
  STAGE III                            0                             3
  STAGE IIIA                          19                            58
  STAGE IIIB                          12                            43
  STAGE IIIC                           3                            34
  STAGE IV                             7                            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 17(9P13.2) MUTATED     6  21  32  15
  AMP PEAK 17(9P13.2) WILD-TYPE  15  66 141  89
D17V4, multiclass
    clus
vv   AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE
  T1                           6                            15
  T2                          21                            66
  T3                          32                           141
  T4                          15                            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 17(9P13.2) MUTATED    22  22  15  15
  AMP PEAK 17(9P13.2) WILD-TYPE 100  85  60  64
D17V5, multiclass
    clus
vv   AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE
  N0                          22                           100
  N1                          22                            85
  N2                          15                            60
  N3                          15                            64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  AMP PEAK 17(9P13.2) MUTATED    69   4   2
  AMP PEAK 17(9P13.2) WILD-TYPE 284  20  16
D17V6, multiclass
    clus
vv   AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE
  M0                          69                           284
  M1                           4                            20
  MX                           2                            16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                               cls
clus                              0   1
  AMP PEAK 17(9P13.2) MUTATED    31  44
  AMP PEAK 17(9P13.2) WILD-TYPE 120 200
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9P13.2) MUTATED     31   44
  AMP PEAK 17(9P13.2) WILD-TYPE  120  200
        clus
vv       AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE
  FEMALE                          31                           120
  MALE                            44                           200
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 17(9P13.2) MUTATED                                       6
  AMP PEAK 17(9P13.2) WILD-TYPE                                    59
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 17(9P13.2) MUTATED                                                       24
  AMP PEAK 17(9P13.2) WILD-TYPE                                                    133
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 17(9P13.2) MUTATED                                                                  15
  AMP PEAK 17(9P13.2) WILD-TYPE                                                                54
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 17(9P13.2) MUTATED                                                 17
  AMP PEAK 17(9P13.2) WILD-TYPE                                               47
                               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                                          2
  AMP PEAK 17(9P13.2) WILD-TYPE                                        7
D17V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 17(9P13.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     24
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          15
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    2
                                                                   clus
vv                                                                  AMP PEAK 17(9P13.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            54
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             47
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     13
  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"
D17V9, binary
                               cls
clus                              0   1
  AMP PEAK 17(9P13.2) MUTATED     3  72
  AMP PEAK 17(9P13.2) WILD-TYPE   3 317
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9P13.2) MUTATED      3   72
  AMP PEAK 17(9P13.2) WILD-TYPE    3  317
     clus
vv    AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE
  NO                            3                             3
  YES                          72                           317
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 17(9P13.2) MUTATED    62   5   3   3
  AMP PEAK 17(9P13.2) WILD-TYPE 256  11  15  22
D17V10, multiclass
    clus
vv   AMP PEAK 17(9P13.2) MUTATED AMP PEAK 17(9P13.2) WILD-TYPE
  R0                          62                           256
  R1                           5                            11
  R2                           3                            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"
D17V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 17(9P13.2) MUTATED      17                         0
  AMP PEAK 17(9P13.2) WILD-TYPE    71                         6
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 17(9P13.2) MUTATED                                           0    43
  AMP PEAK 17(9P13.2) WILD-TYPE                                         1   200
D17V12, multiclass
                                           clus
vv                                          AMP PEAK 17(9P13.2) MUTATED
  ASIAN                                                              17
  BLACK OR AFRICAN AMERICAN                                           0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              43
                                           clus
vv                                          AMP PEAK 17(9P13.2) WILD-TYPE
  ASIAN                                                                71
  BLACK OR AFRICAN AMERICAN                                             6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               200
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = AMP PEAK 18(9Q34.3) MUTATION ANALYSIS
D18V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 18(9Q34.3) MUTATED    63  31
  AMP PEAK 18(9Q34.3) WILD-TYPE 179  91
  AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE 
                           94                           270 
  AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE 
                           31                            91 
$`AMP PEAK 18(9Q34.3) MUTATED`
TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6564 TCGA-BR-6707 TCGA-BR-7197 
        6.61        18.35        10.13         0.82        16.14         9.21 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7959 TCGA-BR-8060 
       35.24        23.93        15.42         0.69        18.71         1.32 
TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8486 
        0.49         0.26         1.55         6.18        19.50        20.22 
TCGA-BR-8588 TCGA-BR-8682 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4J4 TCGA-BR-A4J9 
       12.79        16.44         1.15        22.26         0.53         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-8535 TCGA-CD-A486 
       20.65        20.42        13.15        13.18         0.13         6.35 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4466 
        0.13         0.13         3.02        27.02         7.99        18.97 
TCGA-CG-4477 TCGA-CG-5718 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6528 
       30.97         1.02        12.66        11.93        17.19        15.22 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-A4YT TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6EX 
       10.55        11.31        14.27        15.16        14.76        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-EQ-5647 
       11.44         9.76         2.96        15.65         4.34         0.62 
TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HJ-7597 
       16.24        72.23        21.27         1.55        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4GF TCGA-HU-A4GP 
        1.51        14.17         0.76        12.30        25.81         8.98 
TCGA-HU-A4GU TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        6.25        12.30        27.42         3.45        18.81         3.39 
TCGA-IN-A6RO TCGA-IN-A6RS TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-RD-A7BS TCGA-RD-A8MV 
        1.41         6.87         5.56        60.56        11.05       122.30 
TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8PC TCGA-VQ-A8PU 
      115.69        35.61        37.74         5.46        46.26        23.57 
TCGA-VQ-A8PY TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 
       14.33        20.81         1.71         8.58        44.25         8.61 
TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6J TCGA-ZQ-A9CR 
        5.72        40.08        21.11         0.79 

$`AMP PEAK 18(9Q34.3) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
        5.62        11.70         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        13.12 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.68         7.00        39.12         0.62        32.78        13.84 
TCGA-BR-6706 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       13.22         1.25         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       32.94        12.82        24.76        28.01         0.16        18.54 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 
       12.43         0.95         0.69        12.76        17.49         0.82 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69        12.26        20.55         0.72         0.26        12.95 
TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
       16.31         1.48         7.40         0.36         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
        2.96         0.95        13.74         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 
        0.36        19.17        14.79         0.69         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8589 
        3.72         5.39         0.72         9.21         1.12        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        2.14        13.45         0.20         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       15.81         0.59        15.68         0.62        10.68        12.56 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        0.66         3.02         0.92        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.79         0.72        14.17        12.82         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       13.51         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        3.25         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-8536 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        0.13         0.10         0.13         0.13         0.07         0.10 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
        0.10         0.10        20.02        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-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
       12.03        21.99         9.01         7.07        12.00        22.98 
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-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-D7-6518 TCGA-D7-6519 
       55.04        21.07         7.99        12.36        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 
       18.84        18.54        18.61        17.85         5.95         4.14 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       15.98        12.79        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU 
       17.19         0.23         6.97        21.14        20.91        16.44 
TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A74A TCGA-D7-A74B 
        5.92        13.78        13.71        11.24         7.40         7.13 
TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.79         6.58        14.47         8.12         0.39        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        3.02        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A8CX TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
        0.56         0.23         5.92        14.27        12.59        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 
       12.10        10.62        24.30         5.59        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
        3.25        22.75        11.77        21.37        29.98         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-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-A6RI 
       17.69         9.67         8.88         8.81        21.21        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT 
        5.36         5.19        13.08         6.44         6.74         5.56 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        1.81         2.53        28.90         3.72        19.73         4.31 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 
        8.61         4.67        16.67        37.91        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL 
       71.38        57.44         8.94        16.87         5.79         0.92 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        31.10        21.73        22.36        23.77 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK 
        7.73        19.07        33.63        16.31         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX 
        1.87         9.27        23.41        15.65        19.30        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91W 
       59.18        28.70        11.70         8.68        49.25         7.36 
TCGA-VQ-A91Y TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-AA6B TCGA-ZA-A8F6 
        9.73        55.43         4.54         6.58        29.98         4.21 

  AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE 
                         0.13                          0.07 
  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 
                       12.300                        11.475 
[1] "0.1 - 122.3 (12.3)" "0.1 - 116.4 (11.5)"
[1] "hr=" "1.1"
D18V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 18(9Q34.3) MUTATED         1        6       12        6         8
  AMP PEAK 18(9Q34.3) WILD-TYPE       1        7       27       25        28
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 18(9Q34.3) MUTATED          13         1         24         12
  AMP PEAK 18(9Q34.3) WILD-TYPE        36         2         53         43
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 18(9Q34.3) MUTATED            6        9
  AMP PEAK 18(9Q34.3) WILD-TYPE         31       28
D18V3, multiclass
            clus
vv           AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             6                             7
  STAGE IB                            12                            27
  STAGE II                             6                            25
  STAGE IIA                            8                            28
  STAGE IIB                           13                            36
  STAGE III                            1                             2
  STAGE IIIA                          24                            53
  STAGE IIIB                          12                            43
  STAGE IIIC                           6                            31
  STAGE IV                             9                            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 18(9Q34.3) MUTATED     8  24  46  22
  AMP PEAK 18(9Q34.3) WILD-TYPE  13  63 127  82
D18V4, multiclass
    clus
vv   AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE
  T1                           8                            13
  T2                          24                            63
  T3                          46                           127
  T4                          22                            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 18(9Q34.3) MUTATED   32 29 22 18
  AMP PEAK 18(9Q34.3) WILD-TYPE 90 78 53 61
D18V5, multiclass
    clus
vv   AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE
  N0                          32                            90
  N1                          29                            78
  N2                          22                            53
  N3                          18                            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                             M0  M1  MX
  AMP PEAK 18(9Q34.3) MUTATED    95   5   4
  AMP PEAK 18(9Q34.3) WILD-TYPE 258  19  14
D18V6, multiclass
    clus
vv   AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE
  M0                          95                           258
  M1                           5                            19
  MX                           4                            14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                               cls
clus                              0   1
  AMP PEAK 18(9Q34.3) MUTATED    39  65
  AMP PEAK 18(9Q34.3) WILD-TYPE 112 179
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(9Q34.3) MUTATED     39   65
  AMP PEAK 18(9Q34.3) WILD-TYPE  112  179
        clus
vv       AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE
  FEMALE                          39                           112
  MALE                            65                           179
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 18(9Q34.3) MUTATED                                      11
  AMP PEAK 18(9Q34.3) WILD-TYPE                                    54
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 18(9Q34.3) MUTATED                                                       40
  AMP PEAK 18(9Q34.3) WILD-TYPE                                                    117
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 18(9Q34.3) MUTATED                                                                  17
  AMP PEAK 18(9Q34.3) WILD-TYPE                                                                52
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 18(9Q34.3) MUTATED                                                 20
  AMP PEAK 18(9Q34.3) WILD-TYPE                                               44
                               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                                          3
  AMP PEAK 18(9Q34.3) WILD-TYPE                                        6
D18V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 18(9Q34.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      11
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     40
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    3
                                                                   clus
vv                                                                  AMP PEAK 18(9Q34.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        54
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      117
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            52
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             44
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     12
  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"
D18V9, binary
                               cls
clus                              0   1
  AMP PEAK 18(9Q34.3) MUTATED     3 101
  AMP PEAK 18(9Q34.3) WILD-TYPE   3 288
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(9Q34.3) MUTATED      3  101
  AMP PEAK 18(9Q34.3) WILD-TYPE    3  288
     clus
vv    AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE
  NO                            3                             3
  YES                         101                           288
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 18(9Q34.3) MUTATED    86   5   2   7
  AMP PEAK 18(9Q34.3) WILD-TYPE 232  11  16  18
D18V10, multiclass
    clus
vv   AMP PEAK 18(9Q34.3) MUTATED AMP PEAK 18(9Q34.3) WILD-TYPE
  R0                          86                           232
  R1                           5                            11
  R2                           2                            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"
D18V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 18(9Q34.3) MUTATED      21                         2
  AMP PEAK 18(9Q34.3) WILD-TYPE    67                         4
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 18(9Q34.3) MUTATED                                           0    65
  AMP PEAK 18(9Q34.3) WILD-TYPE                                         1   178
D18V12, multiclass
                                           clus
vv                                          AMP PEAK 18(9Q34.3) MUTATED
  ASIAN                                                              21
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              65
                                           clus
vv                                          AMP PEAK 18(9Q34.3) WILD-TYPE
  ASIAN                                                                67
  BLACK OR AFRICAN AMERICAN                                             4
  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"

Clustering(19) Variable = AMP PEAK 19(10P11.22) MUTATION ANALYSIS
D19V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 19(10P11.22) MUTATED    66  34
  AMP PEAK 19(10P11.22) WILD-TYPE 176  88
  AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE 
                            100                             264 
  AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE 
                             34                              88 
$`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        10.13        13.68         0.62        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         0.69        18.54         0.69 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8483 TCGA-BR-8485 
        0.26         1.55         1.48         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         0.59        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         0.13         0.13         0.13         0.10 
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         7.79        72.23         0.39        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        17.69         9.67        27.42         3.45 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RR TCGA-KB-A93H TCGA-MX-A663 TCGA-RD-A7BS 
        3.39        18.38         6.74        28.90         4.31        11.05 
TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-VQ-A8DU TCGA-VQ-A8E3 TCGA-VQ-A8P5 
        8.61        16.67       122.30         5.46        21.73         7.73 
TCGA-VQ-A8PC TCGA-VQ-A8PK TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91E 
       46.26        17.85        64.57        14.33        28.70         8.68 
TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-AA6J 
        1.71         8.58         8.61        21.11 

$`AMP PEAK 19(10P11.22) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
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-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
       13.12         7.00        39.12         0.82        32.78        13.84 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 
       13.22        16.14         1.25         8.98        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7851 
       32.94        12.82        24.76        23.93         0.16        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        0.95         0.69        12.76        18.71        17.49         0.82 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        1.32        12.26         0.49        20.55         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       12.95        16.31         6.18        19.50         0.36         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19         2.96         0.95        13.74         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 
        3.32         0.36        19.17        14.79         0.69         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       15.85         3.72         0.72         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        2.14        13.45         0.20         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       15.81        15.68         0.62        10.68        12.56         1.15 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        0.66         3.02        22.26         0.92        13.41        13.51 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 
        0.79        14.17         0.53        12.82         0.66         0.46 
TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       20.42        11.57         5.13         2.83         3.25        13.15 
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-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.10         0.10         0.13         0.13         0.10         6.35 
TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
        0.13         0.07         0.10         0.10         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 
       15.95         1.02         7.99         8.05        54.08        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       29.98        19.07        12.03         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       22.98         6.97         1.02         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-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10        55.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       11.93        18.84        18.54        18.61        17.85         5.95 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
        4.14        15.98        12.79        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 
       16.80        19.50        17.19         0.23         6.97        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-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-A4SO 
       11.44         9.76         2.96         4.34         7.13        16.24 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 
        6.58        14.47        21.27         8.12         3.02        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-A5NB 
       59.54         5.03        13.58         0.56         1.55        18.08 
TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 
       26.47        14.27        12.59        12.10        10.62        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
        5.59        11.84         3.25        21.37        29.98         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-8462 TCGA-IN-A6RJ TCGA-IN-A6RL 
        8.88         8.81        21.21        18.81         5.36         5.19 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU 
       13.08         1.41         6.44         6.87         5.56         1.81 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BW 
        2.53         5.56        60.56         3.72        19.73         4.67 
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-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        16.87         5.79         0.92        37.74 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       13.25        13.02        31.10        22.36        23.77        19.07 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       33.63        16.31         2.70         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91K 
       15.65        19.30        23.57        59.18        11.70        49.25 
TCGA-VQ-A91Q TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A924 TCGA-VQ-A925 
       20.81         7.36         9.73        44.25        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        6.58         5.72        40.08        29.98         4.21         0.79 

  AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE 
                           0.07                            0.07 
  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 
                          11.36                           11.70 
[1] "0.1 - 122.3 (11.4)" "0.1 - 116.4 (11.7)"
[1] "hr=" "1"  
D19V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 19(10P11.22) MUTATED         0        7        8        4        12
  AMP PEAK 19(10P11.22) WILD-TYPE       2        6       31       27        24
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 19(10P11.22) MUTATED          19         1         21         17
  AMP PEAK 19(10P11.22) WILD-TYPE        30         2         56         38
                                 vv
clus                              STAGE IIIC STAGE IV
  AMP PEAK 19(10P11.22) MUTATED            6       10
  AMP PEAK 19(10P11.22) WILD-TYPE         31       27
D19V3, multiclass
            clus
vv           AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE
  STAGE I                                0                               2
  STAGE IA                               7                               6
  STAGE IB                               8                              31
  STAGE II                               4                              27
  STAGE IIA                             12                              24
  STAGE IIB                             19                              30
  STAGE III                              1                               2
  STAGE IIIA                            21                              56
  STAGE IIIB                            17                              38
  STAGE IIIC                             6                              31
  STAGE IV                              10                              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 19(10P11.22) MUTATED     7  17  56  26
  AMP PEAK 19(10P11.22) WILD-TYPE  14  70 117  78
D19V4, multiclass
    clus
vv   AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE
  T1                             7                              14
  T2                            17                              70
  T3                            56                             117
  T4                            26                              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
  AMP PEAK 19(10P11.22) MUTATED   37 28 22 18
  AMP PEAK 19(10P11.22) WILD-TYPE 85 79 53 61
D19V5, multiclass
    clus
vv   AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE
  N0                            37                              85
  N1                            28                              79
  N2                            22                              53
  N3                            18                              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                               M0  M1  MX
  AMP PEAK 19(10P11.22) MUTATED    95   6   6
  AMP PEAK 19(10P11.22) WILD-TYPE 258  18  12
D19V6, multiclass
    clus
vv   AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE
  M0                            95                             258
  M1                             6                              18
  MX                             6                              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                                 cls
clus                                0   1
  AMP PEAK 19(10P11.22) MUTATED    40  67
  AMP PEAK 19(10P11.22) WILD-TYPE 111 177
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(10P11.22) MUTATED     40   67
  AMP PEAK 19(10P11.22) WILD-TYPE  111  177
        clus
vv       AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE
  FEMALE                            40                             111
  MALE                              67                             177
[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                                    51
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 19(10P11.22) MUTATED                                                       41
  AMP PEAK 19(10P11.22) WILD-TYPE                                                    116
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 19(10P11.22) MUTATED                                                                  21
  AMP PEAK 19(10P11.22) WILD-TYPE                                                                48
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 19(10P11.22) MUTATED                                                 23
  AMP PEAK 19(10P11.22) WILD-TYPE                                               41
                                 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                                          2
  AMP PEAK 19(10P11.22) WILD-TYPE                                        7
D19V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 19(10P11.22) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        14
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       41
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            21
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             23
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      2
                                                                   clus
vv                                                                  AMP PEAK 19(10P11.22) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          51
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        116
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              48
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               41
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       7
  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"
D19V9, binary
                                 cls
clus                                0   1
  AMP PEAK 19(10P11.22) MUTATED     3 104
  AMP PEAK 19(10P11.22) WILD-TYPE   3 285
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(10P11.22) MUTATED      3  104
  AMP PEAK 19(10P11.22) WILD-TYPE    3  285
     clus
vv    AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE
  NO                              3                               3
  YES                           104                             285
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 19(10P11.22) MUTATED    89   2   5   5
  AMP PEAK 19(10P11.22) WILD-TYPE 229  14  13  20
D19V10, multiclass
    clus
vv   AMP PEAK 19(10P11.22) MUTATED AMP PEAK 19(10P11.22) WILD-TYPE
  R0                            89                             229
  R1                             2                              14
  R2                             5                              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"
D19V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 19(10P11.22) MUTATED      31                         3
  AMP PEAK 19(10P11.22) WILD-TYPE    57                         3
                                 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      60
  AMP PEAK 19(10P11.22) WILD-TYPE   183
D19V12, multiclass
                                           clus
vv                                          AMP PEAK 19(10P11.22) MUTATED
  ASIAN                                                                31
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                60
                                           clus
vv                                          AMP PEAK 19(10P11.22) WILD-TYPE
  ASIAN                                                                  57
  BLACK OR AFRICAN AMERICAN                                               3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               0
  WHITE                                                                 183
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = AMP PEAK 20(10Q22.2) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 20(10Q22.2) MUTATED    49  28
  AMP PEAK 20(10Q22.2) WILD-TYPE 193  94
  AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE 
                            77                            287 
  AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE 
                            28                             94 
$`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        10.13         7.00         0.82         9.21 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8286 
       35.24        15.42         0.69         0.82         0.69        12.95 
TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8369 TCGA-BR-8485 TCGA-BR-8682 
        0.26         1.48         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 
        0.59        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        55.04        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         0.23        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-RD-A7BS TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8N9 
        6.44         1.81        11.05         8.61       122.30        35.61 
TCGA-VQ-A8E3 TCGA-VQ-A8PC TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       21.73        46.26         1.87        23.57        64.57        14.33 
TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A925 TCGA-VQ-A928 
       28.70         8.68        20.81         4.54         5.72 

$`AMP PEAK 20(10Q22.2) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
        5.62        11.70         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        13.12 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.68        39.12         0.62        32.78        13.84        13.22 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       16.14         1.25         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         0.16 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       18.54        12.43         0.95         0.69        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49         1.32        12.26         0.49        20.55         0.72 
TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        0.26        16.31         1.55         6.18        19.50         0.36 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19         2.96         0.95        13.74         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 
        3.32         0.36        19.17        14.79         0.69         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 
       15.85         3.72         5.39         0.72        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         2.14        13.45         0.20         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
        0.49        11.54        15.81        15.68         0.62        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56         1.15         0.66         3.02        22.26         0.92 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       13.41        13.51         0.79        14.17         0.53        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL 
        0.66        13.51         0.46        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-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 
        0.07         0.07         0.07         0.10         0.13         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         6.35         0.13         0.13 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.13         0.13         0.07         0.10         0.10         0.10 
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-4455 TCGA-CG-4465 
       54.08         4.01        14.01        29.98        12.03         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         1.02 
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-D7-6521 
        7.99        12.36        12.66        11.93        19.13        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85         5.95        17.19         4.14        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       15.98        12.79        11.31        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       17.19         6.97        21.14        20.91        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6F0 
       15.16        13.78        14.76        13.71        11.44         2.96 
TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 
       15.65         4.34         7.13         0.62         7.79         6.58 
TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        21.27         8.12         0.39        19.53         3.02 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF 
       22.29        17.06        59.54         5.03        13.58         1.55 
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-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 
       14.17        12.10        10.62        24.30         5.59        11.84 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-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-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 
       17.69        12.30         8.88         8.81        21.21        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38         5.36         5.19         1.41         6.74         6.87 
TCGA-IN-A7NT TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG 
        5.56         2.53         5.56        60.56        28.90         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 
       19.73         4.31         4.67        16.67        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB 
      115.69       116.38        71.38        57.44         8.94        16.87 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        37.74         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       31.10        22.36        23.77         7.73        19.07        33.63 
TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       16.31         2.70        17.85         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91W 
       19.30        59.18        11.70        49.25         1.71         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 
        8.58         9.73        44.25         8.61        55.43         6.58 
TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       40.08        29.98        21.11         4.21         0.79 

  AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE 
                          0.07                           0.07 
  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 
                         11.24                          11.77 
[1] "0.1 - 122.3 (11.2)" "0.1 - 116.4 (11.8)"
[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        3        8         3
  AMP PEAK 20(10Q22.2) WILD-TYPE       2        8       36       23        33
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 20(10Q22.2) MUTATED          10         2         20         13
  AMP PEAK 20(10Q22.2) WILD-TYPE        39         1         57         42
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 20(10Q22.2) MUTATED            6        9
  AMP PEAK 20(10Q22.2) WILD-TYPE         31       28
D20V3, multiclass
            clus
vv           AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              5                              8
  STAGE IB                              3                             36
  STAGE II                              8                             23
  STAGE IIA                             3                             33
  STAGE IIB                            10                             39
  STAGE III                             2                              1
  STAGE IIIA                           20                             57
  STAGE IIIB                           13                             42
  STAGE IIIC                            6                             31
  STAGE IV                              9                             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 20(10Q22.2) MUTATED     6  14  38  21
  AMP PEAK 20(10Q22.2) WILD-TYPE  15  73 135  83
D20V4, multiclass
    clus
vv   AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE
  T1                            6                             15
  T2                           14                             73
  T3                           38                            135
  T4                           21                             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 20(10Q22.2) MUTATED    21  20  21  17
  AMP PEAK 20(10Q22.2) WILD-TYPE 101  87  54  62
D20V5, multiclass
    clus
vv   AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE
  N0                           21                            101
  N1                           20                             87
  N2                           21                             54
  N3                           17                             62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  AMP PEAK 20(10Q22.2) MUTATED    74   3   3
  AMP PEAK 20(10Q22.2) WILD-TYPE 279  21  15
D20V6, multiclass
    clus
vv   AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE
  M0                           74                            279
  M1                            3                             21
  MX                            3                             15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                                cls
clus                               0   1
  AMP PEAK 20(10Q22.2) MUTATED    31  49
  AMP PEAK 20(10Q22.2) WILD-TYPE 120 195
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(10Q22.2) MUTATED     31   49
  AMP PEAK 20(10Q22.2) WILD-TYPE  120  195
        clus
vv       AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE
  FEMALE                           31                            120
  MALE                             49                            195
[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                                    53
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 20(10Q22.2) MUTATED                                                       28
  AMP PEAK 20(10Q22.2) WILD-TYPE                                                    129
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 20(10Q22.2) MUTATED                                                                  15
  AMP PEAK 20(10Q22.2) WILD-TYPE                                                                54
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 20(10Q22.2) MUTATED                                                 17
  AMP PEAK 20(10Q22.2) WILD-TYPE                                               47
                                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                                          2
  AMP PEAK 20(10Q22.2) WILD-TYPE                                        7
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)                           15
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
                                                                   clus
vv                                                                  AMP PEAK 20(10Q22.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         53
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             54
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              47
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      17
  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"
D20V9, binary
                                cls
clus                               0   1
  AMP PEAK 20(10Q22.2) MUTATED     2  78
  AMP PEAK 20(10Q22.2) WILD-TYPE   4 311
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(10Q22.2) MUTATED      2   78
  AMP PEAK 20(10Q22.2) WILD-TYPE    4  311
     clus
vv    AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE
  NO                             2                              4
  YES                           78                            311
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 20(10Q22.2) MUTATED    72   0   3   4
  AMP PEAK 20(10Q22.2) WILD-TYPE 246  16  15  21
D20V10, multiclass
    clus
vv   AMP PEAK 20(10Q22.2) MUTATED AMP PEAK 20(10Q22.2) WILD-TYPE
  R0                           72                            246
  R1                            0                             16
  R2                            3                             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"
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                         5
                                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      49
  AMP PEAK 20(10Q22.2) WILD-TYPE   194
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                                                               49
                                           clus
vv                                          AMP PEAK 20(10Q22.2) WILD-TYPE
  ASIAN                                                                 68
  BLACK OR AFRICAN AMERICAN                                              5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                194
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = AMP PEAK 21(10Q26.13) MUTATION ANALYSIS
D21V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 21(10Q26.13) MUTATED    47  28
  AMP PEAK 21(10Q26.13) WILD-TYPE 195  94
  AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE 
                             75                             289 
  AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE 
                             28                              94 
$`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        10.13        13.68         0.82 
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 
        0.49        12.95         0.26         1.48         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         1.02         4.01        55.04 
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 
        7.79        72.23         0.39        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-RD-A7BS TCGA-VQ-A8DU 
        3.39        18.38         6.44         5.56        11.05         5.46 
TCGA-VQ-A8E3 TCGA-VQ-A8PC TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91Q 
       21.73        46.26        64.57        14.33         8.68        20.81 
TCGA-VQ-A91Y TCGA-VQ-A925 TCGA-VQ-A928 
        9.73         4.54         5.72 

$`AMP PEAK 21(10Q26.13) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 
        5.62        11.70         6.97         7.43        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        13.12         7.00 
TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12         0.62        32.78        13.84        13.22        16.14 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 
        1.25         8.98        21.11        30.90        32.94        12.82 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       24.76        23.93         0.69         0.16        18.54        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        0.95         0.69        12.76        18.71        17.49         0.82 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 
        1.32        12.26        20.55         0.72         0.26        16.31 
TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        1.55         6.18        19.50         0.36         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
        2.96         0.95        13.74         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 
        0.36        19.17        14.79         0.69         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         0.72         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         2.14        13.45         0.20         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        15.81         0.59        15.68         0.62 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56         1.15         0.66         3.02        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        0.92        13.41        13.51        12.89         0.79        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
        0.53        12.82         0.66        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8528 
       13.15         0.30         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.13         0.10         0.10         0.13         0.10         6.35 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        0.13         0.13         0.13         0.13         0.07         0.10 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
        0.10         0.10         3.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4455 
        8.05        54.08         4.01        14.01        47.05        12.03 
TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5719 
       21.99         9.01        18.97        22.98         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-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        79.07        65.10        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-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 
        5.95         4.14        15.98        12.79        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       24.72        19.50        17.19         0.23         6.97        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-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.44         2.96        15.65         4.34         7.40         7.13 
TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 
       16.24         6.58        14.47        21.27         8.12        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
        3.02        22.29        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 
        1.55         0.23        18.08        26.47         5.92        14.27 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 
       12.59        14.17        12.10        10.62        24.30         5.59 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       11.84         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-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-HU-A4HB 
        2.10        12.95        19.36        17.69         8.88         8.81 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RL 
       27.42        21.21         3.45        18.81         5.36         5.19 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU 
       13.08         1.41         6.74         6.87         5.56         1.81 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        2.53        60.56        28.90         3.72        19.73         4.31 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         4.67        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-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       16.87         5.79         0.92        37.74        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       31.10        22.36        23.77         7.73        19.07        33.63 
TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       16.31         2.70        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       15.65        19.30        23.57        59.18        28.70        11.70 
TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 
       49.25         1.71         7.36         8.58        44.25         8.61 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 
       55.43         6.58        40.08        29.98        21.11         4.21 
TCGA-ZQ-A9CR 
        0.79 

  AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE 
                           0.07                            0.07 
  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 
                          11.24                           11.77 
[1] "0.1 - 72.2 (11.2)"  "0.1 - 122.3 (11.8)"
[1] "hr=" "1.2"
D21V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 21(10Q26.13) MUTATED         0        6        7        8         5
  AMP PEAK 21(10Q26.13) WILD-TYPE       2        7       32       23        31
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 21(10Q26.13) MUTATED           9         0         19          8
  AMP PEAK 21(10Q26.13) WILD-TYPE        40         3         58         47
                                 vv
clus                              STAGE IIIC STAGE IV
  AMP PEAK 21(10Q26.13) MUTATED            5        9
  AMP PEAK 21(10Q26.13) WILD-TYPE         32       28
D21V3, multiclass
            clus
vv           AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE
  STAGE I                                0                               2
  STAGE IA                               6                               7
  STAGE IB                               7                              32
  STAGE II                               8                              23
  STAGE IIA                              5                              31
  STAGE IIB                              9                              40
  STAGE III                              0                               3
  STAGE IIIA                            19                              58
  STAGE IIIB                             8                              47
  STAGE IIIC                             5                              32
  STAGE IV                               9                              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 21(10Q26.13) MUTATED     7  19  34  16
  AMP PEAK 21(10Q26.13) WILD-TYPE  14  68 139  88
D21V4, multiclass
    clus
vv   AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE
  T1                             7                              14
  T2                            19                              68
  T3                            34                             139
  T4                            16                              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 21(10Q26.13) MUTATED   26 19 18 13
  AMP PEAK 21(10Q26.13) WILD-TYPE 96 88 57 66
D21V5, multiclass
    clus
vv   AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE
  N0                            26                              96
  N1                            19                              88
  N2                            18                              57
  N3                            13                              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"
                                 vv
clus                               M0  M1  MX
  AMP PEAK 21(10Q26.13) MUTATED    72   3   4
  AMP PEAK 21(10Q26.13) WILD-TYPE 281  21  14
D21V6, multiclass
    clus
vv   AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE
  M0                            72                             281
  M1                             3                              21
  MX                             4                              14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                                 cls
clus                                0   1
  AMP PEAK 21(10Q26.13) MUTATED    30  49
  AMP PEAK 21(10Q26.13) WILD-TYPE 121 195
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(10Q26.13) MUTATED     30   49
  AMP PEAK 21(10Q26.13) WILD-TYPE  121  195
        clus
vv       AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE
  FEMALE                            30                             121
  MALE                              49                             195
[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                                    56
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 21(10Q26.13) MUTATED                                                       29
  AMP PEAK 21(10Q26.13) WILD-TYPE                                                    128
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 21(10Q26.13) MUTATED                                                                  16
  AMP PEAK 21(10Q26.13) WILD-TYPE                                                                53
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 21(10Q26.13) MUTATED                                                 15
  AMP PEAK 21(10Q26.13) WILD-TYPE                                               49
                                 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                                          1
  AMP PEAK 21(10Q26.13) WILD-TYPE                                        8
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)                            16
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      1
                                                                   clus
vv                                                                  AMP PEAK 21(10Q26.13) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              53
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               49
  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"
D21V9, binary
                                 cls
clus                                0   1
  AMP PEAK 21(10Q26.13) MUTATED     2  77
  AMP PEAK 21(10Q26.13) WILD-TYPE   4 312
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(10Q26.13) MUTATED      2   77
  AMP PEAK 21(10Q26.13) WILD-TYPE    4  312
     clus
vv    AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE
  NO                              2                               4
  YES                            77                             312
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 21(10Q26.13) MUTATED    67   1   4   6
  AMP PEAK 21(10Q26.13) WILD-TYPE 251  15  14  19
D21V10, multiclass
    clus
vv   AMP PEAK 21(10Q26.13) MUTATED AMP PEAK 21(10Q26.13) WILD-TYPE
  R0                            67                             251
  R1                             1                              15
  R2                             4                              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"
D21V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 21(10Q26.13) MUTATED      16                         2
  AMP PEAK 21(10Q26.13) WILD-TYPE    72                         4
                                 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      47
  AMP PEAK 21(10Q26.13) WILD-TYPE   196
D21V12, multiclass
                                           clus
vv                                          AMP PEAK 21(10Q26.13) MUTATED
  ASIAN                                                                16
  BLACK OR AFRICAN AMERICAN                                             2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                47
                                           clus
vv                                          AMP PEAK 21(10Q26.13) WILD-TYPE
  ASIAN                                                                  72
  BLACK OR AFRICAN AMERICAN                                               4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  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"

Clustering(22) Variable = AMP PEAK 22(11P13) MUTATION ANALYSIS
D22V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 22(11P13) MUTATED    40  29
  AMP PEAK 22(11P13) WILD-TYPE 202  93
  AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE 
                          69                          295 
  AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE 
                          29                           93 
$`AMP PEAK 22(11P13) MUTATED`
TCGA-B7-5818 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-7717 
       11.70        13.12        10.13         7.00         0.82         0.69 
TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8296 TCGA-BR-8297 
        0.95         1.32         0.69         0.49         1.48         7.40 
TCGA-BR-8485 TCGA-BR-8590 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A453 
        9.21         2.14        11.54        15.68        12.56         3.02 
TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J2 TCGA-BR-A4J8 TCGA-CD-8525 TCGA-CD-8528 
       22.26        12.89        14.17        13.51         0.07         0.10 
TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-A487 TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4438 
        0.16         0.13         0.13         0.10        20.02        54.08 
TCGA-CG-4449 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5722 TCGA-D7-6822 TCGA-D7-8576 
       19.07        12.00         6.97         0.99        12.33         6.97 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A8CX 
        0.62         7.79         3.02        17.06         0.56         0.23 
TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-A4G2 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RI 
        5.92        14.17        24.30        27.42         3.45        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RO TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H 
        5.36         1.41         5.56         1.81         5.56        28.90 
TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-VQ-A8DU TCGA-VQ-A8DZ 
        8.61        16.67       115.69        57.44         5.46        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8PJ TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91X TCGA-VQ-A91Y 
       31.10         2.70        23.57        64.57         8.58         9.73 
TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-AA6B 
        8.61         4.54        29.98 

$`AMP PEAK 22(11P13) WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62         6.61         6.97         4.64         7.43        18.35 
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-6457 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.68        39.12         0.62        32.78        13.84        13.22 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       16.14         1.25         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-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 
       15.42        28.01         0.16        18.54        12.43         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 
       12.76        18.71        17.49         0.82        12.26        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        0.72         0.26        12.95         0.26        16.31         1.55 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        19.50         0.36         0.26        22.19         2.96 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        13.74         4.31        14.04         3.32         0.36 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       19.17        14.79         0.69         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        5.39         0.72        20.22         1.12        12.79        15.81 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       13.45         0.20         7.53         0.49        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CS 
        0.59         0.62        10.68         1.15         0.66         0.92 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J5 
       13.41        13.51         0.79         0.72         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-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.13         0.10         0.10         0.13         0.10         6.35 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.13         0.13         0.13         0.07         0.10         0.10 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 
        4.01        14.01        29.98        47.05        12.03        21.99 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5718 
        9.01        18.97         7.07        22.98        30.97         1.02 
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-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        55.04        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-D7-6526 
       18.84        18.54        18.61        17.85         5.95        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
        4.14        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-D7-8578 
       24.72        16.80        19.50        17.19         0.23        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-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        13.71        11.24        11.31        11.44         9.76 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-A4SO 
        2.96        15.65         4.34         7.40         7.13        16.24 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        6.58        14.47        72.23        21.27         8.12         0.39 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF 
       19.53        22.29        59.54         5.03        13.58         1.55 
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-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       12.10        10.62         0.76         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-A4H5 
        0.26         2.10        12.95        19.36        17.69        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 
        9.67         8.88         8.81        21.21        18.81         3.39 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IP-7968 
        5.19        13.08         6.44         6.74         6.87         2.53 
TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BW 
       60.56         3.72        19.73         4.31        11.05         4.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N6 
      122.30        37.91        40.64       116.38        71.38         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV 
       35.61        16.87         5.79         0.92        37.74        13.25 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        22.36        23.77         7.73        19.07        33.63 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       46.26        16.31        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       15.65        19.30        14.33        59.18        28.70        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Z 
        8.68        49.25        20.81         1.71         7.36        44.25 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6J TCGA-ZA-A8F6 
       55.43         6.58         5.72        40.08        21.11         4.21 
TCGA-ZQ-A9CR 
        0.79 

  AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE 
                        0.07                         0.07 
  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 
                        7.79                        12.26 
[1] "0.1 - 115.7 (7.8)"  "0.1 - 122.3 (12.3)"
[1] "hr=" "1.6"
D22V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 22(11P13) MUTATED         0        2        7        4         3
  AMP PEAK 22(11P13) WILD-TYPE       2       11       32       27        33
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 22(11P13) MUTATED          11         1         15          8
  AMP PEAK 22(11P13) WILD-TYPE        38         2         62         47
                              vv
clus                           STAGE IIIC STAGE IV
  AMP PEAK 22(11P13) MUTATED           10       12
  AMP PEAK 22(11P13) WILD-TYPE         27       25
D22V3, multiclass
            clus
vv           AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE
  STAGE I                             0                            2
  STAGE IA                            2                           11
  STAGE IB                            7                           32
  STAGE II                            4                           27
  STAGE IIA                           3                           33
  STAGE IIB                          11                           38
  STAGE III                           1                            2
  STAGE IIIA                         15                           62
  STAGE IIIB                          8                           47
  STAGE IIIC                         10                           27
  STAGE IV                           12                           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 22(11P13) MUTATED     4   9  36  25
  AMP PEAK 22(11P13) WILD-TYPE  17  78 137  79
D22V4, multiclass
    clus
vv   AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE
  T1                          4                           17
  T2                          9                           78
  T3                         36                          137
  T4                         25                           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 22(11P13) MUTATED    17  22  19  16
  AMP PEAK 22(11P13) WILD-TYPE 105  85  56  63
D22V5, multiclass
    clus
vv   AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE
  N0                         17                          105
  N1                         22                           85
  N2                         19                           56
  N3                         16                           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                            M0  M1  MX
  AMP PEAK 22(11P13) MUTATED    65   6   6
  AMP PEAK 22(11P13) WILD-TYPE 288  18  12
D22V6, multiclass
    clus
vv   AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE
  M0                         65                          288
  M1                          6                           18
  MX                          6                           12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                              cls
clus                             0   1
  AMP PEAK 22(11P13) MUTATED    24  53
  AMP PEAK 22(11P13) WILD-TYPE 127 191
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(11P13) MUTATED     24   53
  AMP PEAK 22(11P13) WILD-TYPE  127  191
        clus
vv       AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE
  FEMALE                         24                          127
  MALE                           53                          191
[1] 2 2
[1] FALSE
                              vv
clus                           STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 22(11P13) MUTATED                                      12
  AMP PEAK 22(11P13) WILD-TYPE                                    53
                              vv
clus                           STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 22(11P13) MUTATED                                                       31
  AMP PEAK 22(11P13) WILD-TYPE                                                    126
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 22(11P13) MUTATED                                                                  11
  AMP PEAK 22(11P13) WILD-TYPE                                                                58
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 22(11P13) MUTATED                                                 14
  AMP PEAK 22(11P13) WILD-TYPE                                               50
                              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                                          3
  AMP PEAK 22(11P13) WILD-TYPE                                        6
D22V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 22(11P13) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    31
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                          14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                  0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   3
                                                                   clus
vv                                                                  AMP PEAK 22(11P13) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       53
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           58
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            50
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    8
  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"
D22V9, binary
                              cls
clus                             0   1
  AMP PEAK 22(11P13) MUTATED     2  75
  AMP PEAK 22(11P13) WILD-TYPE   4 314
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(11P13) MUTATED      2   75
  AMP PEAK 22(11P13) WILD-TYPE    4  314
     clus
vv    AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE
  NO                           2                            4
  YES                         75                          314
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 22(11P13) MUTATED    57   3   7   5
  AMP PEAK 22(11P13) WILD-TYPE 261  13  11  20
D22V10, multiclass
    clus
vv   AMP PEAK 22(11P13) MUTATED AMP PEAK 22(11P13) WILD-TYPE
  R0                         57                          261
  R1                          3                           13
  R2                          7                           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"
D22V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 22(11P13) MUTATED      18                         1
  AMP PEAK 22(11P13) WILD-TYPE    70                         5
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 22(11P13) MUTATED                                           1    45
  AMP PEAK 22(11P13) WILD-TYPE                                         0   198
D22V12, multiclass
                                           clus
vv                                          AMP PEAK 22(11P13) MUTATED
  ASIAN                                                             18
  BLACK OR AFRICAN AMERICAN                                          1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                             45
                                           clus
vv                                          AMP PEAK 22(11P13) WILD-TYPE
  ASIAN                                                               70
  BLACK OR AFRICAN AMERICAN                                            5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              198
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = AMP PEAK 23(11P11.2) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 23(11P11.2) MUTATED    42  30
  AMP PEAK 23(11P11.2) WILD-TYPE 200  92
  AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE 
                            72                            292 
  AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE 
                            30                             92 
$`AMP PEAK 23(11P11.2) MUTATED`
TCGA-BR-4183 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-7717 TCGA-BR-7901 
        6.61        13.12        10.13         7.00         0.69         0.95 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8296 TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8686 
        1.32         0.69         1.48         9.21        11.54        15.68 
TCGA-BR-8687 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J8 TCGA-CD-8525 
        0.62        22.26         0.92        12.89        13.51         0.07 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-A487 TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4438 
        0.10         0.16         0.13         0.10        20.02        54.08 
TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5722 TCGA-D7-6520 
        4.01        47.05        12.00         6.97         0.99        18.84 
TCGA-D7-6822 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A6F2 TCGA-EQ-8122 
       12.33         6.97        21.14        14.27        15.65         7.79 
TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HU-8243 TCGA-HU-8249 
        3.02        17.06         0.56         0.23         5.92        14.17 
TCGA-HU-A4G2 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RJ 
       24.30        12.30        27.42         3.45        18.38         5.36 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H 
       13.08         1.41         5.56         1.81         5.56        28.90 
TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-VQ-A8DU TCGA-VQ-A8DZ 
        8.61        16.67       115.69         8.94         5.46        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8PJ TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91E 
       31.10         2.70        23.57        64.57        14.33         8.68 
TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-AA6B 
        1.71         8.58         9.73         8.61         4.54        29.98 

$`AMP PEAK 23(11P11.2) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
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-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.68        39.12         0.82         0.62        32.78        13.84 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       13.22        16.14         1.25         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-7722 TCGA-BR-7723 TCGA-BR-7851 
       23.93        15.42        28.01         0.16        18.54        12.43 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 
        0.69        12.76        18.71        17.49         0.82        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.49        20.55         0.72         0.26        12.95         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       16.31         1.55         7.40         6.18        19.50         0.36 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19         2.96         0.95        13.74         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 
       14.04         3.32         0.36        19.17        14.79         0.69 
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         0.72        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         2.14        13.45         0.20 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 
        7.53         0.49        15.81        16.44         0.59        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
       12.56         1.15         0.66         3.02        13.41        13.51 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        0.79         0.72        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36         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-8526 TCGA-CD-8527 TCGA-CD-8529 
        0.30         0.07         0.07         0.07         0.07         0.13 
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         6.35 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.13         0.13         0.13         0.07         0.10         0.10 
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-4455 TCGA-CG-4460 TCGA-CG-4465 
       14.01        29.98        19.07        12.03        21.99         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        22.98        30.97         1.02         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-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        55.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 
       12.36        12.66        11.93        19.13        20.55        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85         5.95        17.19         4.14        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 
       15.98        12.79        10.55        11.31        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV 
       19.50        17.19         0.23        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-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.44         9.76         2.96         4.34         7.40         7.13 
TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62        16.24         6.58        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
        8.12         0.39        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         1.55        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-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 
       17.69         9.67         8.88         8.81        21.21        18.81 
TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IP-7968 
        3.39         5.19         6.44         6.74         6.87         2.53 
TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BW 
       60.56         3.72        19.73         4.31        11.05         4.67 
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-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV 
       35.61        16.87         5.79         0.92        37.74        13.25 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        22.36        23.77         7.73        19.07        33.63 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       46.26        16.31        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K 
       15.65        19.30        59.18        28.70        11.70        49.25 
TCGA-VQ-A91Q TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
       20.81         7.36        44.25        55.43         6.58         5.72 
TCGA-VQ-AA68 TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       40.08        21.11         4.21         0.79 

  AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE 
                          0.07                           0.07 
  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 
                         8.645                         12.030 
[1] "0.1 - 115.7 (8.6)"  "0.1 - 122.3 (12.0)"
[1] "hr=" "1.5"
D23V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 23(11P11.2) MUTATED         0        2        9        2         2
  AMP PEAK 23(11P11.2) WILD-TYPE       2       11       30       29        34
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 23(11P11.2) MUTATED          10         1         19         10
  AMP PEAK 23(11P11.2) WILD-TYPE        39         2         58         45
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 23(11P11.2) MUTATED           10       11
  AMP PEAK 23(11P11.2) WILD-TYPE         27       26
D23V3, multiclass
            clus
vv           AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              2                             11
  STAGE IB                              9                             30
  STAGE II                              2                             29
  STAGE IIA                             2                             34
  STAGE IIB                            10                             39
  STAGE III                             1                              2
  STAGE IIIA                           19                             58
  STAGE IIIB                           10                             45
  STAGE IIIC                           10                             27
  STAGE IV                             11                             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 23(11P11.2) MUTATED     5  14  36  22
  AMP PEAK 23(11P11.2) WILD-TYPE  16  73 137  82
D23V4, multiclass
    clus
vv   AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE
  T1                            5                             16
  T2                           14                             73
  T3                           36                            137
  T4                           22                             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 23(11P11.2) MUTATED    17  22  22  16
  AMP PEAK 23(11P11.2) WILD-TYPE 105  85  53  63
D23V5, multiclass
    clus
vv   AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE
  N0                           17                            105
  N1                           22                             85
  N2                           22                             53
  N3                           16                             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                              M0  M1  MX
  AMP PEAK 23(11P11.2) MUTATED    69   5   6
  AMP PEAK 23(11P11.2) WILD-TYPE 284  19  12
D23V6, multiclass
    clus
vv   AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE
  M0                           69                            284
  M1                            5                             19
  MX                            6                             12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                                cls
clus                               0   1
  AMP PEAK 23(11P11.2) MUTATED    27  53
  AMP PEAK 23(11P11.2) WILD-TYPE 124 191
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(11P11.2) MUTATED     27   53
  AMP PEAK 23(11P11.2) WILD-TYPE  124  191
        clus
vv       AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE
  FEMALE                           27                            124
  MALE                             53                            191
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 23(11P11.2) MUTATED                                       8
  AMP PEAK 23(11P11.2) WILD-TYPE                                    57
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 23(11P11.2) MUTATED                                                       33
  AMP PEAK 23(11P11.2) WILD-TYPE                                                    124
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 23(11P11.2) MUTATED                                                                  14
  AMP PEAK 23(11P11.2) WILD-TYPE                                                                55
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 23(11P11.2) MUTATED                                                 19
  AMP PEAK 23(11P11.2) WILD-TYPE                                               45
                                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                                          2
  AMP PEAK 23(11P11.2) WILD-TYPE                                        7
D23V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 23(11P11.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      33
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
                                                                   clus
vv                                                                  AMP PEAK 23(11P11.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         57
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             55
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              45
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      7
  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"
D23V9, binary
                                cls
clus                               0   1
  AMP PEAK 23(11P11.2) MUTATED     2  78
  AMP PEAK 23(11P11.2) WILD-TYPE   4 311
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(11P11.2) MUTATED      2   78
  AMP PEAK 23(11P11.2) WILD-TYPE    4  311
     clus
vv    AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE
  NO                             2                              4
  YES                           78                            311
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 23(11P11.2) MUTATED    58   4   7   6
  AMP PEAK 23(11P11.2) WILD-TYPE 260  12  11  19
D23V10, multiclass
    clus
vv   AMP PEAK 23(11P11.2) MUTATED AMP PEAK 23(11P11.2) WILD-TYPE
  R0                           58                            260
  R1                            4                             12
  R2                            7                             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"
D23V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 23(11P11.2) MUTATED      17                         1
  AMP PEAK 23(11P11.2) WILD-TYPE    71                         5
                                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      48
  AMP PEAK 23(11P11.2) WILD-TYPE   195
D23V12, multiclass
                                           clus
vv                                          AMP PEAK 23(11P11.2) MUTATED
  ASIAN                                                               17
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               48
                                           clus
vv                                          AMP PEAK 23(11P11.2) WILD-TYPE
  ASIAN                                                                 71
  BLACK OR AFRICAN AMERICAN                                              5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                195
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = AMP PEAK 24(11Q13.3) MUTATION ANALYSIS
D24V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 24(11Q13.3) MUTATED    58  32
  AMP PEAK 24(11Q13.3) WILD-TYPE 184  90
  AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE 
                            90                            274 
  AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE 
                            32                             90 
$`AMP PEAK 24(11Q13.3) MUTATED`
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-7704 TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-8058 
       13.12        13.68        35.24         0.69         0.95        17.49 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8296 TCGA-BR-8361 TCGA-BR-8365 
        1.32         0.69         0.49         1.48        19.50         2.96 
TCGA-BR-8485 TCGA-BR-8589 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A4CQ 
        9.21        15.81        11.54        15.68         0.62        22.26 
TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-8525 
        0.92        12.89         1.15        13.64         3.25         0.07 
TCGA-CD-8528 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-A487 TCGA-CD-A48C TCGA-CD-A4MH 
        0.10         0.10         0.13         0.13         0.13         0.10 
TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4472 
       20.02        54.08        47.05        19.07        12.03        12.00 
TCGA-CG-5722 TCGA-CG-5724 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A6EV TCGA-D7-A6F0 
        0.99        12.03         0.23         6.97        11.24         2.96 
TCGA-D7-A6F2 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-8099 TCGA-FP-8631 TCGA-HU-8243 
       15.65         7.79        72.23        17.06         0.56         5.92 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4GC TCGA-HU-A4GY TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.76        24.30         3.25         0.26        17.69        12.30 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO 
        9.67        27.42         3.39         5.36         5.19         1.41 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H 
        6.44         6.74         5.56         1.81         5.56        28.90 
TCGA-MX-A663 TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N5 
        4.31         8.61        16.67       122.30       115.69        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8PJ 
        8.94        35.61         5.46        13.02        31.10         2.70 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91U 
       23.57        64.57        14.33        28.70         8.68         1.71 
TCGA-VQ-A91Y TCGA-VQ-A925 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZQ-A9CR 
        9.73         4.54        40.08        29.98        21.11         0.79 

$`AMP PEAK 24(11Q13.3) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         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-6456 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       15.95        10.13         7.00        39.12         0.82         0.62 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        13.84        13.22        16.14         1.25         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-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       24.76        23.93        15.42        28.01         0.16        18.54 
TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8078 
       12.43         0.69        12.76        18.71         0.82        12.26 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       20.55         0.72         0.26        12.95         0.26        16.31 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        1.55         7.40         6.18         0.36         0.26        22.19 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        13.74         4.31        14.04         3.32         0.36 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       19.17        14.79         0.69         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 
        5.39         0.72        20.22         1.12        12.79         2.14 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       13.45         0.20         7.53         0.49        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        0.59        10.68        12.56         1.15         0.66         3.02 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51         0.79         0.72        14.17         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-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 
       20.42        11.57         5.13         2.83        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 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-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 
        0.16         0.10         0.13         0.10         6.35         0.13 
TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
        0.13         0.07         0.10         0.10         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-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       29.98        21.99         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97         1.02         1.02         0.99         6.02 
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 
       55.04        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 
        5.95        17.19         4.14        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-A6EX TCGA-D7-A6EY 
       15.16        13.78        14.76        13.71        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO 
        9.76         4.34         7.40         7.13         0.62        16.24 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        6.58        14.47        21.27         8.12         0.39        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF 
        3.02        22.29        59.54         5.03        13.58         1.55 
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-A4G3 TCGA-HU-A4G6 
       14.17        11.41        12.10        10.62         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       11.84        24.20        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-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-A6RN TCGA-IN-A6RS TCGA-IP-7968 
        3.45        18.81        18.38        13.08         6.87         2.53 
TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MW 
       60.56         3.72        19.73        11.05         4.67        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-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       37.74        13.25        21.73        22.36        23.77         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PK TCGA-VQ-A8PM 
       19.07        33.63        46.26        16.31        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91D 
        9.27        23.41        15.65        19.30        59.18        11.70 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 
       49.25        20.81         7.36         8.58        44.25         8.61 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-ZA-A8F6 
       55.43         6.58         5.72         4.21 

  AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE 
                          0.07                           0.07 
  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 
                          8.81                          12.18 
[1] "0.1 - 122.3 (8.8)"  "0.1 - 116.4 (12.2)"
[1] "hr=" "1.1"
D24V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 24(11Q13.3) MUTATED         1        4        7        8         7
  AMP PEAK 24(11Q13.3) WILD-TYPE       1        9       32       23        29
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 24(11Q13.3) MUTATED          12         0         21         15
  AMP PEAK 24(11Q13.3) WILD-TYPE        37         3         56         40
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 24(11Q13.3) MUTATED           13       10
  AMP PEAK 24(11Q13.3) WILD-TYPE         24       27
D24V3, multiclass
            clus
vv           AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                              4                              9
  STAGE IB                              7                             32
  STAGE II                              8                             23
  STAGE IIA                             7                             29
  STAGE IIB                            12                             37
  STAGE III                             0                              3
  STAGE IIIA                           21                             56
  STAGE IIIB                           15                             40
  STAGE IIIC                           13                             24
  STAGE IV                             10                             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 24(11Q13.3) MUTATED     6  19  44  30
  AMP PEAK 24(11Q13.3) WILD-TYPE  15  68 129  74
D24V4, multiclass
    clus
vv   AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE
  T1                            6                             15
  T2                           19                             68
  T3                           44                            129
  T4                           30                             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
  AMP PEAK 24(11Q13.3) MUTATED   26 27 30 16
  AMP PEAK 24(11Q13.3) WILD-TYPE 96 80 45 63
D24V5, multiclass
    clus
vv   AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE
  N0                           26                             96
  N1                           27                             80
  N2                           30                             45
  N3                           16                             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                              M0  M1  MX
  AMP PEAK 24(11Q13.3) MUTATED    94   4   5
  AMP PEAK 24(11Q13.3) WILD-TYPE 259  20  13
D24V6, multiclass
    clus
vv   AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE
  M0                           94                            259
  M1                            4                             20
  MX                            5                             13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                                cls
clus                               0   1
  AMP PEAK 24(11Q13.3) MUTATED    36  67
  AMP PEAK 24(11Q13.3) WILD-TYPE 115 177
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(11Q13.3) MUTATED     36   67
  AMP PEAK 24(11Q13.3) WILD-TYPE  115  177
        clus
vv       AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE
  FEMALE                           36                            115
  MALE                             67                            177
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 24(11Q13.3) MUTATED                                      11
  AMP PEAK 24(11Q13.3) WILD-TYPE                                    54
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 24(11Q13.3) MUTATED                                                       44
  AMP PEAK 24(11Q13.3) WILD-TYPE                                                    113
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 24(11Q13.3) MUTATED                                                                  18
  AMP PEAK 24(11Q13.3) WILD-TYPE                                                                51
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 24(11Q13.3) MUTATED                                                 20
  AMP PEAK 24(11Q13.3) WILD-TYPE                                               44
                                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                                          1
  AMP PEAK 24(11Q13.3) WILD-TYPE                                        8
D24V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 24(11Q13.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       11
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      44
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           18
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     1
                                                                   clus
vv                                                                  AMP PEAK 24(11Q13.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         54
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       113
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             51
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              44
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      14
  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"
D24V9, binary
                                cls
clus                               0   1
  AMP PEAK 24(11Q13.3) MUTATED     2 101
  AMP PEAK 24(11Q13.3) WILD-TYPE   4 288
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(11Q13.3) MUTATED      2  101
  AMP PEAK 24(11Q13.3) WILD-TYPE    4  288
     clus
vv    AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE
  NO                             2                              4
  YES                          101                            288
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 24(11Q13.3) MUTATED    81   4   7   6
  AMP PEAK 24(11Q13.3) WILD-TYPE 237  12  11  19
D24V10, multiclass
    clus
vv   AMP PEAK 24(11Q13.3) MUTATED AMP PEAK 24(11Q13.3) WILD-TYPE
  R0                           81                            237
  R1                            4                             12
  R2                            7                             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"
D24V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 24(11Q13.3) MUTATED      25                         3
  AMP PEAK 24(11Q13.3) WILD-TYPE    63                         3
                                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      59
  AMP PEAK 24(11Q13.3) WILD-TYPE   184
D24V12, multiclass
                                           clus
vv                                          AMP PEAK 24(11Q13.3) MUTATED
  ASIAN                                                               25
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               59
                                           clus
vv                                          AMP PEAK 24(11Q13.3) WILD-TYPE
  ASIAN                                                                 63
  BLACK OR AFRICAN AMERICAN                                              3
  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"

Clustering(25) Variable = AMP PEAK 25(12P12.1) MUTATION ANALYSIS
D25V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 25(12P12.1) MUTATED    71  35
  AMP PEAK 25(12P12.1) WILD-TYPE 171  87
  AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE 
                           106                            258 
  AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE 
                            35                             87 
$`AMP PEAK 25(12P12.1) MUTATED`
TCGA-BR-4183 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6709 TCGA-BR-6801 
        6.61        39.12        32.78        13.84         1.25        21.11 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8078 TCGA-BR-8295 TCGA-BR-8297 
       18.54         0.95        18.71        12.26         1.55         7.40 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8369 TCGA-BR-8370 
       19.50         0.36         0.26         0.95        14.04         3.32 
TCGA-BR-8381 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8678 TCGA-BR-8687 TCGA-BR-A452 
        0.26        20.22        15.81        11.54         0.62         0.66 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4PF TCGA-CD-5798 
       22.26         0.92         0.72        14.17         1.15         2.83 
TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 
        3.25         0.30         0.07         0.07         0.07         0.16 
TCGA-CD-8531 TCGA-CD-A48A TCGA-CD-A48C TCGA-CG-4300 TCGA-CG-4444 TCGA-CG-4460 
        0.10         0.13         0.13        20.02        47.05        21.99 
TCGA-CG-4472 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5727 TCGA-D7-5578 TCGA-D7-6518 
       12.00         0.99        12.03        79.07        12.66        19.13 
TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8573 
       20.55        18.54        17.19        12.79        11.31        19.50 
TCGA-D7-8575 TCGA-D7-A4YV TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A 
        0.23         5.92        11.31         2.96        15.65         7.40 
TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
        0.62        16.24         8.12         0.39        19.53        22.29 
TCGA-FP-A4BF TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4GC 
        1.55         1.51        14.17        12.10        24.30         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       22.75        25.81         8.98         6.51         6.25        10.19 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RP 
        8.81        27.42         3.45         3.39         5.36         6.44 
TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-RD-A7BS 
        6.74         1.81         2.53        60.56        28.90        11.05 
TCGA-RD-A7C1 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV 
       16.67         8.94         5.79         0.92        37.74        13.25 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PK TCGA-VQ-A8PY TCGA-VQ-A91A 
       31.10        21.73         7.73        17.85        14.33        28.70 
TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A925 TCGA-VQ-A928 
        8.68        20.81         4.54         5.72 

$`AMP PEAK 25(12P12.1) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
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-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 
       13.12        10.13        13.68         7.00         0.82         0.62 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       13.22        16.14         8.98        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-7851 TCGA-BR-7957 TCGA-BR-7958 
       28.01         0.69         0.16        12.43         0.69        12.76 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       17.49         0.82         1.32         0.69         0.49        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 
        0.72         0.26        12.95         0.26        16.31         1.48 
TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8371 
        6.18        22.19         2.96        13.74         4.31         0.36 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.69        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
        0.72         9.21         1.12        12.79         2.14        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        0.20         7.53         0.49        15.81        16.44         0.59 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU 
       15.68        10.68        12.56         1.15         3.02        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       13.51        12.89         0.79         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI 
       19.36        13.51         0.46        20.65        20.42        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8525 
       11.57         5.13        13.15        13.18         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.10         0.13         0.10         0.13         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        6.35         0.13         0.13         0.07         0.10         0.10 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
        0.10         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
       12.03         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 
        6.97         1.02         1.02         0.99         6.02       105.07 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
        7.99        12.36        11.93        18.84        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6822 
        5.95         4.14        15.22        15.98        10.55        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       24.72        16.80        17.19         6.97        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44        15.16        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 
       11.24        11.44         9.76         4.34         7.13         7.79 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7916 TCGA-FP-8099 
        6.58        14.47        72.23        21.27         3.02        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HF-A5NB 
       59.54         5.03        13.58         0.56         0.23        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-A4GH 
        0.76         5.59        12.30        11.84        24.20        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
       21.37        29.98         0.10         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-IN-7806 
       19.36        17.69        12.30         9.67         8.88        21.21 
TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RS 
       18.81        18.38         5.19        13.08         1.41         6.87 
TCGA-IN-A7NT TCGA-KB-A6F5 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BT 
        5.56         5.56         3.72        19.73         4.31         8.61 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        4.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A8DU TCGA-VQ-A8DZ 
       71.38        57.44        35.61        16.87         5.46        13.02 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       22.36        23.77        19.07        33.63        46.26        16.31 
TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
        2.70         1.87         9.27        23.41        15.65        19.30 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91U 
       23.57        64.57        59.18        11.70        49.25         1.71 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 
        7.36         8.58         9.73        44.25         8.61        55.43 
TCGA-VQ-A927 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        6.58        40.08        29.98        21.11         4.21         0.79 

  AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE 
                          0.07                           0.07 
  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 
                         8.960                         12.165 
[1] "0.1 - 79.1 (9.0)"   "0.1 - 122.3 (12.2)"
[1] "hr=" "1.1"
D25V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 25(12P12.1) MUTATED         0        1       10        7        14
  AMP PEAK 25(12P12.1) WILD-TYPE       2       12       29       24        22
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 25(12P12.1) MUTATED          16         1         26         19
  AMP PEAK 25(12P12.1) WILD-TYPE        33         2         51         36
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 25(12P12.1) MUTATED           10        9
  AMP PEAK 25(12P12.1) WILD-TYPE         27       28
D25V3, multiclass
            clus
vv           AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              1                             12
  STAGE IB                             10                             29
  STAGE II                              7                             24
  STAGE IIA                            14                             22
  STAGE IIB                            16                             33
  STAGE III                             1                              2
  STAGE IIIA                           26                             51
  STAGE IIIB                           19                             36
  STAGE IIIC                           10                             27
  STAGE IV                              9                             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 25(12P12.1) MUTATED     4  20  64  25
  AMP PEAK 25(12P12.1) WILD-TYPE  17  67 109  79
D25V4, multiclass
    clus
vv   AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE
  T1                            4                             17
  T2                           20                             67
  T3                           64                            109
  T4                           25                             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 25(12P12.1) MUTATED   32 32 28 22
  AMP PEAK 25(12P12.1) WILD-TYPE 90 75 47 57
D25V5, multiclass
    clus
vv   AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE
  N0                           32                             90
  N1                           32                             75
  N2                           28                             47
  N3                           22                             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"
                                vv
clus                              M0  M1  MX
  AMP PEAK 25(12P12.1) MUTATED   104   6   4
  AMP PEAK 25(12P12.1) WILD-TYPE 249  18  14
D25V6, multiclass
    clus
vv   AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE
  M0                          104                            249
  M1                            6                             18
  MX                            4                             14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                                cls
clus                               0   1
  AMP PEAK 25(12P12.1) MUTATED    42  72
  AMP PEAK 25(12P12.1) WILD-TYPE 109 172
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(12P12.1) MUTATED     42   72
  AMP PEAK 25(12P12.1) WILD-TYPE  109  172
        clus
vv       AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE
  FEMALE                           42                            109
  MALE                             72                            172
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 25(12P12.1) MUTATED                                      21
  AMP PEAK 25(12P12.1) WILD-TYPE                                    44
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 25(12P12.1) MUTATED                                                       45
  AMP PEAK 25(12P12.1) WILD-TYPE                                                    112
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 25(12P12.1) MUTATED                                                                  16
  AMP PEAK 25(12P12.1) WILD-TYPE                                                                53
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 25(12P12.1) MUTATED                                                 24
  AMP PEAK 25(12P12.1) WILD-TYPE                                               40
                                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                                          1
  AMP PEAK 25(12P12.1) WILD-TYPE                                        8
D25V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 25(12P12.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       21
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      45
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           16
  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                                                     1
                                                                   clus
vv                                                                  AMP PEAK 25(12P12.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         44
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       112
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             53
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              40
  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"
D25V9, binary
                                cls
clus                               0   1
  AMP PEAK 25(12P12.1) MUTATED     2 112
  AMP PEAK 25(12P12.1) WILD-TYPE   4 277
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(12P12.1) MUTATED      2  112
  AMP PEAK 25(12P12.1) WILD-TYPE    4  277
     clus
vv    AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE
  NO                             2                              4
  YES                          112                            277
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 25(12P12.1) MUTATED    93   5   6   4
  AMP PEAK 25(12P12.1) WILD-TYPE 225  11  12  21
D25V10, multiclass
    clus
vv   AMP PEAK 25(12P12.1) MUTATED AMP PEAK 25(12P12.1) WILD-TYPE
  R0                           93                            225
  R1                            5                             11
  R2                            6                             12
  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                         1
  AMP PEAK 25(12P12.1) WILD-TYPE    59                         5
                                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      72
  AMP PEAK 25(12P12.1) WILD-TYPE   171
D25V12, multiclass
                                           clus
vv                                          AMP PEAK 25(12P12.1) MUTATED
  ASIAN                                                               29
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               72
                                           clus
vv                                          AMP PEAK 25(12P12.1) WILD-TYPE
  ASIAN                                                                 59
  BLACK OR AFRICAN AMERICAN                                              5
  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"

Clustering(26) Variable = AMP PEAK 26(12Q15) MUTATION ANALYSIS
D26V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 26(12Q15) MUTATED    62  31
  AMP PEAK 26(12Q15) WILD-TYPE 180  91
  AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE 
                          93                          271 
  AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE 
                          31                           91 
$`AMP PEAK 26(12Q15) MUTATED`
TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-7723 
        6.61        18.35         6.18        39.12        32.78        18.54 
TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8295 TCGA-BR-8297 
       18.71         1.32         0.69        12.26         1.55         7.40 
TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8370 TCGA-BR-8381 TCGA-BR-8484 TCGA-BR-8589 
        0.26         0.95         3.32         0.26         0.72        15.81 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A4CS TCGA-BR-A4J1 
       15.68         0.62        12.56         0.66         0.92         0.72 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5802 
        0.53         0.66         1.15         2.83         3.25         0.30 
TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A48A 
        0.07         0.16         0.10         0.13         0.13         0.13 
TCGA-CG-4301 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-4475 
        3.02        47.05        12.03        21.99        12.00        22.98 
TCGA-CG-5722 TCGA-CG-5725 TCGA-CG-5727 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6518 
        0.99        15.02        79.07        55.04        12.66        19.13 
TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-8573 
       20.55        18.54        17.19         4.14        12.79        19.50 
TCGA-D7-A4YV TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-F1-A72C TCGA-FP-7916 
        5.92        15.65         7.40         0.62         8.12         3.02 
TCGA-FP-7998 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8604 
       22.29         1.55         0.23         1.51        14.17        12.10 
TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       24.30        22.75         8.98         6.51         6.25        10.19 
TCGA-HU-A4H4 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN 
       17.69        27.42         3.45         3.39         5.36        13.08 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-KB-A6F7 TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-VQ-A8E2 
        1.41         6.44        60.56         4.67        16.67        31.10 
TCGA-VQ-A8P5 TCGA-VQ-A8PJ TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A91X 
        7.73         2.70        14.33         8.68        20.81         8.58 
TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A928 
        8.61         4.54         5.72 

$`AMP PEAK 26(12Q15) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
        5.62        11.70         6.97         4.64         7.43        30.90 
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        13.12        10.13 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 
       13.68         7.00         0.82         0.62        13.84        13.22 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       16.14         1.25         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         0.69         0.16        12.43         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8081 
        0.69        12.76        17.49         0.82         0.49        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 
        0.72         0.26        12.95         0.26        16.31         1.48 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 
        6.18        19.50         0.36        22.19         2.96        13.74 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 
        4.31        14.04         0.36        19.17        14.79         0.69 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
       15.85         3.72         5.39         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79         2.14        13.45         0.20         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44U 
       11.54        15.81        16.44         0.59        10.68         1.15 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        3.02        22.26        13.41        13.51        12.89         0.79 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
       14.17        12.82        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-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48C 
        0.10         0.13         0.10         6.35         0.13         0.13 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 
        0.07         0.10         0.10         0.10        20.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       14.01        29.98        19.07         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97         1.02         1.02         0.99         6.02 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 
      105.07        12.03        28.96        65.10         4.01        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
        7.99        12.36        11.93        18.84        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
        5.95        15.22        15.98        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       24.72        16.80        17.19         0.23         6.97        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27        16.44        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-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 
        4.34         7.13         7.79        16.24         6.58        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8209 
       72.23        21.27         0.39        19.53        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 
        5.03        13.58         0.56        18.08        26.47         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 
       14.27        12.59        11.41        10.62         0.76         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-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
       21.37        29.98         0.10         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       19.36        12.30         9.67         8.88         8.81        21.21 
TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT 
       18.81        18.38         5.19         6.74         6.87         5.56 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        1.81         2.53         5.56        28.90         3.72        19.73 
TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        4.31        11.05         8.61       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-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       16.87         5.79         0.92        37.74         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       13.02        21.73        22.36        23.77        19.07        33.63 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       46.26        16.31        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        19.30        23.57        64.57        59.18        28.70 
TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z 
       11.70        49.25         1.71         7.36         9.73        44.25 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 
       55.43         6.58        40.08        29.98        21.11         4.21 
TCGA-ZQ-A9CR 
        0.79 

  AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE 
                        0.07                         0.07 
  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 
                        7.40                        12.33 
[1] "0.1 - 79.1 (7.4)"   "0.1 - 122.3 (12.3)"
[1] "hr=" "1.2"
D26V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 26(12Q15) MUTATED         0        1        9        7        12
  AMP PEAK 26(12Q15) WILD-TYPE       2       12       30       24        24
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 26(12Q15) MUTATED          13         1         19         13
  AMP PEAK 26(12Q15) WILD-TYPE        36         2         58         42
                              vv
clus                           STAGE IIIC STAGE IV
  AMP PEAK 26(12Q15) MUTATED            9       12
  AMP PEAK 26(12Q15) WILD-TYPE         28       25
D26V3, multiclass
            clus
vv           AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE
  STAGE I                             0                            2
  STAGE IA                            1                           12
  STAGE IB                            9                           30
  STAGE II                            7                           24
  STAGE IIA                          12                           24
  STAGE IIB                          13                           36
  STAGE III                           1                            2
  STAGE IIIA                         19                           58
  STAGE IIIB                         13                           42
  STAGE IIIC                          9                           28
  STAGE IV                           12                           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 26(12Q15) MUTATED     5  20  44  27
  AMP PEAK 26(12Q15) WILD-TYPE  16  67 129  77
D26V4, multiclass
    clus
vv   AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE
  T1                          5                           16
  T2                         20                           67
  T3                         44                          129
  T4                         27                           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 26(12Q15) MUTATED   27 30 24 16
  AMP PEAK 26(12Q15) WILD-TYPE 95 77 51 63
D26V5, multiclass
    clus
vv   AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE
  N0                         27                           95
  N1                         30                           77
  N2                         24                           51
  N3                         16                           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                            M0  M1  MX
  AMP PEAK 26(12Q15) MUTATED    87   7   4
  AMP PEAK 26(12Q15) WILD-TYPE 266  17  14
D26V6, multiclass
    clus
vv   AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE
  M0                         87                          266
  M1                          7                           17
  MX                          4                           14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                              cls
clus                             0   1
  AMP PEAK 26(12Q15) MUTATED    35  63
  AMP PEAK 26(12Q15) WILD-TYPE 116 181
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(12Q15) MUTATED     35   63
  AMP PEAK 26(12Q15) WILD-TYPE  116  181
        clus
vv       AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE
  FEMALE                         35                          116
  MALE                           63                          181
[1] 2 2
[1] FALSE
                              vv
clus                           STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 26(12Q15) MUTATED                                      20
  AMP PEAK 26(12Q15) WILD-TYPE                                    45
                              vv
clus                           STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 26(12Q15) MUTATED                                                       35
  AMP PEAK 26(12Q15) WILD-TYPE                                                    122
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 26(12Q15) MUTATED                                                                  11
  AMP PEAK 26(12Q15) WILD-TYPE                                                                58
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 26(12Q15) MUTATED                                                 23
  AMP PEAK 26(12Q15) WILD-TYPE                                               41
                              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                                          2
  AMP PEAK 26(12Q15) WILD-TYPE                                        7
D26V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 26(12Q15) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     20
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    35
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                          23
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                  2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   2
                                                                   clus
vv                                                                  AMP PEAK 26(12Q15) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       45
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     122
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           58
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            41
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    18
  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"
D26V9, binary
                              cls
clus                             0   1
  AMP PEAK 26(12Q15) MUTATED     2  96
  AMP PEAK 26(12Q15) WILD-TYPE   4 293
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(12Q15) MUTATED      2   96
  AMP PEAK 26(12Q15) WILD-TYPE    4  293
     clus
vv    AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE
  NO                           2                            4
  YES                         96                          293
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 26(12Q15) MUTATED    76   3   7   5
  AMP PEAK 26(12Q15) WILD-TYPE 242  13  11  20
D26V10, multiclass
    clus
vv   AMP PEAK 26(12Q15) MUTATED AMP PEAK 26(12Q15) WILD-TYPE
  R0                         76                          242
  R1                          3                           13
  R2                          7                           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"
D26V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 26(12Q15) MUTATED      28                         0
  AMP PEAK 26(12Q15) WILD-TYPE    60                         6
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 26(12Q15) MUTATED                                           0    54
  AMP PEAK 26(12Q15) WILD-TYPE                                         1   189
D26V12, multiclass
                                           clus
vv                                          AMP PEAK 26(12Q15) MUTATED
  ASIAN                                                             28
  BLACK OR AFRICAN AMERICAN                                          0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          0
  WHITE                                                             54
                                           clus
vv                                          AMP PEAK 26(12Q15) WILD-TYPE
  ASIAN                                                               60
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              189
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = AMP PEAK 27(13Q12.3) MUTATION ANALYSIS
D27V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 27(13Q12.3) MUTATED    96  45
  AMP PEAK 27(13Q12.3) WILD-TYPE 146  77
  AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE 
                           141                            223 
  AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE 
                            45                             77 
$`AMP PEAK 27(13Q12.3) MUTATED`
TCGA-B7-5818 TCGA-BR-4187 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6563 
       11.70         4.64         9.57         6.61        15.95        39.12 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7704 
        0.62        32.78        13.84        21.11         9.21        35.24 
TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        0.69        18.54         0.95         1.32         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8362 TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8483 
        0.49        12.95         0.36        14.79        15.85         5.39 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 
        9.21        20.22        12.79        16.44        15.68         0.62 
TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 
       10.68         1.15        22.26         0.72        14.17        12.82 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QM 
       13.51         0.46        20.65        20.42         1.15         5.13 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8535 
        3.25        13.15         0.07         0.07         0.10         0.13 
TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 
        6.35         0.13         0.07         0.10        20.02         3.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4444 TCGA-CG-4469 
       15.95         7.99         8.05        54.08        47.05         7.07 
TCGA-CG-4472 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 
       12.00         1.02        12.03        79.07         4.01        55.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6524 
        7.99        12.36        12.66        19.13        18.54        17.85 
TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8573 
       17.19        15.98        12.79        10.55        11.31        19.50 
TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4Z0 TCGA-D7-A6EV 
       17.19         6.97        21.14        14.27        14.76        11.24 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 
        2.96        15.65         0.62         7.79        72.23         0.39 
TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-A4BF TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
       19.53        17.06         1.55        12.59        14.17        12.10 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GT TCGA-HU-A4GY 
       12.30        11.84        22.75        25.81         6.51         0.26 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RI 
       19.36        17.69        12.30        27.42         3.45        18.38 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H 
        1.41         6.44         6.87         1.81         5.56        28.90 
TCGA-MX-A663 TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 
        4.31         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        37.74         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PP 
       13.02        21.73         7.73         2.70        17.85        23.41 
TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91Z TCGA-VQ-A922 
       14.33        28.70        20.81         1.71        44.25         8.61 
TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       29.98        21.11         0.79 

$`AMP PEAK 27(13Q12.3) WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        5.62         6.61         6.97         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.18        34.68        13.12        10.13        13.68         7.00 
TCGA-BR-6564 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 
        0.82        13.22        16.14         1.25         8.98        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       31.20        32.94        12.82        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.01         0.16        12.43         0.69        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 
       17.49         0.82        20.55         0.72         0.26         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         1.55         1.48         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         2.96         0.95        13.74         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 
       14.04         3.32         0.36        19.17         0.69         0.26 
TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        3.72         0.72         1.12        15.81         2.14        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 
        0.20         7.53         0.49        11.54        15.81         0.59 
TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       12.56         0.66         3.02         0.92        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4QI 
       12.89         0.79         0.53         0.66        19.36        13.64 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
       11.57         2.83        13.18         0.30         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.07         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.10         0.13         0.13         0.13         0.10         0.10 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
       27.02         1.02         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 
       12.03        21.99         9.01        18.97        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 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-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-5579 TCGA-D7-6519 
       15.02        28.96        65.10        21.07        11.93        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6822 
       18.84        18.61         5.95         4.14        15.22        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8575 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV 
       24.72        16.80         0.23        20.91        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       15.16        13.78        13.71        11.31        11.44         9.76 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 
        4.34         7.40         7.13        16.24         6.58        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
       21.27         8.12         3.02        22.29        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-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-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        5.59        24.20         3.25        11.77        21.37        29.98 
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-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 
        9.67         8.88         8.81        21.21        18.81         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IP-7968 
        5.36         5.19        13.08         6.74         5.56         2.53 
TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
       60.56         3.72        19.73        11.05         4.67        16.67 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-VQ-A8DL TCGA-VQ-A8E2 
       40.64       116.38        71.38        16.87         0.92        31.10 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       22.36        23.77        19.07        33.63        46.26        16.31 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX 
        1.87         9.27        15.65        19.30        23.57        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91W TCGA-VQ-A91X 
       59.18        11.70         8.68        49.25         7.36         8.58 
TCGA-VQ-A91Y TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 
        9.73        55.43         4.54         6.58         5.72        40.08 
TCGA-ZA-A8F6 
        4.21 

  AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE 
                          0.07                           0.07 
  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 
                         12.30                          10.19 
[1] "0.1 - 122.3 (12.3)" "0.1 - 116.4 (10.2)"
[1] "hr=" "1.2"
D27V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 27(13Q12.3) MUTATED         1        5       11       12        17
  AMP PEAK 27(13Q12.3) WILD-TYPE       1        8       28       19        19
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 27(13Q12.3) MUTATED          19         2         32         19
  AMP PEAK 27(13Q12.3) WILD-TYPE        30         1         45         36
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 27(13Q12.3) MUTATED           11       18
  AMP PEAK 27(13Q12.3) WILD-TYPE         26       19
D27V3, multiclass
            clus
vv           AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                              5                              8
  STAGE IB                             11                             28
  STAGE II                             12                             19
  STAGE IIA                            17                             19
  STAGE IIB                            19                             30
  STAGE III                             2                              1
  STAGE IIIA                           32                             45
  STAGE IIIB                           19                             36
  STAGE IIIC                           11                             26
  STAGE IV                             18                             19
[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  67  36
  AMP PEAK 27(13Q12.3) WILD-TYPE  14  48 106  68
D27V4, multiclass
    clus
vv   AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE
  T1                            7                             14
  T2                           39                             48
  T3                           67                            106
  T4                           36                             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"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 27(13Q12.3) MUTATED   46 38 30 34
  AMP PEAK 27(13Q12.3) WILD-TYPE 76 69 45 45
D27V5, multiclass
    clus
vv   AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE
  N0                           46                             76
  N1                           38                             69
  N2                           30                             45
  N3                           34                             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"
                                vv
clus                              M0  M1  MX
  AMP PEAK 27(13Q12.3) MUTATED   140   9   5
  AMP PEAK 27(13Q12.3) WILD-TYPE 213  15  13
D27V6, multiclass
    clus
vv   AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE
  M0                          140                            213
  M1                            9                             15
  MX                            5                             13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                                cls
clus                               0   1
  AMP PEAK 27(13Q12.3) MUTATED    55  99
  AMP PEAK 27(13Q12.3) WILD-TYPE  96 145
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(13Q12.3) MUTATED     55   99
  AMP PEAK 27(13Q12.3) WILD-TYPE   96  145
        clus
vv       AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE
  FEMALE                           55                             96
  MALE                             99                            145
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 27(13Q12.3) MUTATED                                      17
  AMP PEAK 27(13Q12.3) WILD-TYPE                                    48
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 27(13Q12.3) MUTATED                                                       62
  AMP PEAK 27(13Q12.3) WILD-TYPE                                                     95
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 27(13Q12.3) MUTATED                                                                  31
  AMP PEAK 27(13Q12.3) WILD-TYPE                                                                38
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 27(13Q12.3) MUTATED                                                 27
  AMP PEAK 27(13Q12.3) WILD-TYPE                                               37
                                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                                          2
  AMP PEAK 27(13Q12.3) WILD-TYPE                                        7
D27V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 27(13Q12.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       17
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      62
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           31
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            27
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
                                                                   clus
vv                                                                  AMP PEAK 27(13Q12.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        95
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      11
  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"
D27V9, binary
                                cls
clus                               0   1
  AMP PEAK 27(13Q12.3) MUTATED     3 151
  AMP PEAK 27(13Q12.3) WILD-TYPE   3 238
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(13Q12.3) MUTATED      3  151
  AMP PEAK 27(13Q12.3) WILD-TYPE    3  238
     clus
vv    AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE
  NO                             3                              3
  YES                          151                            238
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 27(13Q12.3) MUTATED   121   8   8   9
  AMP PEAK 27(13Q12.3) WILD-TYPE 197   8  10  16
D27V10, multiclass
    clus
vv   AMP PEAK 27(13Q12.3) MUTATED AMP PEAK 27(13Q12.3) WILD-TYPE
  R0                          121                            197
  R1                            8                              8
  R2                            8                             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"
D27V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 27(13Q12.3) MUTATED      33                         4
  AMP PEAK 27(13Q12.3) WILD-TYPE    55                         2
                                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      91
  AMP PEAK 27(13Q12.3) WILD-TYPE   152
D27V12, multiclass
                                           clus
vv                                          AMP PEAK 27(13Q12.3) MUTATED
  ASIAN                                                               33
  BLACK OR AFRICAN AMERICAN                                            4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               91
                                           clus
vv                                          AMP PEAK 27(13Q12.3) WILD-TYPE
  ASIAN                                                                 55
  BLACK OR AFRICAN AMERICAN                                              2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                152
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = AMP PEAK 28(13Q22.1) MUTATION ANALYSIS
D28V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 28(13Q22.1) MUTATED   103  45
  AMP PEAK 28(13Q22.1) WILD-TYPE 139  77
  AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE 
                           148                            216 
  AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE 
                            45                             77 
$`AMP PEAK 28(13Q22.1) MUTATED`
TCGA-B7-5818 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       11.70         4.64         7.43         9.57         6.61        15.95 
TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7704 
       39.12         0.62        32.78        21.11         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8077 
       15.42        28.01         0.69        18.54         0.95         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8362 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       12.26         0.49         0.36        14.79         0.26        15.85 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8686 
        5.39         9.21        12.79        11.54        16.44        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J1 
        0.62        10.68         1.15        22.26        12.89         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-5802 TCGA-CD-8525 
        1.15         5.13         3.25        13.15         0.30         0.07 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH 
        0.13         0.13         6.35         0.13         0.07         0.10 
TCGA-CG-4300 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
       20.02        15.95         1.02         7.99        54.08         4.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5719 
       29.98        19.07         7.07        12.00         1.02         1.02 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
      105.07        15.02         4.01        55.04         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6524 TCGA-D7-6526 
       12.66        11.93        19.13        18.54        17.85        17.19 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8573 
        4.14        15.98        10.55        11.31        12.33        19.50 
TCGA-D7-8574 TCGA-D7-A4YT TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-D7-A6F2 
       17.19        14.27        14.76        11.24         2.96        15.65 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-8631 TCGA-FP-A4BF 
        0.62         7.79        72.23        19.53         0.56         1.55 
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-A4GU TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 
       25.81         6.51         6.25         0.26        19.36        17.69 
TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO 
       12.30        27.42         3.39        18.38         5.19         1.41 
TCGA-IN-A6RP TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A663 
        6.44         1.81         2.53         5.56        28.90         4.31 
TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 
        8.61       122.30        37.91       115.69        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       35.61         5.79        37.74         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PP TCGA-VQ-A8PY 
       31.10        21.73         2.70        17.85        23.41        14.33 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 
       49.25        20.81         1.71         8.58        44.25         8.61 
TCGA-VQ-A925 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J 
        4.54        40.08        29.98        21.11 

$`AMP PEAK 28(13Q22.1) WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        5.62         6.61         6.97        18.35        30.90         6.18 
TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 
       34.68        13.12        10.13        13.68         7.00         0.82 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 
       13.84        13.22        16.14         1.25         8.98        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         0.16 
TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       12.43         0.69        12.76        18.71        17.49         0.82 
TCGA-BR-8060 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        1.32        20.55         0.72         0.26        12.95         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         1.55         1.48         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         2.96         0.95        13.74         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8384 
       14.04         3.32         0.36        19.17         0.69         3.72 
TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        0.72        20.22         1.12        15.81         2.14        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-A44T 
        0.20         7.53         0.49        15.81         0.59        12.56 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
        0.66         3.02         0.92        13.41        13.51         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 
        0.53         0.66        19.36        13.64        11.57         2.83 
TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       13.18         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A487 
        0.13         0.16         0.10         0.10         0.10         0.13 
TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
        0.13         0.13         0.10         0.10         3.02        27.02 
TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 
        8.05        14.01        47.05        12.03        21.99         9.01 
TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 
       18.97        22.98        30.97         6.97         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5733 
        0.99        12.03        28.96        79.07        65.10        21.07 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6817 
       20.55        18.84        18.61         5.95        15.22        12.79 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       24.72        16.80         0.23         6.97        21.14        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-F1-6177 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 
        6.58        14.47        21.27         8.12         0.39         3.02 
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-8244 TCGA-HU-8602 
       18.08        26.47         1.51         5.92        14.27        11.41 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G9 TCGA-HU-A4GC 
       10.62         0.76        24.30         5.59        24.20         3.25 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX 
       11.77        21.37        29.98         8.98         0.10        10.19 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
        2.10        12.95         9.67         8.88         8.81        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS 
        3.45        18.81         5.36        13.08         6.74         6.87 
TCGA-IN-A7NT TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW 
        5.56        60.56         3.72        19.73        11.05         4.67 
TCGA-RD-A7C1 TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-VQ-A8DL 
       16.67        40.64       116.38        71.38        16.87         0.92 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       22.36        23.77         7.73        19.07        33.63        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU 
       16.31         1.87         9.27        15.65        19.30        23.57 
TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91W 
       64.57        59.18        28.70        11.70         8.68         7.36 
TCGA-VQ-A91Y TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        9.73        55.43         6.58         5.72         4.21         0.79 

  AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE 
                          0.07                           0.07 
  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 
                        12.280                         10.405 
[1] "0.1 - 122.3 (12.3)" "0.1 - 116.4 (10.4)"
[1] "hr=" "1.3"
D28V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 28(13Q22.1) MUTATED         1        4       12       14        16
  AMP PEAK 28(13Q22.1) WILD-TYPE       1        9       27       17        20
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 28(13Q22.1) MUTATED          23         1         33         19
  AMP PEAK 28(13Q22.1) WILD-TYPE        26         2         44         36
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 28(13Q22.1) MUTATED           11       17
  AMP PEAK 28(13Q22.1) WILD-TYPE         26       20
D28V3, multiclass
            clus
vv           AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                              4                              9
  STAGE IB                             12                             27
  STAGE II                             14                             17
  STAGE IIA                            16                             20
  STAGE IIB                            23                             26
  STAGE III                             1                              2
  STAGE IIIA                           33                             44
  STAGE IIIB                           19                             36
  STAGE IIIC                           11                             26
  STAGE IV                             17                             20
[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  40  72  35
  AMP PEAK 28(13Q22.1) WILD-TYPE  15  47 101  69
D28V4, multiclass
    clus
vv   AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE
  T1                            6                             15
  T2                           40                             47
  T3                           72                            101
  T4                           35                             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 28(13Q22.1) MUTATED   45 45 36 28
  AMP PEAK 28(13Q22.1) WILD-TYPE 77 62 39 51
D28V5, multiclass
    clus
vv   AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE
  N0                           45                             77
  N1                           45                             62
  N2                           36                             39
  N3                           28                             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  AMP PEAK 28(13Q22.1) MUTATED   147   8   4
  AMP PEAK 28(13Q22.1) WILD-TYPE 206  16  14
D28V6, multiclass
    clus
vv   AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE
  M0                          147                            206
  M1                            8                             16
  MX                            4                             14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                                cls
clus                               0   1
  AMP PEAK 28(13Q22.1) MUTATED    51 108
  AMP PEAK 28(13Q22.1) WILD-TYPE 100 136
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(13Q22.1) MUTATED     51  108
  AMP PEAK 28(13Q22.1) WILD-TYPE  100  136
        clus
vv       AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE
  FEMALE                           51                            100
  MALE                            108                            136
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 28(13Q22.1) MUTATED                                      15
  AMP PEAK 28(13Q22.1) WILD-TYPE                                    50
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 28(13Q22.1) MUTATED                                                       65
  AMP PEAK 28(13Q22.1) WILD-TYPE                                                     92
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 28(13Q22.1) MUTATED                                                                  33
  AMP PEAK 28(13Q22.1) WILD-TYPE                                                                36
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 28(13Q22.1) MUTATED                                                 28
  AMP PEAK 28(13Q22.1) WILD-TYPE                                               36
                                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                                          2
  AMP PEAK 28(13Q22.1) WILD-TYPE                                        7
D28V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 28(13Q22.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      65
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           33
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            28
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
                                                                   clus
vv                                                                  AMP PEAK 28(13Q22.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        92
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      3
  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"
D28V9, binary
                                cls
clus                               0   1
  AMP PEAK 28(13Q22.1) MUTATED     1 158
  AMP PEAK 28(13Q22.1) WILD-TYPE   5 231
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(13Q22.1) MUTATED      1  158
  AMP PEAK 28(13Q22.1) WILD-TYPE    5  231
     clus
vv    AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE
  NO                             1                              5
  YES                          158                            231
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 28(13Q22.1) MUTATED   124   8   9  10
  AMP PEAK 28(13Q22.1) WILD-TYPE 194   8   9  15
D28V10, multiclass
    clus
vv   AMP PEAK 28(13Q22.1) MUTATED AMP PEAK 28(13Q22.1) WILD-TYPE
  R0                          124                            194
  R1                            8                              8
  R2                            9                              9
  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                         3
  AMP PEAK 28(13Q22.1) WILD-TYPE    53                         3
                                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      94
  AMP PEAK 28(13Q22.1) WILD-TYPE   149
D28V12, multiclass
                                           clus
vv                                          AMP PEAK 28(13Q22.1) MUTATED
  ASIAN                                                               35
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               94
                                           clus
vv                                          AMP PEAK 28(13Q22.1) WILD-TYPE
  ASIAN                                                                 53
  BLACK OR AFRICAN AMERICAN                                              3
  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"

Clustering(29) Variable = AMP PEAK 29(15Q26.1) MUTATION ANALYSIS
D29V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 29(15Q26.1) MUTATED    60  32
  AMP PEAK 29(15Q26.1) WILD-TYPE 182  90
  AMP PEAK 29(15Q26.1) MUTATED AMP PEAK 29(15Q26.1) WILD-TYPE 
                            92                            272 
  AMP PEAK 29(15Q26.1) MUTATED AMP PEAK 29(15Q26.1) WILD-TYPE 
                            32                             90 
$`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         7.00         1.25         9.21 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8361 
       15.42         0.69        18.71         1.32         0.69        19.50 
TCGA-BR-8364 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4J4 
       22.19         0.59         0.62         0.66        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         6.35         0.07        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        55.04        11.93        20.55        18.84 
TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8575 
        5.95        15.22        15.98        10.55        12.33         0.23 
TCGA-D7-A4YT TCGA-D7-A4YY TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6875 
       14.27        13.78        15.65         0.62         6.58        72.23 
TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 TCGA-HU-A4G8 
        8.12        19.53        17.06        13.58         0.56        11.84 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GY TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 
       25.81        11.77         0.26        12.30        27.42         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RN TCGA-IN-A6RO TCGA-KB-A6F5 
       18.81         3.39        18.38        13.08         1.41         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8N6 TCGA-VQ-A8DL 
       60.56        28.90         8.61       122.30         8.94         0.92 
TCGA-VQ-A8DZ TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       13.02        23.77         7.73        46.26         2.70        17.85 
TCGA-VQ-A8PU TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A925 
       23.57        49.25        20.81         8.58         8.61         4.54 
TCGA-VQ-AA68 TCGA-VQ-AA6B 
       40.08        29.98 

$`AMP PEAK 29(15Q26.1) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
        5.62        11.70         6.97         4.64         7.43        30.90 
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        13.12        10.13 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.68        39.12         0.82         0.62        32.78        13.84 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       13.22        16.14         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-7716 
       32.94        12.82        24.76        35.24        23.93        28.01 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
        0.16        18.54        12.43         0.95         0.69        12.76 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49         0.82        12.26         0.49        20.55         0.72 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.26        12.95         0.26        16.31         1.55         1.48 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.36         0.26         2.96         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       13.74         4.31        14.04         3.32         0.36        19.17 
TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       14.79         0.69         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 
        0.72         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 
        2.14        13.45         0.20         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       15.81        16.44        15.68        10.68        12.56         1.15 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        3.02         0.92        13.41        13.51        12.89         0.79 
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-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.65        20.42        11.57         5.13         2.83 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8530 
       13.18         0.30         0.07         0.07         0.07         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         0.13         0.13 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
        0.13         0.13         0.10         0.10         0.10        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-4443 TCGA-CG-4455 TCGA-CG-4460 
       54.08         4.01        14.01        29.98        12.03        21.99 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5720 
        9.01        18.97         7.07        12.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99       105.07        15.02        28.96        65.10 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6521 
       21.07         7.99        12.36        12.66        19.13        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6820 
       18.61        17.85        17.19         4.14        12.79        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         6.97        21.14 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET 
       20.91        16.44         5.92        15.16        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A748 
       11.24        11.31        11.44         9.76         2.96         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 
        7.40         7.13         7.79        16.24        14.47        21.27 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF 
        0.39         3.02        22.29        59.54         5.03         1.55 
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-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        12.30        24.20         3.25        22.75 
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-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
       10.19         2.10        12.95        19.36        17.69         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP 
        8.88         8.81        21.21         5.36         5.19         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-MX-A5UG 
        6.74         6.87         5.56         1.81         2.53         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW 
       19.73         4.31        11.05         4.67        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-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E2 
       16.87         5.79        37.74         5.46        13.25        31.10 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PM 
       21.73        22.36        19.07        33.63        16.31         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        19.30        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91U TCGA-VQ-A91W 
       59.18        28.70        11.70         8.68         1.71         7.36 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6J 
        9.73        44.25        55.43         6.58         5.72        21.11 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        4.21         0.79 

  AMP PEAK 29(15Q26.1) MUTATED AMP PEAK 29(15Q26.1) WILD-TYPE 
                          0.07                           0.07 
  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 
                        11.885                         11.490 
[1] "0.1 - 122.3 (11.9)" "0.1 - 116.4 (11.5)"
[1] "hr=" "1"  
D29V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 29(15Q26.1) MUTATED         1        3        8        9        10
  AMP PEAK 29(15Q26.1) WILD-TYPE       1       10       31       22        26
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 29(15Q26.1) MUTATED          10         1         24         10
  AMP PEAK 29(15Q26.1) WILD-TYPE        39         2         53         45
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 29(15Q26.1) MUTATED            6       14
  AMP PEAK 29(15Q26.1) WILD-TYPE         31       23
D29V3, multiclass
            clus
vv           AMP PEAK 29(15Q26.1) MUTATED AMP PEAK 29(15Q26.1) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                              3                             10
  STAGE IB                              8                             31
  STAGE II                              9                             22
  STAGE IIA                            10                             26
  STAGE IIB                            10                             39
  STAGE III                             1                              2
  STAGE IIIA                           24                             53
  STAGE IIIB                           10                             45
  STAGE IIIC                            6                             31
  STAGE IV                             14                             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 29(15Q26.1) MUTATED     6  25  42  24
  AMP PEAK 29(15Q26.1) WILD-TYPE  15  62 131  80
D29V4, multiclass
    clus
vv   AMP PEAK 29(15Q26.1) MUTATED AMP PEAK 29(15Q26.1) WILD-TYPE
  T1                            6                             15
  T2                           25                             62
  T3                           42                            131
  T4                           24                             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
  AMP PEAK 29(15Q26.1) MUTATED   28 29 24 16
  AMP PEAK 29(15Q26.1) WILD-TYPE 94 78 51 63
D29V5, multiclass
    clus
vv   AMP PEAK 29(15Q26.1) MUTATED AMP PEAK 29(15Q26.1) WILD-TYPE
  N0                           28                             94
  N1                           29                             78
  N2                           24                             51
  N3                           16                             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                              M0  M1  MX
  AMP PEAK 29(15Q26.1) MUTATED    85   9   5
  AMP PEAK 29(15Q26.1) WILD-TYPE 268  15  13
D29V6, multiclass
    clus
vv   AMP PEAK 29(15Q26.1) MUTATED AMP PEAK 29(15Q26.1) WILD-TYPE
  M0                           85                            268
  M1                            9                             15
  MX                            5                             13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                                cls
clus                               0   1
  AMP PEAK 29(15Q26.1) MUTATED    31  68
  AMP PEAK 29(15Q26.1) WILD-TYPE 120 176
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(15Q26.1) MUTATED     31   68
  AMP PEAK 29(15Q26.1) WILD-TYPE  120  176
        clus
vv       AMP PEAK 29(15Q26.1) MUTATED AMP PEAK 29(15Q26.1) WILD-TYPE
  FEMALE                           31                            120
  MALE                             68                            176
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 29(15Q26.1) MUTATED                                      13
  AMP PEAK 29(15Q26.1) WILD-TYPE                                    52
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 29(15Q26.1) MUTATED                                                       33
  AMP PEAK 29(15Q26.1) WILD-TYPE                                                    124
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 29(15Q26.1) MUTATED                                                                  20
  AMP PEAK 29(15Q26.1) WILD-TYPE                                                                49
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 29(15Q26.1) MUTATED                                                 21
  AMP PEAK 29(15Q26.1) WILD-TYPE                                               43
                                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                                        7
D29V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 29(15Q26.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       13
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      33
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           20
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            21
  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                                                         52
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             49
  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                                                       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"
D29V9, binary
                                cls
clus                               0   1
  AMP PEAK 29(15Q26.1) MUTATED     2  97
  AMP PEAK 29(15Q26.1) WILD-TYPE   4 292
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(15Q26.1) MUTATED      2   97
  AMP PEAK 29(15Q26.1) WILD-TYPE    4  292
     clus
vv    AMP PEAK 29(15Q26.1) MUTATED AMP PEAK 29(15Q26.1) WILD-TYPE
  NO                             2                              4
  YES                           97                            292
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 29(15Q26.1) MUTATED    76   5   8   5
  AMP PEAK 29(15Q26.1) WILD-TYPE 242  11  10  20
D29V10, multiclass
    clus
vv   AMP PEAK 29(15Q26.1) MUTATED AMP PEAK 29(15Q26.1) WILD-TYPE
  R0                           76                            242
  R1                            5                             11
  R2                            8                             10
  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                         3
  AMP PEAK 29(15Q26.1) WILD-TYPE    66                         3
                                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      55
  AMP PEAK 29(15Q26.1) WILD-TYPE   188
D29V12, multiclass
                                           clus
vv                                          AMP PEAK 29(15Q26.1) MUTATED
  ASIAN                                                               22
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               55
                                           clus
vv                                          AMP PEAK 29(15Q26.1) WILD-TYPE
  ASIAN                                                                 66
  BLACK OR AFRICAN AMERICAN                                              3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                188
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = AMP PEAK 30(17Q12) MUTATION ANALYSIS
D30V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 30(17Q12) MUTATED    77  44
  AMP PEAK 30(17Q12) WILD-TYPE 165  78
  AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE 
                         121                          243 
  AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE 
                          44                           78 
$`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         0.62         9.21        15.42         0.69        18.71 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 
        0.82         1.32         0.69        12.95         0.26         1.48 
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         2.14        16.44 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY 
       15.68        10.68         1.15        22.26         0.92        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         6.35         0.13        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        55.04        18.54         5.95        17.19         4.14 
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         6.97 
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         7.79        16.24 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HJ-7597 
       72.23         0.39         3.02         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-IP-7968 TCGA-RD-A7BT TCGA-RD-A8N6 
        6.87         5.56         1.81         2.53         8.61         8.94 
TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8P5 TCGA-VQ-A8PC 
        0.92         5.46        13.25        13.02         7.73        46.26 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91Q 
        2.70        17.85         1.87        19.30        59.18        20.81 
TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J 
        8.58         8.61         4.54        40.08        29.98        21.11 
TCGA-ZQ-A9CR 
        0.79 

$`AMP PEAK 30(17Q12) WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62         6.61         6.97         4.64         7.43        18.35 
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-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.12        10.13        13.68         7.00        39.12         0.82 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        13.84        13.22        16.14         1.25         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-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       35.24        23.93        28.01         0.16        18.54        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8078 TCGA-BR-8080 
        0.95         0.69        12.76        17.49        12.26         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
       20.55         0.72         0.26        16.31         1.55         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        19.50         0.36         0.26        22.19         2.96 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        13.74         4.31         3.32         0.36        19.17 
TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 
        0.69         0.26        15.85         3.72         0.72         9.21 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        15.81        13.45         0.20         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44T 
        0.49        11.54        15.81         0.59         0.62        12.56 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 
        0.66         3.02        13.41        13.51         0.79        14.17 
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-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 
        1.15        11.57         5.13         2.83        13.18         0.30 
TCGA-CD-5803 TCGA-CD-8524 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-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 
        0.10         0.10         0.13         0.13         0.10         0.13 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.13         0.13         0.07         0.10         0.10         0.10 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 
       27.02        15.95         1.02         8.05        54.08        14.01 
TCGA-CG-4443 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 
       29.98         9.01         7.07        12.00         6.97         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-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-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6528 
       19.13        20.55        18.84        18.61        17.85        15.22 
TCGA-D7-6818 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 
       10.55        24.72        16.80        17.19         0.23        21.14 
TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EZ 
        5.92        13.78        14.76        13.71        11.31         9.76 
TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        7.40         7.13         6.58        14.47        21.27         8.12 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       19.53        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 
        1.55        18.08        14.27        14.17        11.41        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        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-A4H5 TCGA-HU-A4H6 
       10.19         0.26        19.36        17.69        12.30         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-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        5.56        60.56        28.90         3.72        19.73         4.31 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         4.67        16.67       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-A7EB TCGA-VQ-A8DT TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        5.79        37.74        31.10        21.73        22.36        23.77 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       19.07        33.63        16.31         9.27        23.41        15.65 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       23.57        64.57        14.33        28.70        11.70         8.68 
TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A924 
       49.25         1.71         7.36         9.73        44.25        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-ZA-A8F6 
        6.58         5.72         4.21 

  AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE 
                        0.07                         0.07 
  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 
                       11.31                        11.84 
[1] "0.1 - 72.2 (11.3)"  "0.1 - 122.3 (11.8)"
[1] "hr=" "1.3"
D30V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 30(17Q12) MUTATED         0        6       13        8        11
  AMP PEAK 30(17Q12) WILD-TYPE       2        7       26       23        25
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 30(17Q12) MUTATED          13         1         23         18
  AMP PEAK 30(17Q12) WILD-TYPE        36         2         54         37
                              vv
clus                           STAGE IIIC STAGE IV
  AMP PEAK 30(17Q12) MUTATED           12       20
  AMP PEAK 30(17Q12) WILD-TYPE         25       17
D30V3, multiclass
            clus
vv           AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE
  STAGE I                             0                            2
  STAGE IA                            6                            7
  STAGE IB                           13                           26
  STAGE II                            8                           23
  STAGE IIA                          11                           25
  STAGE IIB                          13                           36
  STAGE III                           1                            2
  STAGE IIIA                         23                           54
  STAGE IIIB                         18                           37
  STAGE IIIC                         12                           25
  STAGE IV                           20                           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 30(17Q12) MUTATED     8  32  50  36
  AMP PEAK 30(17Q12) WILD-TYPE  13  55 123  68
D30V4, multiclass
    clus
vv   AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE
  T1                          8                           13
  T2                         32                           55
  T3                         50                          123
  T4                         36                           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"
                              vv
clus                           N0 N1 N2 N3
  AMP PEAK 30(17Q12) MUTATED   40 29 26 30
  AMP PEAK 30(17Q12) WILD-TYPE 82 78 49 49
D30V5, multiclass
    clus
vv   AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE
  N0                         40                           82
  N1                         29                           78
  N2                         26                           49
  N3                         30                           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"
                              vv
clus                            M0  M1  MX
  AMP PEAK 30(17Q12) MUTATED   103  14  11
  AMP PEAK 30(17Q12) WILD-TYPE 250  10   7
D30V6, multiclass
    clus
vv   AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE
  M0                        103                          250
  M1                         14                           10
  MX                         11                            7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                              cls
clus                             0   1
  AMP PEAK 30(17Q12) MUTATED    41  87
  AMP PEAK 30(17Q12) WILD-TYPE 110 157
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 30(17Q12) MUTATED     41   87
  AMP PEAK 30(17Q12) WILD-TYPE  110  157
        clus
vv       AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE
  FEMALE                         41                          110
  MALE                           87                          157
[1] 2 2
[1] FALSE
                              vv
clus                           STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 30(17Q12) MUTATED                                       9
  AMP PEAK 30(17Q12) WILD-TYPE                                    56
                              vv
clus                           STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 30(17Q12) MUTATED                                                       45
  AMP PEAK 30(17Q12) WILD-TYPE                                                    112
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 30(17Q12) MUTATED                                                                  29
  AMP PEAK 30(17Q12) WILD-TYPE                                                                40
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 30(17Q12) MUTATED                                                 28
  AMP PEAK 30(17Q12) WILD-TYPE                                               36
                              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                                        3
D30V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 30(17Q12) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    45
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         29
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                          28
  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                                                       56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     112
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     3
[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     2 126
  AMP PEAK 30(17Q12) WILD-TYPE   4 263
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 30(17Q12) MUTATED      2  126
  AMP PEAK 30(17Q12) WILD-TYPE    4  263
     clus
vv    AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE
  NO                           2                            4
  YES                        126                          263
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 30(17Q12) MUTATED   108   0  12   3
  AMP PEAK 30(17Q12) WILD-TYPE 210  16   6  22
D30V10, multiclass
    clus
vv   AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE
  R0                        108                          210
  R1                          0                           16
  R2                         12                            6
  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                         4
  AMP PEAK 30(17Q12) WILD-TYPE    63                         2
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 30(17Q12) MUTATED                                           1    77
  AMP PEAK 30(17Q12) WILD-TYPE                                         0   166
D30V12, multiclass
                                           clus
vv                                          AMP PEAK 30(17Q12) MUTATED
  ASIAN                                                             25
  BLACK OR AFRICAN AMERICAN                                          4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                             77
                                           clus
vv                                          AMP PEAK 30(17Q12) WILD-TYPE
  ASIAN                                                               63
  BLACK OR AFRICAN AMERICAN                                            2
  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"

Clustering(31) Variable = AMP PEAK 31(18Q11.2) MUTATION ANALYSIS
D31V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 31(18Q11.2) MUTATED    67  45
  AMP PEAK 31(18Q11.2) WILD-TYPE 175  77
  AMP PEAK 31(18Q11.2) MUTATED AMP PEAK 31(18Q11.2) WILD-TYPE 
                           112                            252 
  AMP PEAK 31(18Q11.2) MUTATED AMP PEAK 31(18Q11.2) WILD-TYPE 
                            45                             77 
$`AMP PEAK 31(18Q11.2) MUTATED`
TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-7715 
        6.97         7.43        18.35         0.82         0.62        15.42 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 
        0.16        18.54         0.95         0.69         0.49         0.72 
TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8370 
       12.95         1.55         1.48         7.40         0.36         3.32 
TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 
       14.79         3.72         0.72        20.22         1.12        15.81 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A4CQ 
        0.49        11.54        15.68         0.62         1.15        22.26 
TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF 
       12.89         0.72         0.66        13.51        20.65         1.15 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8526 TCGA-CD-8529 TCGA-CD-A486 
        2.83         3.25        13.15         0.07         0.13         6.35 
TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4440 TCGA-CG-4441 
        0.13         0.10        20.02         3.02         4.01        14.01 
TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5724 TCGA-D7-5579 
       19.07        21.99         7.07        12.00        12.03        11.93 
TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       19.13        18.54         5.95        17.19         4.14        15.22 
TCGA-D7-6817 TCGA-D7-8576 TCGA-D7-A4YY TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       12.79         6.97        13.78        11.24        11.31        11.44 
TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-5647 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-8631 
        2.96         7.40         0.62        72.23         8.12         0.56 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8610 
        1.55         0.23        26.47         5.92        12.59         0.76 
TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD 
       22.75         8.98        17.69        12.30         9.67        27.42 
TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
       18.81        18.38         5.19        13.08         1.41         6.44 
TCGA-IN-A6RR TCGA-IN-A7NU TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A663 TCGA-RD-A7BW 
        6.74         1.81        60.56        28.90         4.31         4.67 
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-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PZ TCGA-VQ-A91E 
       13.02         2.70         1.87         9.27        59.18         8.68 
TCGA-VQ-A91U TCGA-VQ-A922 TCGA-VQ-AA68 TCGA-ZQ-A9CR 
        1.71         8.61        40.08         0.79 

$`AMP PEAK 31(18Q11.2) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4201 TCGA-BR-4267 
        5.62        11.70         6.61         4.64        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        13.12        10.13 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.68         7.00        39.12        32.78        13.84        13.22 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       16.14         1.25         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-7716 TCGA-BR-7717 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.01         0.69        12.43         0.69        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8285 
       17.49         0.82         1.32        12.26        20.55         0.26 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        0.26        16.31         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 
        2.96         0.95        13.74         4.31        14.04         0.36 
TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8485 
       19.17         0.69         0.26        15.85         5.39         9.21 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 
       12.79         2.14        13.45         0.20         7.53        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 
       16.44         0.59        10.68        12.56         0.66         3.02 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
        0.92        13.41        13.51         0.79        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL 
       12.82        19.36         0.46        20.42        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 
        5.13        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-A489 TCGA-CD-A48C TCGA-CD-A4MG 
        0.13         0.10         0.13         0.13         0.13         0.07 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
        0.10         0.10        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4465 
        8.05        54.08        29.98        47.05        12.03         9.01 
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         1.02         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        55.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
       12.36        12.66        20.55        18.84        18.61        17.85 
TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       15.98        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19         0.23        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EZ 
       16.44         5.92        15.16        14.76        13.71         9.76 
TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 
       15.65         4.34         7.13         7.79        16.24         6.58 
TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       14.47        21.27         0.39        19.53         3.02        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-A5NB TCGA-HU-8238 
       17.06        59.54         5.03        13.58        18.08         1.51 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 
       14.27        14.17        11.41        12.10        10.62        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-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-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 
       10.19         0.26         2.10        12.95        19.36         8.88 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RS 
        8.81        21.21         3.45         3.39         5.36         6.87 
TCGA-IN-A7NT TCGA-IP-7968 TCGA-KB-A6F5 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS 
        5.56         2.53         5.56         3.72        19.73        11.05 
TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
        8.61       122.30        37.91        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E2 
       57.44         8.94        16.87        37.74        13.25        31.10 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        22.36        23.77         7.73        19.07        33.63 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PK TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       46.26        16.31        17.85        23.41        15.65        19.30 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K 
       23.57        64.57        14.33        28.70        11.70        49.25 
TCGA-VQ-A91Q TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A924 
       20.81         7.36         8.58         9.73        44.25        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 
        4.54         6.58         5.72        29.98        21.11         4.21 

  AMP PEAK 31(18Q11.2) MUTATED AMP PEAK 31(18Q11.2) WILD-TYPE 
                          0.07                           0.07 
  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 
                          7.40                          12.61 
[1] "0.1 - 115.7 (7.4)"  "0.1 - 122.3 (12.6)"
[1] "hr=" "1.6"
D31V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 31(18Q11.2) MUTATED         0        4       10        8        12
  AMP PEAK 31(18Q11.2) WILD-TYPE       2        9       29       23        24
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 31(18Q11.2) MUTATED          12         0         26         16
  AMP PEAK 31(18Q11.2) WILD-TYPE        37         3         51         39
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 31(18Q11.2) MUTATED           15       14
  AMP PEAK 31(18Q11.2) WILD-TYPE         22       23
D31V3, multiclass
            clus
vv           AMP PEAK 31(18Q11.2) MUTATED AMP PEAK 31(18Q11.2) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              4                              9
  STAGE IB                             10                             29
  STAGE II                              8                             23
  STAGE IIA                            12                             24
  STAGE IIB                            12                             37
  STAGE III                             0                              3
  STAGE IIIA                           26                             51
  STAGE IIIB                           16                             39
  STAGE IIIC                           15                             22
  STAGE IV                             14                             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 31(18Q11.2) MUTATED     7  24  51  36
  AMP PEAK 31(18Q11.2) WILD-TYPE  14  63 122  68
D31V4, multiclass
    clus
vv   AMP PEAK 31(18Q11.2) MUTATED AMP PEAK 31(18Q11.2) WILD-TYPE
  T1                            7                             14
  T2                           24                             63
  T3                           51                            122
  T4                           36                             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"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 31(18Q11.2) MUTATED   35 32 24 29
  AMP PEAK 31(18Q11.2) WILD-TYPE 87 75 51 50
D31V5, multiclass
    clus
vv   AMP PEAK 31(18Q11.2) MUTATED AMP PEAK 31(18Q11.2) WILD-TYPE
  N0                           35                             87
  N1                           32                             75
  N2                           24                             51
  N3                           29                             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  AMP PEAK 31(18Q11.2) MUTATED   108   9   7
  AMP PEAK 31(18Q11.2) WILD-TYPE 245  15  11
D31V6, multiclass
    clus
vv   AMP PEAK 31(18Q11.2) MUTATED AMP PEAK 31(18Q11.2) WILD-TYPE
  M0                          108                            245
  M1                            9                             15
  MX                            7                             11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                                cls
clus                               0   1
  AMP PEAK 31(18Q11.2) MUTATED    48  76
  AMP PEAK 31(18Q11.2) WILD-TYPE 103 168
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(18Q11.2) MUTATED     48   76
  AMP PEAK 31(18Q11.2) WILD-TYPE  103  168
        clus
vv       AMP PEAK 31(18Q11.2) MUTATED AMP PEAK 31(18Q11.2) WILD-TYPE
  FEMALE                           48                            103
  MALE                             76                            168
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 31(18Q11.2) MUTATED                                      14
  AMP PEAK 31(18Q11.2) WILD-TYPE                                    51
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 31(18Q11.2) MUTATED                                                       55
  AMP PEAK 31(18Q11.2) WILD-TYPE                                                    102
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 31(18Q11.2) MUTATED                                                                  15
  AMP PEAK 31(18Q11.2) WILD-TYPE                                                                54
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 31(18Q11.2) MUTATED                                                 21
  AMP PEAK 31(18Q11.2) WILD-TYPE                                               43
                                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                                          7
  AMP PEAK 31(18Q11.2) WILD-TYPE                                        2
D31V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 31(18Q11.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       14
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      55
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           15
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     7
                                                                   clus
vv                                                                  AMP PEAK 31(18Q11.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         51
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       102
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             54
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              43
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       2
[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     4 120
  AMP PEAK 31(18Q11.2) WILD-TYPE   2 269
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(18Q11.2) MUTATED      4  120
  AMP PEAK 31(18Q11.2) WILD-TYPE    2  269
     clus
vv    AMP PEAK 31(18Q11.2) MUTATED AMP PEAK 31(18Q11.2) WILD-TYPE
  NO                             4                              2
  YES                          120                            269
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 31(18Q11.2) MUTATED    95   8   8   8
  AMP PEAK 31(18Q11.2) WILD-TYPE 223   8  10  17
D31V10, multiclass
    clus
vv   AMP PEAK 31(18Q11.2) MUTATED AMP PEAK 31(18Q11.2) WILD-TYPE
  R0                           95                            223
  R1                            8                              8
  R2                            8                             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"
D31V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 31(18Q11.2) MUTATED      26                         2
  AMP PEAK 31(18Q11.2) WILD-TYPE    62                         4
                                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      79
  AMP PEAK 31(18Q11.2) WILD-TYPE   164
D31V12, multiclass
                                           clus
vv                                          AMP PEAK 31(18Q11.2) MUTATED
  ASIAN                                                               26
  BLACK OR AFRICAN AMERICAN                                            2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               79
                                           clus
vv                                          AMP PEAK 31(18Q11.2) WILD-TYPE
  ASIAN                                                                 62
  BLACK OR AFRICAN AMERICAN                                              4
  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"

Clustering(32) Variable = AMP PEAK 32(19P13.2) MUTATION ANALYSIS
D32V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 32(19P13.2) MUTATED    29   9
  AMP PEAK 32(19P13.2) WILD-TYPE 213 113
  AMP PEAK 32(19P13.2) MUTATED AMP PEAK 32(19P13.2) WILD-TYPE 
                            38                            326 
  AMP PEAK 32(19P13.2) MUTATED AMP PEAK 32(19P13.2) WILD-TYPE 
                             9                            113 
$`AMP PEAK 32(19P13.2) MUTATED`
TCGA-BR-6456 TCGA-BR-6801 TCGA-BR-7959 TCGA-BR-8370 TCGA-BR-A453 TCGA-BR-A4J8 
       10.13        21.11        18.71         3.32         3.02        13.51 
TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-5801 TCGA-CD-8528 TCGA-CD-8533 TCGA-CD-A486 
       20.65        13.64        13.18         0.10         0.13         6.35 
TCGA-CG-4436 TCGA-CG-5722 TCGA-CG-5727 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 
        7.99         0.99        79.07        19.13        20.55        18.54 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-A4YU TCGA-D7-A6EV 
        5.95        17.19        15.22        15.98        16.44        11.24 
TCGA-EQ-A4SO TCGA-F1-A72C TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8249 TCGA-HU-8604 
       16.24         8.12         0.56         1.55        14.17        12.10 
TCGA-HU-A4GD TCGA-IN-7808 TCGA-IN-A6RP TCGA-IN-A7NT TCGA-RD-A7BT TCGA-VQ-A8DT 
       22.75         3.45         6.44         5.56         8.61        37.74 
TCGA-VQ-A8E3 TCGA-VQ-A925 
       21.73         4.54 

$`AMP PEAK 32(19P13.2) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         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-6458 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.12        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        0.62        32.78        13.84        13.22        16.14         1.25 
TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
        8.98        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         0.69 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
        0.16        18.54        12.43         0.95         0.69        12.76 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       17.49         0.82         1.32         0.69        12.26         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       20.55         0.72         0.26        12.95         0.26        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        1.55         1.48         7.40         6.18        19.50         0.36 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19         2.96         0.95        13.74         4.31 
TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 
       14.04         0.36        19.17        14.79         0.69         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         0.72         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         2.14        13.45         0.20 
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         0.59 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         0.62        10.68        12.56         1.15         0.66 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         0.92        13.41        13.51        12.89         0.79 
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-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-8525 
        3.25        13.15         0.30         0.07         0.07         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-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         0.10         0.13         0.13         0.13         0.13 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        0.07         0.10         0.10         0.10        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         1.02         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
       14.01        29.98        47.05        19.07        12.03        21.99 
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-5723 
        6.97         1.02         1.02         0.99         6.02       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        55.04 
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-D7-6522 TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       18.61        17.85         4.14        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         0.23 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX 
        6.97        21.14        20.91        14.27         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-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
        2.96        15.65         4.34         7.40         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.79         6.58        14.47        72.23        21.27         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53         3.02        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       13.58         0.23        18.08        26.47         1.51         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-HU-A4HD 
       17.69        12.30         9.67         8.88         8.81        27.42 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       21.21        18.81         3.39        18.38         5.36         5.19 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NU TCGA-IP-7968 
       13.08         1.41         6.74         6.87         1.81         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        5.56        60.56        28.90         3.72        19.73         4.31 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         4.67        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-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       16.87         5.79         0.92         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       31.10        22.36        23.77         7.73        19.07        33.63 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
       46.26        16.31         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-A8PY 
       23.41        15.65        19.30        23.57        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q 
       59.18        28.70        11.70         8.68        49.25        20.81 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
        1.71         7.36         8.58         9.73        44.25         8.61 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J 
       55.43         6.58         5.72        40.08        29.98        21.11 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        4.21         0.79 

  AMP PEAK 32(19P13.2) MUTATED AMP PEAK 32(19P13.2) WILD-TYPE 
                          0.10                           0.07 
  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 
                        12.640                         11.555 
[1] "0.1 - 79.1 (12.6)"  "0.1 - 122.3 (11.6)"
[1] "hr=" "1.5"
D32V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 32(19P13.2) MUTATED         0        0        2        2         6
  AMP PEAK 32(19P13.2) WILD-TYPE       2       13       37       29        30
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 32(19P13.2) MUTATED           5         1         12          7
  AMP PEAK 32(19P13.2) WILD-TYPE        44         2         65         48
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 32(19P13.2) MUTATED            2        4
  AMP PEAK 32(19P13.2) WILD-TYPE         35       33
D32V3, multiclass
            clus
vv           AMP PEAK 32(19P13.2) MUTATED AMP PEAK 32(19P13.2) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              0                             13
  STAGE IB                              2                             37
  STAGE II                              2                             29
  STAGE IIA                             6                             30
  STAGE IIB                             5                             44
  STAGE III                             1                              2
  STAGE IIIA                           12                             65
  STAGE IIIB                            7                             48
  STAGE IIIC                            2                             35
  STAGE IV                              4                             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 32(19P13.2) MUTATED     1   9  25   7
  AMP PEAK 32(19P13.2) WILD-TYPE  20  78 148  97
D32V4, multiclass
    clus
vv   AMP PEAK 32(19P13.2) MUTATED AMP PEAK 32(19P13.2) WILD-TYPE
  T1                            1                             20
  T2                            9                             78
  T3                           25                            148
  T4                            7                             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
  AMP PEAK 32(19P13.2) MUTATED    12   8  11  10
  AMP PEAK 32(19P13.2) WILD-TYPE 110  99  64  69
D32V5, multiclass
    clus
vv   AMP PEAK 32(19P13.2) MUTATED AMP PEAK 32(19P13.2) WILD-TYPE
  N0                           12                            110
  N1                            8                             99
  N2                           11                             64
  N3                           10                             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                              M0  M1  MX
  AMP PEAK 32(19P13.2) MUTATED    36   4   2
  AMP PEAK 32(19P13.2) WILD-TYPE 317  20  16
D32V6, multiclass
    clus
vv   AMP PEAK 32(19P13.2) MUTATED AMP PEAK 32(19P13.2) WILD-TYPE
  M0                           36                            317
  M1                            4                             20
  MX                            2                             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                                cls
clus                               0   1
  AMP PEAK 32(19P13.2) MUTATED    17  25
  AMP PEAK 32(19P13.2) WILD-TYPE 134 219
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 32(19P13.2) MUTATED     17   25
  AMP PEAK 32(19P13.2) WILD-TYPE  134  219
        clus
vv       AMP PEAK 32(19P13.2) MUTATED AMP PEAK 32(19P13.2) WILD-TYPE
  FEMALE                           17                            134
  MALE                             25                            219
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 32(19P13.2) MUTATED                                       7
  AMP PEAK 32(19P13.2) WILD-TYPE                                    58
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 32(19P13.2) MUTATED                                                       16
  AMP PEAK 32(19P13.2) WILD-TYPE                                                    141
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 32(19P13.2) MUTATED                                                                   8
  AMP PEAK 32(19P13.2) WILD-TYPE                                                                61
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 32(19P13.2) MUTATED                                                  8
  AMP PEAK 32(19P13.2) WILD-TYPE                                               56
                                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                                        7
D32V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 32(19P13.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      16
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            8
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             8
  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                                                         58
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       141
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             61
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              56
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      8
  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"
D32V9, binary
                                cls
clus                               0   1
  AMP PEAK 32(19P13.2) MUTATED     0  42
  AMP PEAK 32(19P13.2) WILD-TYPE   6 347
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 32(19P13.2) MUTATED      0   42
  AMP PEAK 32(19P13.2) WILD-TYPE    6  347
     clus
vv    AMP PEAK 32(19P13.2) MUTATED AMP PEAK 32(19P13.2) WILD-TYPE
  NO                             0                              6
  YES                           42                            347
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 32(19P13.2) MUTATED    32   2   4   2
  AMP PEAK 32(19P13.2) WILD-TYPE 286  14  14  23
D32V10, multiclass
    clus
vv   AMP PEAK 32(19P13.2) MUTATED AMP PEAK 32(19P13.2) WILD-TYPE
  R0                           32                            286
  R1                            2                             14
  R2                            4                             14
  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                         0
  AMP PEAK 32(19P13.2) WILD-TYPE    79                         6
                                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      27
  AMP PEAK 32(19P13.2) WILD-TYPE   216
D32V12, multiclass
                                           clus
vv                                          AMP PEAK 32(19P13.2) MUTATED
  ASIAN                                                                9
  BLACK OR AFRICAN AMERICAN                                            0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               27
                                           clus
vv                                          AMP PEAK 32(19P13.2) WILD-TYPE
  ASIAN                                                                 79
  BLACK OR AFRICAN AMERICAN                                              6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = AMP PEAK 33(19Q12) MUTATION ANALYSIS
D33V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 33(19Q12) MUTATED    72  32
  AMP PEAK 33(19Q12) WILD-TYPE 170  90
  AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE 
                         104                          260 
  AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE 
                          32                           90 
$`AMP PEAK 33(19Q12) MUTATED`
TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 
       10.13         7.00         9.21        15.42        28.01        18.54 
TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8289 
        0.95        18.71         1.32         0.69        12.95         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8370 TCGA-BR-8373 TCGA-BR-8485 TCGA-BR-8487 
       16.31         1.55         3.32        14.79         9.21         1.12 
TCGA-BR-8590 TCGA-BR-8678 TCGA-BR-8690 TCGA-BR-A453 TCGA-BR-A4J1 TCGA-BR-A4J8 
        2.14        11.54        10.68         3.02         0.72        13.51 
TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 
       20.65        13.64        13.15        13.18         0.30         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
        0.07         0.07         0.16         0.13         6.35         0.13 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4438 TCGA-CG-4444 TCGA-CG-4449 
        0.13         0.13         0.10        54.08        47.05        19.07 
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5722 TCGA-CG-5730 TCGA-D7-5577 TCGA-D7-5579 
       21.99        22.98         0.99         4.01        12.36        11.93 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       19.13        18.84        18.54        17.19         4.14        15.22 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A4YY TCGA-D7-A6F0 
       10.55        12.33        21.14        16.44        13.78         2.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7735 
        7.13         0.62         7.79        16.24        72.23         0.39 
TCGA-FP-7916 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
        3.02         0.56         1.55        14.27        12.59        14.17 
TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4H0 
       12.10        24.30        22.75        25.81        11.77         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RL 
       12.95        12.30        27.42         3.45        18.38         5.19 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-RD-A7BT TCGA-RD-A7BW 
        1.41         6.44         5.56        60.56         8.61         4.67 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E2 
       35.61         5.79        37.74         5.46        13.25        31.10 
TCGA-VQ-A8P5 TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A91A TCGA-VQ-A91U TCGA-VQ-A91X 
        7.73        17.85         1.87        28.70         1.71         8.58 
TCGA-VQ-A922 TCGA-VQ-A925 
        8.61         4.54 

$`AMP PEAK 33(19Q12) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         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-6565 
       15.95        13.12        13.68        39.12         0.82         0.62 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        13.84        13.22        16.14         1.25         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-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 
       35.24        23.93         0.69         0.16        12.43         0.69 
TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       12.76        17.49         0.82        12.26         0.49        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        0.72         0.26         1.48         7.40         6.18        19.50 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        0.36         0.26        22.19         2.96         0.95        13.74 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 
        4.31        14.04         0.36        19.17         0.69         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8588 
       15.85         3.72         5.39         0.72        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
       15.81        13.45         0.20         7.53         0.49        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U 
       16.44         0.59        15.68         0.62        12.56         1.15 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        0.66        22.26         0.92        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.79        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-5803 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 
        3.25         0.07         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         0.13         0.07         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 
        7.99         8.05         4.01        14.01        29.98        12.03 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        12.00        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 
        1.02         1.02         0.99         6.02       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        79.07        65.10        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
        7.99        12.66        20.55        18.61        17.85         5.95 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       15.98        12.79        11.31        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       17.19         0.23         6.97        20.91        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       15.16        14.76        13.71        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-F1-6177 TCGA-F1-6874 
        9.76        15.65         4.34         7.40         6.58        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       21.27         8.12        19.53        22.29        17.06        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-8243 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 
        5.92        11.41        10.62         0.76         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       11.84        24.20         3.25        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-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 
       17.69         9.67         8.88         8.81        21.21        18.81 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT 
        3.39         5.36        13.08         6.74         6.87         5.56 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        1.81         2.53        28.90         3.72        19.73         4.31 
TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
       11.05        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-VQ-A8DL 
      116.38        71.38        57.44         8.94        16.87         0.92 
TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       13.02        21.73        22.36        23.77        19.07        33.63 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       46.26        16.31         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 
       19.30        23.57        64.57        14.33        59.18        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z 
        8.68        49.25        20.81         7.36         9.73        44.25 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J 
       55.43         6.58         5.72        40.08        29.98        21.11 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        4.21         0.79 

  AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE 
                        0.07                         0.07 
  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 
                       10.34                        11.92 
[1] "0.1 - 72.2 (10.3)"  "0.1 - 122.3 (11.9)"
[1] "hr=" "1"  
D33V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 33(19Q12) MUTATED         0        4       12        9        11
  AMP PEAK 33(19Q12) WILD-TYPE       2        9       27       22        25
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 33(19Q12) MUTATED          14         1         26         16
  AMP PEAK 33(19Q12) WILD-TYPE        35         2         51         39
                              vv
clus                           STAGE IIIC STAGE IV
  AMP PEAK 33(19Q12) MUTATED            6       12
  AMP PEAK 33(19Q12) WILD-TYPE         31       25
D33V3, multiclass
            clus
vv           AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE
  STAGE I                             0                            2
  STAGE IA                            4                            9
  STAGE IB                           12                           27
  STAGE II                            9                           22
  STAGE IIA                          11                           25
  STAGE IIB                          14                           35
  STAGE III                           1                            2
  STAGE IIIA                         26                           51
  STAGE IIIB                         16                           39
  STAGE IIIC                          6                           31
  STAGE IV                           12                           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 33(19Q12) MUTATED     6  25  62  20
  AMP PEAK 33(19Q12) WILD-TYPE  15  62 111  84
D33V4, multiclass
    clus
vv   AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE
  T1                          6                           15
  T2                         25                           62
  T3                         62                          111
  T4                         20                           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
  AMP PEAK 33(19Q12) MUTATED   34 32 20 26
  AMP PEAK 33(19Q12) WILD-TYPE 88 75 55 53
D33V5, multiclass
    clus
vv   AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE
  N0                         34                           88
  N1                         32                           75
  N2                         20                           55
  N3                         26                           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"
                              vv
clus                            M0  M1  MX
  AMP PEAK 33(19Q12) MUTATED   101   8   7
  AMP PEAK 33(19Q12) WILD-TYPE 252  16  11
D33V6, multiclass
    clus
vv   AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE
  M0                        101                          252
  M1                          8                           16
  MX                          7                           11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                              cls
clus                             0   1
  AMP PEAK 33(19Q12) MUTATED    41  75
  AMP PEAK 33(19Q12) WILD-TYPE 110 169
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 33(19Q12) MUTATED     41   75
  AMP PEAK 33(19Q12) WILD-TYPE  110  169
        clus
vv       AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE
  FEMALE                         41                          110
  MALE                           75                          169
[1] 2 2
[1] FALSE
                              vv
clus                           STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 33(19Q12) MUTATED                                      16
  AMP PEAK 33(19Q12) WILD-TYPE                                    49
                              vv
clus                           STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 33(19Q12) MUTATED                                                       46
  AMP PEAK 33(19Q12) WILD-TYPE                                                    111
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 33(19Q12) MUTATED                                                                  21
  AMP PEAK 33(19Q12) WILD-TYPE                                                                48
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 33(19Q12) MUTATED                                                 18
  AMP PEAK 33(19Q12) WILD-TYPE                                               46
                              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                                          3
  AMP PEAK 33(19Q12) WILD-TYPE                                        6
D33V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 33(19Q12) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     16
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    46
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         21
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                          18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                  4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   3
                                                                   clus
vv                                                                  AMP PEAK 33(19Q12) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     111
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           48
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            46
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    14
  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"
D33V9, binary
                              cls
clus                             0   1
  AMP PEAK 33(19Q12) MUTATED     4 112
  AMP PEAK 33(19Q12) WILD-TYPE   2 277
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 33(19Q12) MUTATED      4  112
  AMP PEAK 33(19Q12) WILD-TYPE    2  277
     clus
vv    AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE
  NO                           4                            2
  YES                        112                          277
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 33(19Q12) MUTATED    89   5   7   6
  AMP PEAK 33(19Q12) WILD-TYPE 229  11  11  19
D33V10, multiclass
    clus
vv   AMP PEAK 33(19Q12) MUTATED AMP PEAK 33(19Q12) WILD-TYPE
  R0                         89                          229
  R1                          5                           11
  R2                          7                           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"
D33V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 33(19Q12) MUTATED      32                         2
  AMP PEAK 33(19Q12) WILD-TYPE    56                         4
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 33(19Q12) MUTATED                                           1    66
  AMP PEAK 33(19Q12) WILD-TYPE                                         0   177
D33V12, multiclass
                                           clus
vv                                          AMP PEAK 33(19Q12) MUTATED
  ASIAN                                                             32
  BLACK OR AFRICAN AMERICAN                                          2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                             66
                                           clus
vv                                          AMP PEAK 33(19Q12) WILD-TYPE
  ASIAN                                                               56
  BLACK OR AFRICAN AMERICAN                                            4
  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"

Clustering(34) Variable = AMP PEAK 34(19Q13.32) MUTATION ANALYSIS
D34V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 34(19Q13.32) MUTATED    61  24
  AMP PEAK 34(19Q13.32) WILD-TYPE 181  98
  AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE 
                             85                             279 
  AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE 
                             24                              98 
$`AMP PEAK 34(19Q13.32) MUTATED`
TCGA-BR-4183 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7716 TCGA-BR-7901 
        6.61         7.00         0.62         9.21        28.01         0.95 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8286 TCGA-BR-8291 
       12.76        18.71         0.69        12.26        12.95        16.31 
TCGA-BR-8295 TCGA-BR-8370 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8690 TCGA-BR-A453 
        1.55         3.32         9.21         1.12        10.68         3.02 
TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-5801 TCGA-CD-8524 
        0.72        13.51        20.65        13.64        13.18         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C 
        0.07         0.07         0.10         0.13         0.13         0.13 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-4475 
       54.08         4.01        47.05        21.99        12.00        22.98 
TCGA-CG-5722 TCGA-CG-5730 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 
        0.99         4.01        12.36        11.93        19.13        18.54 
TCGA-D7-6526 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8578 TCGA-D7-A4YU 
       17.19        10.55        12.33        24.72        21.14        16.44 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-A4BF 
        7.79        16.24        72.23         0.39         3.02         1.55 
TCGA-FP-A8CX TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G2 
        0.23        14.27        12.59        14.17        12.10        24.30 
TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4H6 
       22.75        11.77         2.10        12.95        12.30         9.67 
TCGA-IN-7808 TCGA-IN-A6RL TCGA-IN-A6RP TCGA-KB-A6F7 TCGA-RD-A7BS TCGA-RD-A7BT 
        3.45         5.19         6.44        60.56        11.05         8.61 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E2 
       35.61         5.79        37.74         5.46        13.25        31.10 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PM TCGA-VQ-A91A TCGA-VQ-A91U TCGA-VQ-A91X 
       23.77         7.73         1.87        28.70         1.71         8.58 
TCGA-VQ-A922 
        8.61 

$`AMP PEAK 34(19Q13.32) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
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-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       13.12        10.13        13.68        39.12         0.82        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       13.84        13.22        16.14         1.25         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-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       23.93        15.42         0.69         0.16        18.54        12.43 
TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8081 
        0.69        17.49         0.82         1.32         0.49        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        0.72         0.26         0.26         1.48         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       19.50         0.36         0.26        22.19         2.96         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       13.74         4.31        14.04         0.36        19.17        14.79 
TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
        0.69         0.26        15.85         3.72         5.39         0.72 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        15.81         2.14        13.45         0.20 
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         0.59 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ 
       15.68         0.62        12.56         1.15         0.66        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        0.92        13.41        13.51        12.89         0.79        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-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.30         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         6.35         0.13 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        0.07         0.10         0.10         0.10        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 
       27.02        15.95         1.02         7.99         8.05        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       29.98        19.07        12.03         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97         1.02         1.02         0.99         6.02 
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-D7-5578 TCGA-D7-6519 TCGA-D7-6520 
       55.04        21.07         7.99        12.66        20.55        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.61        17.85         5.95         4.14        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.79        11.31        16.80        19.50        17.19         0.23 
TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
        6.97        20.91        14.27         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-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
        2.96        15.65         4.34         7.40         7.13         0.62 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7998 
        6.58        14.47        21.27         8.12        19.53        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-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
       26.47         1.51         5.92        11.41        10.62         0.76 
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-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-A4H8 TCGA-HU-A4HB 
       10.19         0.26        19.36        17.69         8.88         8.81 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       27.42        21.21        18.81         3.39        18.38         5.36 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU 
       13.08         1.41         6.74         6.87         5.56         1.81 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        2.53         5.56        28.90         3.72        19.73         4.31 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        4.67        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-VQ-A8DL 
      116.38        71.38        57.44         8.94        16.87         0.92 
TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       13.02        21.73        22.36        19.07        33.63        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       16.31         2.70        17.85         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D 
       19.30        23.57        64.57        14.33        59.18        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z 
        8.68        49.25        20.81         7.36         9.73        44.25 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B 
       55.43         4.54         6.58         5.72        40.08        29.98 
TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11         4.21         0.79 

  AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE 
                           0.07                            0.07 
  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 
                          11.05                           11.70 
[1] "0.1 - 72.2 (11.1)"  "0.1 - 122.3 (11.7)"
[1] "hr=" "1.2"
D34V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 34(19Q13.32) MUTATED         0        3        7        4         6
  AMP PEAK 34(19Q13.32) WILD-TYPE       2       10       32       27        30
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 34(19Q13.32) MUTATED          14         1         25         14
  AMP PEAK 34(19Q13.32) WILD-TYPE        35         2         52         41
                                 vv
clus                              STAGE IIIC STAGE IV
  AMP PEAK 34(19Q13.32) MUTATED            6       12
  AMP PEAK 34(19Q13.32) WILD-TYPE         31       25
D34V3, multiclass
            clus
vv           AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE
  STAGE I                                0                               2
  STAGE IA                               3                              10
  STAGE IB                               7                              32
  STAGE II                               4                              27
  STAGE IIA                              6                              30
  STAGE IIB                             14                              35
  STAGE III                              1                               2
  STAGE IIIA                            25                              52
  STAGE IIIB                            14                              41
  STAGE IIIC                             6                              31
  STAGE IV                              12                              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 34(19Q13.32) MUTATED     4  17  50  23
  AMP PEAK 34(19Q13.32) WILD-TYPE  17  70 123  81
D34V4, multiclass
    clus
vv   AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE
  T1                             4                              17
  T2                            17                              70
  T3                            50                             123
  T4                            23                              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
  AMP PEAK 34(19Q13.32) MUTATED   24 32 14 23
  AMP PEAK 34(19Q13.32) WILD-TYPE 98 75 61 56
D34V5, multiclass
    clus
vv   AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE
  N0                            24                              98
  N1                            32                              75
  N2                            14                              61
  N3                            23                              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"
                                 vv
clus                               M0  M1  MX
  AMP PEAK 34(19Q13.32) MUTATED    82   7   7
  AMP PEAK 34(19Q13.32) WILD-TYPE 271  17  11
D34V6, multiclass
    clus
vv   AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE
  M0                            82                             271
  M1                             7                              17
  MX                             7                              11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                                 cls
clus                                0   1
  AMP PEAK 34(19Q13.32) MUTATED    36  60
  AMP PEAK 34(19Q13.32) WILD-TYPE 115 184
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 34(19Q13.32) MUTATED     36   60
  AMP PEAK 34(19Q13.32) WILD-TYPE  115  184
        clus
vv       AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE
  FEMALE                            36                             115
  MALE                              60                             184
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 34(19Q13.32) MUTATED                                      14
  AMP PEAK 34(19Q13.32) WILD-TYPE                                    51
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 34(19Q13.32) MUTATED                                                       36
  AMP PEAK 34(19Q13.32) WILD-TYPE                                                    121
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 34(19Q13.32) MUTATED                                                                  16
  AMP PEAK 34(19Q13.32) WILD-TYPE                                                                53
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 34(19Q13.32) MUTATED                                                 16
  AMP PEAK 34(19Q13.32) WILD-TYPE                                               48
                                 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                                          4
  AMP PEAK 34(19Q13.32) WILD-TYPE                                        5
D34V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 34(19Q13.32) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        14
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       36
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            16
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      4
                                                                   clus
vv                                                                  AMP PEAK 34(19Q13.32) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          51
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        121
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              53
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               48
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       15
  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"
D34V9, binary
                                 cls
clus                                0   1
  AMP PEAK 34(19Q13.32) MUTATED     4  92
  AMP PEAK 34(19Q13.32) WILD-TYPE   2 297
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 34(19Q13.32) MUTATED      4   92
  AMP PEAK 34(19Q13.32) WILD-TYPE    2  297
     clus
vv    AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE
  NO                              4                               2
  YES                            92                             297
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 34(19Q13.32) MUTATED    73   5   6   6
  AMP PEAK 34(19Q13.32) WILD-TYPE 245  11  12  19
D34V10, multiclass
    clus
vv   AMP PEAK 34(19Q13.32) MUTATED AMP PEAK 34(19Q13.32) WILD-TYPE
  R0                            73                             245
  R1                             5                              11
  R2                             6                              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"
D34V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 34(19Q13.32) MUTATED      26                         2
  AMP PEAK 34(19Q13.32) WILD-TYPE    62                         4
                                 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      52
  AMP PEAK 34(19Q13.32) WILD-TYPE   191
D34V12, multiclass
                                           clus
vv                                          AMP PEAK 34(19Q13.32) MUTATED
  ASIAN                                                                26
  BLACK OR AFRICAN AMERICAN                                             2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                52
                                           clus
vv                                          AMP PEAK 34(19Q13.32) WILD-TYPE
  ASIAN                                                                  62
  BLACK OR AFRICAN AMERICAN                                               4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               0
  WHITE                                                                 191
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = AMP PEAK 35(20Q13.2) MUTATION ANALYSIS
D35V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 35(20Q13.2) MUTATED   162  83
  AMP PEAK 35(20Q13.2) WILD-TYPE  80  39
  AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE 
                           245                            119 
  AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE 
                            83                             39 
$`AMP PEAK 35(20Q13.2) MUTATED`
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4280 
        6.61         6.97         4.64        18.35        30.90         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.12        10.13        13.68         7.00        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6801 TCGA-BR-6852 
        0.82         0.62        13.22        16.14        21.11        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       12.82         9.21        35.24        15.42        28.01         0.69 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 
        0.16        18.54         0.95        12.76        18.71         0.82 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 
        1.32         0.69         0.49         0.26         0.26        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8381 
        1.55         1.48         7.40        14.04        14.79         0.26 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8590 
        5.39         0.72         9.21        20.22        15.81         2.14 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         0.59        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
        0.62        10.68         1.15         0.66        22.26         0.92 
TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
       12.89         0.72         0.53        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       20.42         1.15        13.64         3.25        13.15        13.18 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
        0.16         0.10         0.13         0.13         6.35         0.13 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 
        0.13         0.13         0.07         0.10         0.10        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        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-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
       21.99        18.97         7.07        12.00        22.98        30.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        1.02         1.02         0.99        12.03        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       79.07         4.01        55.04         7.99        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         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 
       17.19         4.14        15.22        15.98        12.79        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8576 TCGA-D7-8578 
       12.33        24.72        16.80        19.50         6.97        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A6ET 
       20.91        14.27        16.44         5.92        15.16        13.71 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A 
       11.24        11.31         9.76         2.96        15.65         7.40 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
        0.62         7.79        16.24        14.47        72.23         8.12 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8631 
        0.39        19.53         3.02        22.29        17.06         0.56 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        1.55         0.23        26.47         1.51         5.92        14.27 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       12.59        14.17        12.10        10.62         0.76        24.30 
TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
       12.30         3.25        22.75        25.81        11.77         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       17.69        12.30         9.67         8.81        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RR 
        3.45         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 
        6.87         5.56         1.81         2.53         5.56        60.56 
TCGA-KB-A93H TCGA-MX-A663 TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 
       28.90         4.31         8.61        16.67        37.91       115.69 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       57.44         8.94        35.61         5.79         0.92        37.74 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PC 
        5.46        13.25        13.02        31.10        21.73        46.26 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A8PU TCGA-VQ-A8PX 
        2.70        17.85         1.87        15.65        23.57        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91U TCGA-VQ-A91W 
       14.33        59.18        28.70         8.68         1.71         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A928 
        8.58         9.73        44.25         8.61         4.54         5.72 
TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       40.08        29.98        21.11         4.21         0.79 

$`AMP PEAK 35(20Q13.2) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4188 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 
        5.62        11.70         7.43         6.18         9.57        34.68 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 
       32.78        13.84         1.25         8.98        30.90        31.20 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8078 
       24.76        23.93        12.43         0.69        17.49        12.26 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       20.55         0.72        12.95         6.18        19.50         0.36 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19         2.96         0.95        13.74         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8382 TCGA-BR-8384 
        3.32         0.36        19.17         0.69        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         0.20        15.81        12.56 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 
        3.02        13.41        13.51         0.79        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         0.13         0.10         1.02 
TCGA-CG-4465 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5728 
        9.01         6.97         0.99         6.02       105.07        65.10 
TCGA-CG-5733 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6818 TCGA-D7-8574 TCGA-D7-8575 
       21.07        18.61        17.85        10.55        17.19         0.23 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6EY TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6177 
       13.78        14.76        11.44         4.34         7.13         6.58 
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-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 
        3.72        19.73        11.05         4.67       122.30        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
      116.38        71.38        16.87        22.36        23.77         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PT 
       19.07        33.63        16.31         9.27        23.41        19.30 
TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A924 TCGA-VQ-A927 
       11.70        49.25        20.81        55.43         6.58 

  AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE 
                          0.07                           0.07 
  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 
                         11.24                          12.26 
[1] "0.1 - 115.7 (11.2)" "0.1 - 122.3 (12.3)"
[1] "hr=" "1.2"
D35V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 35(20Q13.2) MUTATED         1       11       23       18        23
  AMP PEAK 35(20Q13.2) WILD-TYPE       1        2       16       13        13
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 35(20Q13.2) MUTATED          35         3         56         37
  AMP PEAK 35(20Q13.2) WILD-TYPE        14         0         21         18
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 35(20Q13.2) MUTATED           20       24
  AMP PEAK 35(20Q13.2) WILD-TYPE         17       13
D35V3, multiclass
            clus
vv           AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                             11                              2
  STAGE IB                             23                             16
  STAGE II                             18                             13
  STAGE IIA                            23                             13
  STAGE IIB                            35                             14
  STAGE III                             3                              0
  STAGE IIIA                           56                             21
  STAGE IIIB                           37                             18
  STAGE IIIC                           20                             17
  STAGE IV                             24                             13
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 35(20Q13.2) MUTATED    13  61 121  60
  AMP PEAK 35(20Q13.2) WILD-TYPE   8  26  52  44
D35V4, multiclass
    clus
vv   AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE
  T1                           13                              8
  T2                           61                             26
  T3                          121                             52
  T4                           60                             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"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 35(20Q13.2) MUTATED   74 78 54 47
  AMP PEAK 35(20Q13.2) WILD-TYPE 48 29 21 32
D35V5, multiclass
    clus
vv   AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE
  N0                           74                             48
  N1                           78                             29
  N2                           54                             21
  N3                           47                             32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  AMP PEAK 35(20Q13.2) MUTATED   231  15  15
  AMP PEAK 35(20Q13.2) WILD-TYPE 122   9   3
D35V6, multiclass
    clus
vv   AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE
  M0                          231                            122
  M1                           15                              9
  MX                           15                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                                cls
clus                               0   1
  AMP PEAK 35(20Q13.2) MUTATED    88 173
  AMP PEAK 35(20Q13.2) WILD-TYPE  63  71
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 35(20Q13.2) MUTATED     88  173
  AMP PEAK 35(20Q13.2) WILD-TYPE   63   71
        clus
vv       AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE
  FEMALE                           88                             63
  MALE                            173                             71
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 35(20Q13.2) MUTATED                                      29
  AMP PEAK 35(20Q13.2) WILD-TYPE                                    36
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 35(20Q13.2) MUTATED                                                       98
  AMP PEAK 35(20Q13.2) WILD-TYPE                                                     59
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 35(20Q13.2) MUTATED                                                                  55
  AMP PEAK 35(20Q13.2) WILD-TYPE                                                                14
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 35(20Q13.2) MUTATED                                                 51
  AMP PEAK 35(20Q13.2) WILD-TYPE                                               13
                                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                                          7
  AMP PEAK 35(20Q13.2) WILD-TYPE                                        2
D35V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 35(20Q13.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       29
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      98
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           55
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            51
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     7
                                                                   clus
vv                                                                  AMP PEAK 35(20Q13.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         36
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        59
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       2
[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     4 257
  AMP PEAK 35(20Q13.2) WILD-TYPE   2 132
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 35(20Q13.2) MUTATED      4  257
  AMP PEAK 35(20Q13.2) WILD-TYPE    2  132
     clus
vv    AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE
  NO                             4                              2
  YES                          257                            132
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 35(20Q13.2) MUTATED   215   8  13  14
  AMP PEAK 35(20Q13.2) WILD-TYPE 103   8   5  11
D35V10, multiclass
    clus
vv   AMP PEAK 35(20Q13.2) MUTATED AMP PEAK 35(20Q13.2) WILD-TYPE
  R0                          215                            103
  R1                            8                              8
  R2                           13                              5
  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                         4
  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     155
  AMP PEAK 35(20Q13.2) WILD-TYPE    88
D35V12, multiclass
                                           clus
vv                                          AMP PEAK 35(20Q13.2) MUTATED
  ASIAN                                                               61
  BLACK OR AFRICAN AMERICAN                                            4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              155
                                           clus
vv                                          AMP PEAK 35(20Q13.2) WILD-TYPE
  ASIAN                                                                 27
  BLACK OR AFRICAN AMERICAN                                              2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                 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"

Clustering(36) Variable = AMP PEAK 36(XQ27.3) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 36(XQ27.3) MUTATED    45  25
  AMP PEAK 36(XQ27.3) WILD-TYPE 197  97
  AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE 
                           70                           294 
  AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE 
                           25                            97 
$`AMP PEAK 36(XQ27.3) MUTATED`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-6458 TCGA-BR-6801 
       11.70         6.61         4.64        18.35         7.00        21.11 
TCGA-BR-7717 TCGA-BR-8059 TCGA-BR-8362 TCGA-BR-8370 TCGA-BR-8486 TCGA-BR-8677 
        0.69         0.82         0.36         3.32        20.22         0.49 
TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J2 
       15.81         0.59         1.15        22.26        12.89        14.17 
TCGA-BR-A4QI TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-A4MG TCGA-CG-4300 TCGA-CG-4437 
       13.64         0.07         0.07         0.07        20.02         8.05 
TCGA-CG-4438 TCGA-CG-4460 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5727 TCGA-CG-5734 
       54.08        21.99         7.07        12.00        79.07         7.99 
TCGA-D7-5579 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6822 
       11.93        18.54        17.19        15.22        15.98        12.33 
TCGA-D7-A4YX TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 
       15.16        11.24         9.76        15.65         7.40         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-A4BF TCGA-HU-8244 TCGA-HU-8604 
        7.79        72.23         0.39         1.55        14.27        12.10 
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-A4H5 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RP TCGA-VQ-A8E2 
       12.30         3.45         3.39         5.19         6.44        31.10 
TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91E 
        7.73        46.26        23.57        14.33        59.18         8.68 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91Z TCGA-VQ-AA68 
       20.81         1.71        44.25        40.08 

$`AMP PEAK 36(XQ27.3) WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        5.62         6.97         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        13.12        10.13        13.68 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12         0.82         0.62        32.78        13.84        13.22 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       16.14         1.25         8.98        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-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       28.01         0.16        18.54        12.43         0.95         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        17.49         1.32         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.49        20.55         0.72         0.26        12.95         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         1.55         1.48         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         2.96         0.95        13.74         4.31 
TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 
       14.04         0.36        19.17        14.79         0.69         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         0.72         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         2.14        13.45         0.20         7.53 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       11.54        16.44        15.68         0.62        10.68        12.56 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
        0.66         3.02         0.92        13.41        13.51         0.79 
TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72         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-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-8525 TCGA-CD-8526 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         6.35         0.13 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.13         0.13         0.13         0.10         0.10         0.10 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4440 
        3.02        27.02        15.95         1.02         7.99         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 
       14.01        29.98        47.05        19.07        12.03         9.01 
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         1.02         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-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-D7-5577 
       28.96        65.10         4.01        55.04        21.07        12.36 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
       12.66        19.13        20.55        18.84        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 
        5.95         4.14        12.79        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         0.23         6.97        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27        16.44         5.92        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A748 TCGA-D7-A74B 
       13.71        11.31        11.44         2.96         4.34         7.13 
TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 
       16.24         6.58        14.47        21.27         8.12        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        3.02        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-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 
       12.59        14.17        11.41        10.62         0.76         5.59 
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-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-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       19.36        17.69         9.67         8.88         8.81        27.42 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO 
       21.21        18.81        18.38         5.36        13.08         1.41 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 
        6.74         6.87         5.56         1.81         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS 
       60.56        28.90         3.72        19.73         4.31        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         4.67        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-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       16.87         5.79         0.92        37.74         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       13.02        21.73        22.36        23.77        19.07        33.63 
TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       16.31         2.70        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K 
       15.65        19.30        64.57        28.70        11.70        49.25 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 
        7.36         8.58         9.73         8.61        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        6.58         5.72        29.98        21.11         4.21         0.79 

  AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE 
                         0.07                          0.07 
  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 
                        12.20                         11.31 
[1] "0.1 - 79.1 (12.2)"  "0.1 - 122.3 (11.3)"
[1] "hr=" "1"  
D36V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 36(XQ27.3) MUTATED         1        5        7        5         6
  AMP PEAK 36(XQ27.3) WILD-TYPE       1        8       32       26        30
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 36(XQ27.3) MUTATED          11         2         14          9
  AMP PEAK 36(XQ27.3) WILD-TYPE        38         1         63         46
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 36(XQ27.3) MUTATED            3       10
  AMP PEAK 36(XQ27.3) WILD-TYPE         34       27
D36V3, multiclass
            clus
vv           AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             5                             8
  STAGE IB                             7                            32
  STAGE II                             5                            26
  STAGE IIA                            6                            30
  STAGE IIB                           11                            38
  STAGE III                            2                             1
  STAGE IIIA                          14                            63
  STAGE IIIB                           9                            46
  STAGE IIIC                           3                            34
  STAGE IV                            10                            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 36(XQ27.3) MUTATED     6  17  35  16
  AMP PEAK 36(XQ27.3) WILD-TYPE  15  70 138  88
D36V4, multiclass
    clus
vv   AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE
  T1                           6                            15
  T2                          17                            70
  T3                          35                           138
  T4                          16                            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 36(XQ27.3) MUTATED   25 23 16 11
  AMP PEAK 36(XQ27.3) WILD-TYPE 97 84 59 68
D36V5, multiclass
    clus
vv   AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE
  N0                          25                            97
  N1                          23                            84
  N2                          16                            59
  N3                          11                            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"
                               vv
clus                             M0  M1  MX
  AMP PEAK 36(XQ27.3) MUTATED    71   4   2
  AMP PEAK 36(XQ27.3) WILD-TYPE 282  20  16
D36V6, multiclass
    clus
vv   AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE
  M0                          71                           282
  M1                           4                            20
  MX                           2                            16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                               cls
clus                              0   1
  AMP PEAK 36(XQ27.3) MUTATED    31  46
  AMP PEAK 36(XQ27.3) WILD-TYPE 120 198
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 36(XQ27.3) MUTATED     31   46
  AMP PEAK 36(XQ27.3) WILD-TYPE  120  198
        clus
vv       AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE
  FEMALE                          31                           120
  MALE                            46                           198
[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                                    57
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 36(XQ27.3) MUTATED                                                       27
  AMP PEAK 36(XQ27.3) WILD-TYPE                                                    130
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 36(XQ27.3) MUTATED                                                                  14
  AMP PEAK 36(XQ27.3) WILD-TYPE                                                                55
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 36(XQ27.3) MUTATED                                                 20
  AMP PEAK 36(XQ27.3) WILD-TYPE                                               44
                               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                                        6
D36V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 36(XQ27.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     27
  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                                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    3
                                                                   clus
vv                                                                  AMP PEAK 36(XQ27.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        57
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            55
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             44
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     6
  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"
D36V9, binary
                               cls
clus                              0   1
  AMP PEAK 36(XQ27.3) MUTATED     1  76
  AMP PEAK 36(XQ27.3) WILD-TYPE   5 313
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 36(XQ27.3) MUTATED      1   76
  AMP PEAK 36(XQ27.3) WILD-TYPE    5  313
     clus
vv    AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE
  NO                            1                             5
  YES                          76                           313
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 36(XQ27.3) MUTATED    61   4   2   6
  AMP PEAK 36(XQ27.3) WILD-TYPE 257  12  16  19
D36V10, multiclass
    clus
vv   AMP PEAK 36(XQ27.3) MUTATED AMP PEAK 36(XQ27.3) WILD-TYPE
  R0                          61                           257
  R1                           4                            12
  R2                           2                            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"
D36V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 36(XQ27.3) MUTATED      19                         2
  AMP PEAK 36(XQ27.3) WILD-TYPE    69                         4
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 36(XQ27.3) MUTATED                                           0    45
  AMP PEAK 36(XQ27.3) WILD-TYPE                                         1   198
D36V12, multiclass
                                           clus
vv                                          AMP PEAK 36(XQ27.3) MUTATED
  ASIAN                                                              19
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              45
                                           clus
vv                                          AMP PEAK 36(XQ27.3) WILD-TYPE
  ASIAN                                                                69
  BLACK OR AFRICAN AMERICAN                                             4
  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"

Clustering(37) Variable = DEL PEAK  1(1P36.11) MUTATION ANALYSIS
D37V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.11) MUTATED    70  36
  DEL PEAK  1(1P36.11) WILD-TYPE 172  86
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           106                            258 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            36                             86 
$`DEL PEAK  1(1P36.11) MUTATED`
TCGA-B7-5816 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6458 
        5.62        18.35         6.18         9.57        10.13         7.00 
TCGA-BR-6565 TCGA-BR-7704 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8289 TCGA-BR-8483 
        0.62        35.24        18.71         1.32         0.26         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8690 
        0.72         9.21         0.49        11.54         0.59        10.68 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
        0.66        22.26        20.65        20.42         1.15        13.64 
TCGA-CD-5799 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 
        3.25         0.07         0.07         0.13         0.10         0.13 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MH 
        0.13         6.35         0.13         0.13         0.13         0.10 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 
       20.02         3.02         7.99         8.05        54.08        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5719 
       29.98        47.05        19.07         7.07        30.97         1.02 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6526 
       12.03        15.02         4.01        11.93        20.55        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 
        4.14        15.22        12.79        12.33        24.72        19.50 
TCGA-D7-8575 TCGA-D7-A4YY TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-5647 
        0.23        13.78        11.31         2.96         7.40         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-A72C TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-A4BF 
        7.79        16.24         8.12        17.06        13.58         1.55 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GF TCGA-HU-A4GP 
        1.51         5.92        14.17        12.10        25.81         8.98 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-KB-A6F7 TCGA-KB-A93H 
       12.95        17.69        12.30        27.42        60.56        28.90 
TCGA-MX-A663 TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N9 TCGA-VQ-A8DL 
        4.31         8.61        16.67       122.30        35.61         0.92 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       13.25        13.02         7.73        46.26         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A91A TCGA-VQ-A91Q TCGA-VQ-A91Y TCGA-VQ-A91Z 
        1.87        23.57        28.70        20.81         9.73        44.25 
TCGA-VQ-A925 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-ZQ-A9CR 
        4.54        40.08        29.98         0.79 

$`DEL PEAK  1(1P36.11) WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
       11.70         6.61         6.97         4.64         7.43        30.90 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        6.61        34.68        15.95        13.12        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        0.82        32.78        13.84        13.22        16.14         1.25 
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         0.69 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
        0.16        18.54        12.43         0.95         0.69        12.76 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49         0.82         0.69        12.26         0.49        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.72         0.26        12.95        16.31         1.55         1.48 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        19.50         0.36         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
        2.96         0.95        13.74         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 
        0.36        19.17        14.79         0.69         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        3.72        20.22         1.12        12.79        15.81         2.14 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 
       13.45         0.20         7.53        15.81        16.44        15.68 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
        0.62        12.56         1.15         3.02         0.92        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         0.79         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4QL 
       12.82         0.66        19.36        13.51         0.46        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        5.13         2.83        13.15        13.18         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8536 
        0.07         0.07         0.10         0.16         0.10         0.10 
TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 
        0.13         0.07         0.10         0.10        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4440 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 
        1.02         4.01        12.03        21.99         9.01        18.97 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 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-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 
        0.99       105.07        28.96        79.07        65.10        55.04 
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-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6818 
       18.54        18.61        17.85         5.95        15.98        10.55 
TCGA-D7-6820 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       11.31        16.80        17.19         6.97        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44         5.92        15.16        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74B 
       11.24        11.44         9.76        15.65         4.34         7.13 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        6.58        14.47        72.23        21.27         0.39        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A8CX 
        3.02        22.29        59.54         5.03         0.56         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 
       18.08        26.47        14.27        12.59        11.41        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-A4GQ 
        3.25        22.75        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-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88         8.81        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO 
        3.39        18.38         5.36         5.19        13.08         1.41 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 
        6.44         6.74         6.87         5.56         1.81         2.53 
TCGA-KB-A6F5 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MW 
        5.56         3.72        19.73        11.05         4.67        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-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       16.87         5.79        37.74         5.46        31.10        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PO 
       22.36        23.77        19.07        33.63        16.31         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       23.41        15.65        19.30        64.57        14.33        59.18 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X 
       11.70         8.68        49.25         1.71         7.36         8.58 
TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6J TCGA-ZA-A8F6 
        8.61        55.43         6.58         5.72        21.11         4.21 

  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                          0.07                           0.07 
  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 
                        10.405                         11.805 
[1] "0.1 - 122.3 (10.4)" "0.1 - 116.4 (11.8)"
[1] "hr=" "1.1"
D37V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  1(1P36.11) MUTATED         0        1       13       11        14
  DEL PEAK  1(1P36.11) WILD-TYPE       2       12       26       20        22
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  1(1P36.11) MUTATED          11         0         26         14
  DEL PEAK  1(1P36.11) WILD-TYPE        38         3         51         41
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK  1(1P36.11) MUTATED            5       15
  DEL PEAK  1(1P36.11) WILD-TYPE         32       22
D37V3, multiclass
            clus
vv           DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              1                             12
  STAGE IB                             13                             26
  STAGE II                             11                             20
  STAGE IIA                            14                             22
  STAGE IIB                            11                             38
  STAGE III                             0                              3
  STAGE IIIA                           26                             51
  STAGE IIIB                           14                             41
  STAGE IIIC                            5                             32
  STAGE IV                             15                             22
[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     2  29  56  25
  DEL PEAK  1(1P36.11) WILD-TYPE  19  58 117  79
D37V4, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  T1                            2                             19
  T2                           29                             58
  T3                           56                            117
  T4                           25                             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  1(1P36.11) MUTATED   35 32 22 22
  DEL PEAK  1(1P36.11) WILD-TYPE 87 75 53 57
D37V5, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  N0                           35                             87
  N1                           32                             75
  N2                           22                             53
  N3                           22                             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"
                                vv
clus                              M0  M1  MX
  DEL PEAK  1(1P36.11) MUTATED   101   9   6
  DEL PEAK  1(1P36.11) WILD-TYPE 252  15  12
D37V6, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  M0                          101                            252
  M1                            9                             15
  MX                            6                             12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED    42  74
  DEL PEAK  1(1P36.11) WILD-TYPE 109 170
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     42   74
  DEL PEAK  1(1P36.11) WILD-TYPE  109  170
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  FEMALE                           42                            109
  MALE                             74                            170
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK  1(1P36.11) MUTATED                                      10
  DEL PEAK  1(1P36.11) WILD-TYPE                                    55
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  1(1P36.11) MUTATED                                                       40
  DEL PEAK  1(1P36.11) WILD-TYPE                                                    117
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  1(1P36.11) MUTATED                                                                  24
  DEL PEAK  1(1P36.11) WILD-TYPE                                                                45
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  1(1P36.11) MUTATED                                                 29
  DEL PEAK  1(1P36.11) WILD-TYPE                                               35
                                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                                          4
  DEL PEAK  1(1P36.11) WILD-TYPE                                        5
D37V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  1(1P36.11) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       10
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      40
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           24
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            29
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     4
                                                                   clus
vv                                                                  DEL PEAK  1(1P36.11) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         55
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       117
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             45
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      14
  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"
D37V9, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED     3 113
  DEL PEAK  1(1P36.11) WILD-TYPE   3 276
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      3  113
  DEL PEAK  1(1P36.11) WILD-TYPE    3  276
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  NO                             3                              3
  YES                          113                            276
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  1(1P36.11) MUTATED    85   6   9   9
  DEL PEAK  1(1P36.11) WILD-TYPE 233  10   9  16
D37V10, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  R0                           85                            233
  R1                            6                             10
  R2                            9                              9
  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                         1
  DEL PEAK  1(1P36.11) WILD-TYPE    60                         5
                                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      66
  DEL PEAK  1(1P36.11) WILD-TYPE   177
D37V12, multiclass
                                           clus
vv                                          DEL PEAK  1(1P36.11) MUTATED
  ASIAN                                                               28
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               66
                                           clus
vv                                          DEL PEAK  1(1P36.11) WILD-TYPE
  ASIAN                                                                 60
  BLACK OR AFRICAN AMERICAN                                              5
  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"

Clustering(38) Variable = DEL PEAK  2(1P13.2) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P13.2) MUTATED    54  23
  DEL PEAK  2(1P13.2) WILD-TYPE 188  99
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           77                           287 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           23                            99 
$`DEL PEAK  2(1P13.2) MUTATED`
TCGA-BR-6456 TCGA-BR-7704 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8289 TCGA-BR-8295 
       10.13        35.24         0.95        18.71         0.26         1.55 
TCGA-BR-8369 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8687 
       14.04         5.39         9.21        11.54         0.59         0.62 
TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J6 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       22.26        12.89         0.66        20.42         1.15        13.64 
TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-8527 TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8535 
        3.25         0.30         0.07         0.10         0.13         0.13 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4438 
        6.35         0.13         0.10         3.02         7.99        54.08 
TCGA-CG-4443 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-5724 TCGA-CG-5730 TCGA-D7-5579 
       29.98        18.97        22.98        12.03         4.01        11.93 
TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 
       20.55        18.54        17.19         4.14        15.22        12.79 
TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A74A 
       24.72        19.50        11.31         9.76        15.65         7.40 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-FP-7829 TCGA-FP-A4BF TCGA-HU-8238 
        0.62         7.79        16.24        19.53         1.55         1.51 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4HD TCGA-IN-A6RL TCGA-IN-A6RO 
       14.17        12.10        22.75        27.42         5.19         1.41 
TCGA-IP-7968 TCGA-KB-A93H TCGA-MX-A663 TCGA-RD-A7BT TCGA-VQ-A8DL TCGA-VQ-A8DT 
        2.53        28.90         4.31         8.61         0.92        37.74 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8P5 TCGA-VQ-A8PJ TCGA-VQ-A8PK 
        5.46        13.25        13.02         7.73         2.70        17.85 
TCGA-VQ-A8PO TCGA-VQ-A91A TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-AA6B 
        9.27        28.70        44.25         4.54        29.98 

$`DEL PEAK  2(1P13.2) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         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-6458 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.12        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        0.62        32.78        13.84        13.22        16.14         1.25 
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         0.69 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
        0.16        18.54        12.43         0.69        12.76        17.49 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
        0.82         1.32         0.69        12.26         0.49        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 
        0.72         0.26        12.95        16.31         1.48         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        19.50         0.36         0.26        22.19         2.96 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        13.74         4.31         3.32         0.36        19.17 
TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 
       14.79         0.69         0.26        15.85         3.72         0.72 
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         2.14        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 
        0.20         7.53         0.49        15.81        16.44        15.68 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS 
       10.68        12.56         1.15         0.66         3.02         0.92 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51         0.79         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4QL 
       12.82        19.36        13.51         0.46        20.65        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 
        5.13         2.83        13.15        13.18         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 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-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI 
        0.10         0.13         0.13         0.13         0.07         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
        0.10        20.02        27.02        15.95         1.02         8.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
        4.01        14.01        47.05        19.07        12.03        21.99 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01         7.07        12.00        30.97         6.97         1.02 
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-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07        65.10        55.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
       12.36        12.66        19.13        18.84        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 
        5.95        15.98        10.55        11.31        12.33        16.80 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19         0.23         6.97        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-A6EY TCGA-D7-A6F0 TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6177 
       11.24        11.44         2.96         4.34         7.13         6.58 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 
       14.47        72.23        21.27         8.12         0.39         3.02 
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-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-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-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-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-A4H5 
        0.26         2.10        12.95        19.36        17.69        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88         8.81        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
        3.39        18.38         5.36        13.08         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG 
        6.87         5.56         1.81         5.56        60.56         3.72 
TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       19.73        11.05         4.67        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-A7EB TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 
       35.61        16.87         5.79        31.10        21.73        22.36 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PM 
       23.77        19.07        33.63        46.26        16.31         1.87 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       23.41        15.65        19.30        23.57        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U 
       59.18        11.70         8.68        49.25        20.81         1.71 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 
        7.36         8.58         9.73         8.61        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        5.72        40.08        21.11         4.21         0.79 

  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                         0.07                          0.07 
  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 
                         9.76                         11.84 
[1] "0.1 - 54.1 (9.8)"   "0.1 - 122.3 (11.8)"
[1] "hr=" "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       2       11       32       24        25
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  2(1P13.2) MUTATED          10         0         20         11
  DEL PEAK  2(1P13.2) WILD-TYPE        39         3         57         44
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  2(1P13.2) MUTATED            2        9
  DEL PEAK  2(1P13.2) WILD-TYPE         35       28
D38V3, multiclass
            clus
vv           DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             2                            11
  STAGE IB                             7                            32
  STAGE II                             7                            24
  STAGE IIA                           11                            25
  STAGE IIB                           10                            39
  STAGE III                            0                             3
  STAGE IIIA                          20                            57
  STAGE IIIB                          11                            44
  STAGE IIIC                           2                            35
  STAGE IV                             9                            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  2(1P13.2) MUTATED     2  16  46  16
  DEL PEAK  2(1P13.2) WILD-TYPE  19  71 127  88
D38V4, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  T1                           2                            19
  T2                          16                            71
  T3                          46                           127
  T4                          16                            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  2(1P13.2) MUTATED   27 20 20 12
  DEL PEAK  2(1P13.2) WILD-TYPE 95 87 55 67
D38V5, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  N0                          27                            95
  N1                          20                            87
  N2                          20                            55
  N3                          12                            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"
                               vv
clus                             M0  M1  MX
  DEL PEAK  2(1P13.2) MUTATED    72   7   3
  DEL PEAK  2(1P13.2) WILD-TYPE 281  17  15
D38V6, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  M0                          72                           281
  M1                           7                            17
  MX                           3                            15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED    27  55
  DEL PEAK  2(1P13.2) WILD-TYPE 124 189
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     27   55
  DEL PEAK  2(1P13.2) WILD-TYPE  124  189
        clus
vv       DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  FEMALE                          27                           124
  MALE                            55                           189
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK  2(1P13.2) MUTATED                                       6
  DEL PEAK  2(1P13.2) WILD-TYPE                                    59
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  2(1P13.2) MUTATED                                                       29
  DEL PEAK  2(1P13.2) WILD-TYPE                                                    128
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  2(1P13.2) MUTATED                                                                  18
  DEL PEAK  2(1P13.2) WILD-TYPE                                                                51
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  2(1P13.2) MUTATED                                                 20
  DEL PEAK  2(1P13.2) WILD-TYPE                                               44
                               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                                          3
  DEL PEAK  2(1P13.2) WILD-TYPE                                        6
D38V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  2(1P13.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     29
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          18
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    3
                                                                   clus
vv                                                                  DEL PEAK  2(1P13.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            51
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             44
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     7
  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"
D38V9, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED     1  81
  DEL PEAK  2(1P13.2) WILD-TYPE   5 308
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      1   81
  DEL PEAK  2(1P13.2) WILD-TYPE    5  308
     clus
vv    DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  NO                            1                             5
  YES                          81                           308
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  2(1P13.2) MUTATED    62   3   8   3
  DEL PEAK  2(1P13.2) WILD-TYPE 256  13  10  22
D38V10, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  R0                          62                           256
  R1                           3                            13
  R2                           8                            10
  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                         1
  DEL PEAK  2(1P13.2) WILD-TYPE    69                         5
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  2(1P13.2) MUTATED                                           1    51
  DEL PEAK  2(1P13.2) WILD-TYPE                                         0   192
D38V12, multiclass
                                           clus
vv                                          DEL PEAK  2(1P13.2) MUTATED
  ASIAN                                                              19
  BLACK OR AFRICAN AMERICAN                                           1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              51
                                           clus
vv                                          DEL PEAK  2(1P13.2) WILD-TYPE
  ASIAN                                                                69
  BLACK OR AFRICAN AMERICAN                                             5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               192
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(39) Variable = DEL PEAK  3(1Q44) MUTATION ANALYSIS
D39V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  3(1Q44) MUTATED    15  11
  DEL PEAK  3(1Q44) WILD-TYPE 227 111
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         26                         338 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         11                         111 
$`DEL PEAK  3(1Q44) MUTATED`
TCGA-BR-6456 TCGA-BR-7704 TCGA-BR-8362 TCGA-BR-A452 TCGA-BR-A4PD TCGA-CD-5801 
       10.13        35.24         0.36         0.66        20.65        13.18 
TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4466 
        6.35         0.13         0.10         1.02        14.01        18.97 
TCGA-CG-4469 TCGA-CG-5724 TCGA-D7-6519 TCGA-D7-8576 TCGA-D7-A6F2 TCGA-HU-8604 
        7.07        12.03        20.55         6.97        15.65        12.10 
TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-IN-8663 TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 
        8.98         2.10         3.39         1.81         2.53         5.56 
TCGA-KB-A93H TCGA-VQ-A8PM 
       28.90         1.87 

$`DEL PEAK  3(1Q44) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         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-6458 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.12        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        0.62        32.78        13.84        13.22        16.14         1.25 
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         0.69 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
        0.16        18.54        12.43         0.95         0.69        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       18.71        17.49         0.82         1.32         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.49        20.55         0.72         0.26        12.95         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         1.55         1.48         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         2.96         0.95        13.74         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 
       14.04         3.32         0.36        19.17        14.79         0.69 
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         0.72         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         2.14        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        0.20         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        0.59        15.68         0.62        10.68        12.56         1.15 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        3.02        22.26         0.92        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        0.79         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-5802 
       11.57         5.13         2.83         3.25        13.15         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-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-A4MG TCGA-CD-A4MI 
        0.10         0.13         0.13         0.13         0.07         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
        0.10        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
        8.05        54.08         4.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
       12.03        21.99         9.01        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         1.02         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 
       55.04        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         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19         4.14        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 
        0.23        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-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.44         9.76         2.96         4.34         7.40         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        0.62         7.79        16.24         6.58        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27         8.12         0.39        19.53         3.02        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         1.55 
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        17.69 
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-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-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-KB-A6F7 
        1.41         6.44         6.74         6.87         5.56        60.56 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        3.72        19.73         4.31        11.05         8.61         4.67 
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-A7EB 
       71.38        57.44         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        37.74         5.46        13.25        13.02        31.10 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        22.36        23.77         7.73        19.07        33.63 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PP 
       46.26        16.31         2.70        17.85         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        19.30        23.57        64.57        14.33        59.18 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U 
       28.70        11.70         8.68        49.25        20.81         1.71 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 
        7.36         8.58         9.73        44.25         8.61        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J 
        4.54         6.58         5.72        40.08        29.98        21.11 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        4.21         0.79 

  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                       0.10                        0.07 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                      35.24                      122.30 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                      7.020                      11.805 
[1] "0.1 - 35.2 (7.0)"   "0.1 - 122.3 (11.8)"
[1] "hr=" "1.7"
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       2       13       37       30        31
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  3(1Q44) MUTATED           4         0          4          3
  DEL PEAK  3(1Q44) WILD-TYPE        45         3         73         52
                             vv
clus                          STAGE IIIC STAGE IV
  DEL PEAK  3(1Q44) MUTATED            4        4
  DEL PEAK  3(1Q44) WILD-TYPE         33       33
D39V3, multiclass
            clus
vv           DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  STAGE I                            0                           2
  STAGE IA                           0                          13
  STAGE IB                           2                          37
  STAGE II                           1                          30
  STAGE IIA                          5                          31
  STAGE IIB                          4                          45
  STAGE III                          0                           3
  STAGE IIIA                         4                          73
  STAGE IIIB                         3                          52
  STAGE IIIC                         4                          33
  STAGE IV                           4                          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  3(1Q44) MUTATED     0   6  15   6
  DEL PEAK  3(1Q44) WILD-TYPE  21  81 158  98
D39V4, multiclass
    clus
vv   DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  T1                         0                          21
  T2                         6                          81
  T3                        15                         158
  T4                         6                          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  3(1Q44) MUTATED     8   6   5   8
  DEL PEAK  3(1Q44) WILD-TYPE 114 101  70  71
D39V5, multiclass
    clus
vv   DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  N0                         8                         114
  N1                         6                         101
  N2                         5                          70
  N3                         8                          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                           M0  M1  MX
  DEL PEAK  3(1Q44) MUTATED    25   2   1
  DEL PEAK  3(1Q44) WILD-TYPE 328  22  17
D39V6, multiclass
    clus
vv   DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  M0                        25                         328
  M1                         2                          22
  MX                         1                          17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED    11  17
  DEL PEAK  3(1Q44) WILD-TYPE 140 227
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED     11   17
  DEL PEAK  3(1Q44) WILD-TYPE  140  227
        clus
vv       DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  FEMALE                        11                         140
  MALE                          17                         227
[1] 2 2
[1] FALSE
                             vv
clus                          STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK  3(1Q44) MUTATED                                       4
  DEL PEAK  3(1Q44) WILD-TYPE                                    61
                             vv
clus                          STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  3(1Q44) MUTATED                                                       13
  DEL PEAK  3(1Q44) WILD-TYPE                                                    144
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  3(1Q44) MUTATED                                                                   5
  DEL PEAK  3(1Q44) WILD-TYPE                                                                64
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  3(1Q44) MUTATED                                                  5
  DEL PEAK  3(1Q44) WILD-TYPE                                               59
                             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                                        8
D39V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  3(1Q44) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                   13
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                          5
  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                                                      61
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    144
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          64
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           59
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   21
  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"
D39V9, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED     0  28
  DEL PEAK  3(1Q44) WILD-TYPE   6 361
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED      0   28
  DEL PEAK  3(1Q44) WILD-TYPE    6  361
     clus
vv    DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  NO                          0                           6
  YES                        28                         361
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  3(1Q44) MUTATED    21   1   2   1
  DEL PEAK  3(1Q44) WILD-TYPE 297  15  16  24
D39V10, multiclass
    clus
vv   DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  R0                        21                         297
  R1                         1                          15
  R2                         2                          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"
D39V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  3(1Q44) MUTATED       9                         0
  DEL PEAK  3(1Q44) WILD-TYPE    79                         6
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  3(1Q44) MUTATED                                           0    13
  DEL PEAK  3(1Q44) WILD-TYPE                                         1   230
D39V12, multiclass
                                           clus
vv                                          DEL PEAK  3(1Q44) MUTATED
  ASIAN                                                             9
  BLACK OR AFRICAN AMERICAN                                         0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         0
  WHITE                                                            13
                                           clus
vv                                          DEL PEAK  3(1Q44) WILD-TYPE
  ASIAN                                                              79
  BLACK OR AFRICAN AMERICAN                                           6
  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"

Clustering(40) Variable = DEL PEAK  4(1Q44) MUTATION ANALYSIS
D40V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  4(1Q44) MUTATED    14   9
  DEL PEAK  4(1Q44) WILD-TYPE 228 113
  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE 
                         23                         341 
  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE 
                          9                         113 
$`DEL PEAK  4(1Q44) MUTATED`
TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6705 TCGA-BR-7704 TCGA-BR-8077 TCGA-BR-8362 
       10.13         7.00        13.84        35.24         0.69         0.36 
TCGA-BR-A4PD TCGA-CD-A486 TCGA-CD-A48A TCGA-CG-4441 TCGA-CG-5724 TCGA-D7-6519 
       20.65         6.35         0.13        14.01        12.03        20.55 
TCGA-D7-8576 TCGA-D7-A6F2 TCGA-HU-8604 TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-IN-8663 
        6.97        15.65        12.10         8.98         2.10         3.39 
TCGA-IN-A6RI TCGA-IP-7968 TCGA-KB-A93H TCGA-VQ-A8P3 TCGA-VQ-A928 
       18.38         2.53        28.90        23.77         5.72 

$`DEL PEAK  4(1Q44) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         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-6565 
       15.95        13.12        13.68        39.12         0.82         0.62 
TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       32.78        13.22        16.14         1.25         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-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01         0.69         0.16        18.54 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         0.95         0.69        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
        0.82         1.32        12.26         0.49        20.55         0.72 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.26        12.95         0.26        16.31         1.55         1.48 
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         2.96 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        13.74         4.31        14.04         3.32         0.36 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       19.17        14.79         0.69         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         0.72         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         2.14        13.45         0.20         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         0.59        15.68         0.62 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56         1.15         0.66         3.02        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.92        13.41        13.51        12.89         0.79         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-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         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-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        0.13         0.13         0.13         0.07         0.10         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4444 
        7.99         8.05        54.08         4.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03        21.99         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         1.02         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        55.04        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         5.95        17.19         4.14        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         0.23        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-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
        4.34         7.40         7.13         0.62         7.79        16.24 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        6.58        14.47        72.23        21.27         8.12         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53         3.02        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         1.55         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        17.69        12.30         9.67         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-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         6.87 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56         1.81         5.56        60.56         3.72        19.73 
TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        4.31        11.05         8.61         4.67        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-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        16.87         5.79         0.92        37.74 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 
        5.46        13.25        13.02        31.10        21.73        22.36 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ 
        7.73        19.07        33.63        46.26        16.31         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        19.30 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       23.57        64.57        14.33        59.18        28.70        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X 
        8.68        49.25        20.81         1.71         7.36         8.58 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
        9.73        44.25         8.61        55.43         4.54         6.58 
TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       40.08        29.98        21.11         4.21         0.79 

  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE 
                       0.13                        0.07 
  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE 
                      35.24                      122.30 
  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE 
                      10.13                       11.70 
[1] "0.1 - 35.2 (10.1)"  "0.1 - 122.3 (11.7)"
[1] "hr=" "1.3"
D40V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  4(1Q44) MUTATED         0        0        2        1         4
  DEL PEAK  4(1Q44) WILD-TYPE       2       13       37       30        32
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  4(1Q44) MUTATED           5         0          2          5
  DEL PEAK  4(1Q44) WILD-TYPE        44         3         75         50
                             vv
clus                          STAGE IIIC STAGE IV
  DEL PEAK  4(1Q44) MUTATED            3        2
  DEL PEAK  4(1Q44) WILD-TYPE         34       35
D40V3, multiclass
            clus
vv           DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  STAGE I                            0                           2
  STAGE IA                           0                          13
  STAGE IB                           2                          37
  STAGE II                           1                          30
  STAGE IIA                          4                          32
  STAGE IIB                          5                          44
  STAGE III                          0                           3
  STAGE IIIA                         2                          75
  STAGE IIIB                         5                          50
  STAGE IIIC                         3                          34
  STAGE IV                           2                          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  4(1Q44) MUTATED     1   5  12   6
  DEL PEAK  4(1Q44) WILD-TYPE  20  82 161  98
D40V4, multiclass
    clus
vv   DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  T1                         1                          20
  T2                         5                          82
  T3                        12                         161
  T4                         6                          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  4(1Q44) MUTATED     7   7   3   7
  DEL PEAK  4(1Q44) WILD-TYPE 115 100  72  72
D40V5, multiclass
    clus
vv   DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  N0                         7                         115
  N1                         7                         100
  N2                         3                          72
  N3                         7                          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"
                             vv
clus                           M0  M1  MX
  DEL PEAK  4(1Q44) MUTATED    22   1   1
  DEL PEAK  4(1Q44) WILD-TYPE 331  23  17
D40V6, multiclass
    clus
vv   DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  M0                        22                         331
  M1                         1                          23
  MX                         1                          17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                             cls
clus                            0   1
  DEL PEAK  4(1Q44) MUTATED    12  12
  DEL PEAK  4(1Q44) WILD-TYPE 139 232
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(1Q44) MUTATED     12   12
  DEL PEAK  4(1Q44) WILD-TYPE  139  232
        clus
vv       DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  FEMALE                        12                         139
  MALE                          12                         232
[1] 2 2
[1] FALSE
                             vv
clus                          STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK  4(1Q44) MUTATED                                       4
  DEL PEAK  4(1Q44) WILD-TYPE                                    61
                             vv
clus                          STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  4(1Q44) MUTATED                                                       11
  DEL PEAK  4(1Q44) WILD-TYPE                                                    146
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  4(1Q44) MUTATED                                                                   3
  DEL PEAK  4(1Q44) WILD-TYPE                                                                66
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  4(1Q44) MUTATED                                                  5
  DEL PEAK  4(1Q44) WILD-TYPE                                               59
                             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                                        9
D40V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  4(1Q44) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                   11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                          5
  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                                                      61
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    146
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          66
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           59
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   21
  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"
D40V9, binary
                             cls
clus                            0   1
  DEL PEAK  4(1Q44) MUTATED     0  24
  DEL PEAK  4(1Q44) WILD-TYPE   6 365
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(1Q44) MUTATED      0   24
  DEL PEAK  4(1Q44) WILD-TYPE    6  365
     clus
vv    DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  NO                          0                           6
  YES                        24                         365
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  4(1Q44) MUTATED    21   0   1   0
  DEL PEAK  4(1Q44) WILD-TYPE 297  16  17  25
D40V10, multiclass
    clus
vv   DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  R0                        21                         297
  R1                         0                          16
  R2                         1                          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"
D40V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  4(1Q44) MUTATED       6                         0
  DEL PEAK  4(1Q44) WILD-TYPE    82                         6
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  4(1Q44) MUTATED                                           0    16
  DEL PEAK  4(1Q44) WILD-TYPE                                         1   227
D40V12, multiclass
                                           clus
vv                                          DEL PEAK  4(1Q44) MUTATED
  ASIAN                                                             6
  BLACK OR AFRICAN AMERICAN                                         0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         0
  WHITE                                                            16
                                           clus
vv                                          DEL PEAK  4(1Q44) WILD-TYPE
  ASIAN                                                              82
  BLACK OR AFRICAN AMERICAN                                           6
  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"

Clustering(41) Variable = DEL PEAK  5(2Q32.1) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(2Q32.1) MUTATED    28  23
  DEL PEAK  5(2Q32.1) WILD-TYPE 214  99
  DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE 
                           51                           313 
  DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE 
                           23                            99 
$`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        10.13         7.00         0.62        17.49         0.69 
TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
        0.49        12.95        13.74         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         0.62        20.65         0.07         0.10 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CG-4300 TCGA-CG-4444 TCGA-CG-4472 TCGA-CG-5720 
        0.13         6.35        20.02        47.05        12.00         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-8575 
       12.03        15.02        12.66        11.93        17.19         0.23 
TCGA-D7-8576 TCGA-D7-A6F0 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-A4G3 TCGA-HU-A4GD 
        6.97         2.96        26.47         5.92         5.59        22.75 
TCGA-HU-A4GU TCGA-HU-A4HD TCGA-IN-A6RI TCGA-MX-A663 TCGA-RD-A7C1 TCGA-VQ-A8DL 
        6.25        27.42        18.38         4.31        16.67         0.92 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8P3 TCGA-VQ-A8PK TCGA-VQ-A8PU TCGA-VQ-A8PY 
       13.25        13.02        23.77        17.85        23.57        14.33 
TCGA-VQ-A91Y TCGA-VQ-AA68 TCGA-ZA-A8F6 
        9.73        40.08         4.21 

$`DEL PEAK  5(2Q32.1) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 
        5.62        11.70         6.61         6.97         4.64        18.35 
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-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
       13.12        13.68        39.12         0.82        32.78        13.84 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       13.22        16.14         1.25         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-7723 
       23.93        15.42        28.01         0.69         0.16        18.54 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 
       12.43         0.95         0.69        12.76        18.71         0.82 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 
        1.32        12.26        20.55         0.72         0.26         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         1.55         1.48         7.40         6.18        19.50 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8371 
        0.36         0.26        22.19         2.96         0.95         0.36 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       19.17        14.79         0.69         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         0.72         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8678 
       15.81         2.14        13.45         0.20         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       15.81         0.59        15.68        10.68        12.56         1.15 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        0.66         3.02        22.26         0.92        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         0.79         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-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-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8536 
        0.10         0.13         0.16         0.10         0.13         0.10 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        0.13         0.13         0.13         0.13         0.07         0.10 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10         0.10         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03        21.99         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5721 
       22.98        30.97         6.97         1.02         1.02         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-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 
       55.04        21.07         7.99        12.36        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 
       18.84        18.54        18.61        17.85         5.95         4.14 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-8579 
       24.72        16.80        19.50        17.19        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        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-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
        4.34         7.40         7.13         0.62         7.79        16.24 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        6.58        14.47        72.23        21.27         8.12         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53         3.02        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8238 
       13.58         0.56         1.55         0.23        18.08         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-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30        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 
       17.69        12.30         9.67         8.88         8.81        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45        18.81         3.39         5.36         5.19        13.08 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU 
        1.41         6.44         6.74         6.87         5.56         1.81 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        60.56        28.90         3.72        19.73 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         8.61         4.67       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-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       16.87         5.79        37.74         5.46        31.10        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       22.36         7.73        19.07        33.63        46.26        16.31 
TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
        2.70         1.87         9.27        23.41        15.65        19.30 
TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       64.57        59.18        28.70        11.70         8.68        49.25 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 
       20.81         1.71         7.36         8.58        44.25         8.61 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6B TCGA-VQ-AA6J 
       55.43         4.54         6.58         5.72        29.98        21.11 
TCGA-ZQ-A9CR 
        0.79 

  DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE 
                         0.07                          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 
                        11.93                         11.57 
[1] "0.1 - 47.0 (11.9)"  "0.1 - 122.3 (11.6)"
[1] "hr=" "1.6"
D41V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  5(2Q32.1) MUTATED         0        0        9        3         3
  DEL PEAK  5(2Q32.1) WILD-TYPE       2       13       30       28        33
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  5(2Q32.1) MUTATED           8         0          9         11
  DEL PEAK  5(2Q32.1) WILD-TYPE        41         3         68         44
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  5(2Q32.1) MUTATED            6        5
  DEL PEAK  5(2Q32.1) WILD-TYPE         31       32
D41V3, multiclass
            clus
vv           DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             0                            13
  STAGE IB                             9                            30
  STAGE II                             3                            28
  STAGE IIA                            3                            33
  STAGE IIB                            8                            41
  STAGE III                            0                             3
  STAGE IIIA                           9                            68
  STAGE IIIB                          11                            44
  STAGE IIIC                           6                            31
  STAGE IV                             5                            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  5(2Q32.1) MUTATED     1  11  28  15
  DEL PEAK  5(2Q32.1) WILD-TYPE  20  76 145  89
D41V4, multiclass
    clus
vv   DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE
  T1                           1                            20
  T2                          11                            76
  T3                          28                           145
  T4                          15                            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
  DEL PEAK  5(2Q32.1) MUTATED    18  11  11  15
  DEL PEAK  5(2Q32.1) WILD-TYPE 104  96  64  64
D41V5, multiclass
    clus
vv   DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE
  N0                          18                           104
  N1                          11                            96
  N2                          11                            64
  N3                          15                            64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK  5(2Q32.1) MUTATED    51   3   3
  DEL PEAK  5(2Q32.1) WILD-TYPE 302  21  15
D41V6, multiclass
    clus
vv   DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE
  M0                          51                           302
  M1                           3                            21
  MX                           3                            15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q32.1) MUTATED    21  36
  DEL PEAK  5(2Q32.1) WILD-TYPE 130 208
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q32.1) MUTATED     21   36
  DEL PEAK  5(2Q32.1) WILD-TYPE  130  208
        clus
vv       DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE
  FEMALE                          21                           130
  MALE                            36                           208
[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                                    57
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  5(2Q32.1) MUTATED                                                       21
  DEL PEAK  5(2Q32.1) WILD-TYPE                                                    136
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  5(2Q32.1) MUTATED                                                                   6
  DEL PEAK  5(2Q32.1) WILD-TYPE                                                                63
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  5(2Q32.1) MUTATED                                                 14
  DEL PEAK  5(2Q32.1) WILD-TYPE                                               50
                               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                                          2
  DEL PEAK  5(2Q32.1) WILD-TYPE                                        7
D41V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  5(2Q32.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     21
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    2
                                                                   clus
vv                                                                  DEL PEAK  5(2Q32.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        57
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      136
  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                                     8
  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"
D41V9, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q32.1) MUTATED     1  56
  DEL PEAK  5(2Q32.1) WILD-TYPE   5 333
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q32.1) MUTATED      1   56
  DEL PEAK  5(2Q32.1) WILD-TYPE    5  333
     clus
vv    DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE
  NO                            1                             5
  YES                          56                           333
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  5(2Q32.1) MUTATED    46   3   4   3
  DEL PEAK  5(2Q32.1) WILD-TYPE 272  13  14  22
D41V10, multiclass
    clus
vv   DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE
  R0                          46                           272
  R1                           3                            13
  R2                           4                            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"
D41V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  5(2Q32.1) MUTATED      11                         1
  DEL PEAK  5(2Q32.1) WILD-TYPE    77                         5
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  5(2Q32.1) MUTATED                                           0    36
  DEL PEAK  5(2Q32.1) WILD-TYPE                                         1   207
D41V12, multiclass
                                           clus
vv                                          DEL PEAK  5(2Q32.1) MUTATED
  ASIAN                                                              11
  BLACK OR AFRICAN AMERICAN                                           1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              36
                                           clus
vv                                          DEL PEAK  5(2Q32.1) WILD-TYPE
  ASIAN                                                                77
  BLACK OR AFRICAN AMERICAN                                             5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  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"

Clustering(42) Variable = DEL PEAK  6(2Q33.3) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(2Q33.3) MUTATED    22  19
  DEL PEAK  6(2Q33.3) WILD-TYPE 220 103
  DEL PEAK  6(2Q33.3) MUTATED DEL PEAK  6(2Q33.3) WILD-TYPE 
                           41                           323 
  DEL PEAK  6(2Q33.3) MUTATED DEL PEAK  6(2Q33.3) WILD-TYPE 
                           19                           103 
$`DEL PEAK  6(2Q33.3) MUTATED`
TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7901 TCGA-BR-8058 TCGA-BR-8080 
        7.00         0.62         1.25         0.95        17.49         0.49 
TCGA-BR-8286 TCGA-BR-8369 TCGA-BR-8687 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8535 
       12.95        14.04         0.62         0.07         0.07         0.13 
TCGA-CD-A486 TCGA-CG-4300 TCGA-CG-5720 TCGA-CG-5724 TCGA-D7-5578 TCGA-D7-5579 
        6.35        20.02         0.99        12.03        12.66        11.93 
TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-8573 TCGA-D7-8576 TCGA-HJ-7597 TCGA-HU-8243 
       17.19        15.22        19.50         6.97        26.47         5.92 
TCGA-HU-A4G8 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4HD 
       11.84        22.75        25.81         6.25         2.10        27.42 
TCGA-IN-A6RI TCGA-IN-A6RO TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8PC 
       18.38         1.41         5.46        13.25        13.02        46.26 
TCGA-VQ-A8PK TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-AA68 TCGA-VQ-AA6J 
       17.85        23.57        14.33        40.08        21.11 

$`DEL PEAK  6(2Q33.3) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         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        13.12        10.13        13.68        39.12         0.82 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        13.84        13.22        16.14         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-7722 
       35.24        23.93        15.42        28.01         0.69         0.16 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 
       18.54        12.43         0.69        12.76        18.71         0.82 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        1.32         0.69        12.26        20.55         0.72         0.26 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        0.26        16.31         1.55         1.48         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       19.50         0.36         0.26        22.19         2.96         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       13.74         4.31         3.32         0.36        19.17        14.79 
TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
        0.69         0.26        15.85         3.72         5.39         0.72 
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         2.14 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         0.20         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       16.44         0.59        15.68        10.68        12.56         1.15 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        0.66         3.02        22.26         0.92        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         0.79         0.72        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-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-8527 
       13.15        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-8533 
        0.10         0.13         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-A4MG 
        0.10         0.13         0.13         0.13         0.13         0.07 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10         0.10         0.10         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-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 
       29.98        47.05        19.07        12.03        21.99         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
       18.97         7.07        12.00        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 
        1.02         1.02         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        55.04        21.07 
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-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
       18.61        17.85         5.95         4.14        15.98        12.79 
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-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
        0.23        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-A748 TCGA-D7-A74A 
       11.44         9.76         2.96        15.65         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 
        7.13         0.62         7.79        16.24         6.58        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27         8.12         0.39        19.53         3.02 
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-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
        1.55         0.23        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-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ 
        5.59        12.30        24.20         3.25        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-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        17.69        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-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT 
        5.19        13.08         6.44         6.74         6.87         5.56 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG 
        1.81         2.53         5.56        60.56        28.90         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
       19.73         4.31        11.05         8.61         4.67        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        16.87         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       37.74        31.10        21.73        22.36        23.77         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO 
       19.07        33.63        16.31         2.70         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A 
       23.41        15.65        19.30        64.57        59.18        28.70 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W 
       11.70         8.68        49.25        20.81         1.71         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 
        8.58         9.73        44.25         8.61        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6B TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        6.58         5.72        29.98         4.21         0.79 

  DEL PEAK  6(2Q33.3) MUTATED DEL PEAK  6(2Q33.3) WILD-TYPE 
                         0.07                          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 
                        12.66                         11.41 
[1] "0.1 - 46.3 (12.7)"  "0.1 - 122.3 (11.4)"
[1] "hr=" "1.5"
D42V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  6(2Q33.3) MUTATED         0        1        6        2         3
  DEL PEAK  6(2Q33.3) WILD-TYPE       2       12       33       29        33
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  6(2Q33.3) MUTATED           6         0          9          9
  DEL PEAK  6(2Q33.3) WILD-TYPE        43         3         68         46
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  6(2Q33.3) MUTATED            6        4
  DEL PEAK  6(2Q33.3) WILD-TYPE         31       33
D42V3, multiclass
            clus
vv           DEL PEAK  6(2Q33.3) MUTATED DEL PEAK  6(2Q33.3) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             1                            12
  STAGE IB                             6                            33
  STAGE II                             2                            29
  STAGE IIA                            3                            33
  STAGE IIB                            6                            43
  STAGE III                            0                             3
  STAGE IIIA                           9                            68
  STAGE IIIB                           9                            46
  STAGE IIIC                           6                            31
  STAGE IV                             4                            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  6(2Q33.3) MUTATED     2   6  27  11
  DEL PEAK  6(2Q33.3) WILD-TYPE  19  81 146  93
D42V4, multiclass
    clus
vv   DEL PEAK  6(2Q33.3) MUTATED DEL PEAK  6(2Q33.3) WILD-TYPE
  T1                           2                            19
  T2                           6                            81
  T3                          27                           146
  T4                          11                            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  6(2Q33.3) MUTATED    13  10  10  13
  DEL PEAK  6(2Q33.3) WILD-TYPE 109  97  65  66
D42V5, multiclass
    clus
vv   DEL PEAK  6(2Q33.3) MUTATED DEL PEAK  6(2Q33.3) WILD-TYPE
  N0                          13                           109
  N1                          10                            97
  N2                          10                            65
  N3                          13                            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"
                               vv
clus                             M0  M1  MX
  DEL PEAK  6(2Q33.3) MUTATED    41   3   2
  DEL PEAK  6(2Q33.3) WILD-TYPE 312  21  16
D42V6, multiclass
    clus
vv   DEL PEAK  6(2Q33.3) MUTATED DEL PEAK  6(2Q33.3) WILD-TYPE
  M0                          41                           312
  M1                           3                            21
  MX                           2                            16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q33.3) MUTATED    19  27
  DEL PEAK  6(2Q33.3) WILD-TYPE 132 217
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q33.3) MUTATED     19   27
  DEL PEAK  6(2Q33.3) WILD-TYPE  132  217
        clus
vv       DEL PEAK  6(2Q33.3) MUTATED DEL PEAK  6(2Q33.3) WILD-TYPE
  FEMALE                          19                           132
  MALE                            27                           217
[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                                    58
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  6(2Q33.3) MUTATED                                                       15
  DEL PEAK  6(2Q33.3) WILD-TYPE                                                    142
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  6(2Q33.3) MUTATED                                                                   4
  DEL PEAK  6(2Q33.3) WILD-TYPE                                                                65
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  6(2Q33.3) MUTATED                                                 13
  DEL PEAK  6(2Q33.3) WILD-TYPE                                               51
                               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                                          3
  DEL PEAK  6(2Q33.3) WILD-TYPE                                        6
D42V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  6(2Q33.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     15
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           4
  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                                                    3
                                                                   clus
vv                                                                  DEL PEAK  6(2Q33.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        58
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      142
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            65
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             51
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     8
  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"
D42V9, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q33.3) MUTATED     2  44
  DEL PEAK  6(2Q33.3) WILD-TYPE   4 345
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q33.3) MUTATED      2   44
  DEL PEAK  6(2Q33.3) WILD-TYPE    4  345
     clus
vv    DEL PEAK  6(2Q33.3) MUTATED DEL PEAK  6(2Q33.3) WILD-TYPE
  NO                            2                             4
  YES                          44                           345
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  6(2Q33.3) MUTATED    37   4   3   0
  DEL PEAK  6(2Q33.3) WILD-TYPE 281  12  15  25
D42V10, multiclass
    clus
vv   DEL PEAK  6(2Q33.3) MUTATED DEL PEAK  6(2Q33.3) WILD-TYPE
  R0                          37                           281
  R1                           4                            12
  R2                           3                            15
  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                         4
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  6(2Q33.3) MUTATED                                           0    24
  DEL PEAK  6(2Q33.3) WILD-TYPE                                         1   219
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                                                              24
                                           clus
vv                                          DEL PEAK  6(2Q33.3) WILD-TYPE
  ASIAN                                                                75
  BLACK OR AFRICAN AMERICAN                                             4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  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"

Clustering(43) Variable = DEL PEAK  7(2Q37.2) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(2Q37.2) MUTATED    37  21
  DEL PEAK  7(2Q37.2) WILD-TYPE 205 101
  DEL PEAK  7(2Q37.2) MUTATED DEL PEAK  7(2Q37.2) WILD-TYPE 
                           58                           306 
  DEL PEAK  7(2Q37.2) MUTATED DEL PEAK  7(2Q37.2) WILD-TYPE 
                           21                           101 
$`DEL PEAK  7(2Q37.2) MUTATED`
TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7704 TCGA-BR-7901 TCGA-BR-8058 TCGA-BR-8059 
        0.62         1.25        35.24         0.95        17.49         0.82 
TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8361 TCGA-BR-8373 TCGA-BR-8381 
        1.32         0.49        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 
        0.72         9.21         0.49         0.62        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         6.35         0.13 
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         6.97        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-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91Q 
       13.25        13.02        23.57        64.57        14.33        20.81 
TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-AA68 
        8.61         4.54         5.72        40.08 

$`DEL PEAK  7(2Q37.2) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         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-6458 TCGA-BR-6563 
       15.95        13.12        10.13        13.68         7.00        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        0.82        32.78        13.84        13.22        16.14         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-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01         0.69         0.16 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8077 
       18.54        12.43         0.69        12.76        18.71         0.69 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 
       12.26        20.55         0.72         0.26         0.26        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 
        1.55         1.48         7.40         6.18         0.36         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19         2.96         0.95        13.74         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8382 TCGA-BR-8384 
        3.32         0.36        19.17         0.69        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         2.14 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
       13.45         0.20         7.53        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
        0.59        15.68        10.68        12.56         1.15         0.66 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        3.02        22.26         0.92        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        0.79         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-5801 TCGA-CD-5802 
       11.57         5.13         2.83         3.25        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-8536 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         0.10         0.10         0.13         0.13         0.13 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
        0.07         0.10         0.10         0.10         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 
       15.95         1.02         7.99        54.08         4.01        29.98 
TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4475 
       47.05        12.03        21.99         9.01         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 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-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        55.04        21.07         7.99        12.36        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         5.95 
TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
        4.14        12.79        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19         0.23        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-A6F2 TCGA-D7-A748 TCGA-D7-A74A 
       11.31        11.44         9.76        15.65         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 
        7.13         0.62         7.79        16.24         6.58        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27         8.12         0.39        19.53         3.02 
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-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
        1.55         0.23        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-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-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-A4H5 
       10.19         0.26         2.10        19.36        17.69        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88         8.81        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38         5.36         5.19        13.08         6.44 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        6.87         5.56         1.81         2.53         5.56        60.56 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT 
       28.90         3.72        19.73         4.31        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        4.67        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      116.38        71.38        57.44         8.94        35.61        16.87 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        5.79         0.92        37.74         5.46        31.10        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       22.36        23.77         7.73        19.07        33.63        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       16.31         2.70        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       15.65        19.30        59.18        28.70        11.70         8.68 
TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       49.25         1.71         7.36         8.58         9.73        44.25 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       55.43         6.58        29.98        21.11         4.21         0.79 

  DEL PEAK  7(2Q37.2) MUTATED DEL PEAK  7(2Q37.2) WILD-TYPE 
                         0.07                          0.07 
  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 
                       10.895                        11.700 
[1] "0.1 - 64.6 (10.9)"  "0.1 - 122.3 (11.7)"
[1] "hr=" "1.3"
D43V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  7(2Q37.2) MUTATED         1        2        6        7         3
  DEL PEAK  7(2Q37.2) WILD-TYPE       1       11       33       24        33
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  7(2Q37.2) MUTATED           8         1         12          9
  DEL PEAK  7(2Q37.2) WILD-TYPE        41         2         65         46
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  7(2Q37.2) MUTATED            7        6
  DEL PEAK  7(2Q37.2) WILD-TYPE         30       31
D43V3, multiclass
            clus
vv           DEL PEAK  7(2Q37.2) MUTATED DEL PEAK  7(2Q37.2) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             2                            11
  STAGE IB                             6                            33
  STAGE II                             7                            24
  STAGE IIA                            3                            33
  STAGE IIB                            8                            41
  STAGE III                            1                             2
  STAGE IIIA                          12                            65
  STAGE IIIB                           9                            46
  STAGE IIIC                           7                            30
  STAGE IV                             6                            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  7(2Q37.2) MUTATED     3  15  26  18
  DEL PEAK  7(2Q37.2) WILD-TYPE  18  72 147  86
D43V4, multiclass
    clus
vv   DEL PEAK  7(2Q37.2) MUTATED DEL PEAK  7(2Q37.2) WILD-TYPE
  T1                           3                            18
  T2                          15                            72
  T3                          26                           147
  T4                          18                            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  7(2Q37.2) MUTATED    19  17  13  13
  DEL PEAK  7(2Q37.2) WILD-TYPE 103  90  62  66
D43V5, multiclass
    clus
vv   DEL PEAK  7(2Q37.2) MUTATED DEL PEAK  7(2Q37.2) WILD-TYPE
  N0                          19                           103
  N1                          17                            90
  N2                          13                            62
  N3                          13                            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"
                               vv
clus                             M0  M1  MX
  DEL PEAK  7(2Q37.2) MUTATED    58   2   2
  DEL PEAK  7(2Q37.2) WILD-TYPE 295  22  16
D43V6, multiclass
    clus
vv   DEL PEAK  7(2Q37.2) MUTATED DEL PEAK  7(2Q37.2) WILD-TYPE
  M0                          58                           295
  M1                           2                            22
  MX                           2                            16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(2Q37.2) MUTATED    31  31
  DEL PEAK  7(2Q37.2) WILD-TYPE 120 213
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(2Q37.2) MUTATED     31   31
  DEL PEAK  7(2Q37.2) WILD-TYPE  120  213
        clus
vv       DEL PEAK  7(2Q37.2) MUTATED DEL PEAK  7(2Q37.2) WILD-TYPE
  FEMALE                          31                           120
  MALE                            31                           213
[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                                    59
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  7(2Q37.2) MUTATED                                                       21
  DEL PEAK  7(2Q37.2) WILD-TYPE                                                    136
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  7(2Q37.2) MUTATED                                                                  12
  DEL PEAK  7(2Q37.2) WILD-TYPE                                                                57
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  7(2Q37.2) MUTATED                                                 15
  DEL PEAK  7(2Q37.2) WILD-TYPE                                               49
                               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                                          2
  DEL PEAK  7(2Q37.2) WILD-TYPE                                        7
D43V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  7(2Q37.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     21
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          12
  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  7(2Q37.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      136
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            57
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             49
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     18
  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"
D43V9, binary
                               cls
clus                              0   1
  DEL PEAK  7(2Q37.2) MUTATED     2  60
  DEL PEAK  7(2Q37.2) WILD-TYPE   4 329
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(2Q37.2) MUTATED      2   60
  DEL PEAK  7(2Q37.2) WILD-TYPE    4  329
     clus
vv    DEL PEAK  7(2Q37.2) MUTATED DEL PEAK  7(2Q37.2) WILD-TYPE
  NO                            2                             4
  YES                          60                           329
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  7(2Q37.2) MUTATED    56   2   2   0
  DEL PEAK  7(2Q37.2) WILD-TYPE 262  14  16  25
D43V10, multiclass
    clus
vv   DEL PEAK  7(2Q37.2) MUTATED DEL PEAK  7(2Q37.2) WILD-TYPE
  R0                          56                           262
  R1                           2                            14
  R2                           2                            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"
D43V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  7(2Q37.2) MUTATED      14                         1
  DEL PEAK  7(2Q37.2) WILD-TYPE    74                         5
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  7(2Q37.2) MUTATED                                           0    34
  DEL PEAK  7(2Q37.2) WILD-TYPE                                         1   209
D43V12, multiclass
                                           clus
vv                                          DEL PEAK  7(2Q37.2) MUTATED
  ASIAN                                                              14
  BLACK OR AFRICAN AMERICAN                                           1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              34
                                           clus
vv                                          DEL PEAK  7(2Q37.2) WILD-TYPE
  ASIAN                                                                74
  BLACK OR AFRICAN AMERICAN                                             5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(44) Variable = DEL PEAK  8(3P26.1) MUTATION ANALYSIS
D44V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(3P26.1) MUTATED    75  38
  DEL PEAK  8(3P26.1) WILD-TYPE 167  84
  DEL PEAK  8(3P26.1) MUTATED DEL PEAK  8(3P26.1) WILD-TYPE 
                          113                           251 
  DEL PEAK  8(3P26.1) MUTATED DEL PEAK  8(3P26.1) WILD-TYPE 
                           38                            84 
$`DEL PEAK  8(3P26.1) MUTATED`
TCGA-BR-4191 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6803 TCGA-BR-7704 
       18.35         7.00         0.62        13.84        31.20        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 
       15.42        28.01         0.69        18.71        17.49         0.69 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8483 TCGA-BR-8484 
        0.26        16.31         7.40         0.36         5.39         0.72 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 
        9.21        20.22        11.54        15.81        15.68         0.62 
TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 
       10.68         0.66        22.26         0.92        12.89         0.72 
TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
        0.53        13.51        20.65        20.42         1.15        13.64 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8533 TCGA-CD-A487 
        3.25        13.18         0.07         0.07         0.13         0.13 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       20.02         3.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-5718 TCGA-CG-5723 
       14.01        47.05        12.03        18.97         1.02       105.07 
TCGA-CG-5725 TCGA-CG-5730 TCGA-D7-5578 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 
       15.02         4.01        12.66        18.54         5.95        17.19 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       15.22        12.79        11.31         9.76         2.96        15.65 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 
        0.62         7.79        19.53         3.02        17.06         0.56 
TCGA-FP-A4BF TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD 
        1.55        12.59        14.17        12.30         3.25        22.75 
TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-IN-7806 TCGA-IN-A6RI 
        6.25         2.10        17.69        12.30        21.21        18.38 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NT TCGA-KB-A6F5 TCGA-KB-A6F7 
        1.41         6.44         6.87         5.56         5.56        60.56 
TCGA-KB-A93H TCGA-MX-A663 TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 
       28.90         4.31         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-A8P5 
        8.94         5.79         0.92         5.46        13.25         7.73 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91X 
        2.70        17.85        23.57        14.33        28.70         8.58 
TCGA-VQ-A91Y TCGA-VQ-A925 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZQ-A9CR 
        9.73         4.54        29.98        21.11         0.79 

$`DEL PEAK  8(3P26.1) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         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-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       13.12        10.13        13.68        39.12         0.82        32.78 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       13.22        16.14         1.25         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         0.69 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8059 
        0.16        18.54        12.43         0.95        12.76         0.82 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        1.32        12.26         0.49        20.55         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       12.95         1.55         1.48         6.18        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19         2.96         0.95        13.74         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 
        3.32         0.36        19.17        14.79         0.69         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         2.14 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 
       13.45         0.20         7.53         0.49        16.44         0.59 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
       12.56         1.15         3.02        13.41        13.51         0.79 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QL 
       14.17        12.82         0.66        19.36         0.46        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        5.13         2.83        13.15         0.30         0.07         0.07 
TCGA-CD-8525 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-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         0.10         6.35         0.13         0.13         0.13 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 
        0.07         0.10         0.10         0.10        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4469 
        1.02        29.98        19.07        21.99         9.01         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 
       12.00        22.98        30.97         6.97         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        6.02         0.99        12.03        28.96        79.07        65.10 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 
       55.04        21.07         7.99        12.36        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6815 
       20.55        18.84        18.61        17.85         4.14        15.98 
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-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19         0.23         6.97        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-A6EY TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-A4SO 
       11.24        11.44         4.34         7.40         7.13        16.24 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        6.58        14.47        72.23        21.27         8.12         0.39 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A8CX TCGA-HF-A5NB 
       22.29        59.54         5.03        13.58         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 
       26.47         1.51         5.92        14.27        11.41        12.10 
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-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-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H6 
        6.51        10.19         0.26        12.95        19.36         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88         8.81        27.42         3.45        18.81         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IP-7968 
        5.36         5.19        13.08         6.74         1.81         2.53 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 
        3.72        19.73        11.05         4.67       122.30        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A8DT 
      116.38        71.38        57.44        35.61        16.87        37.74 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       13.02        31.10        21.73        22.36        23.77        19.07 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       33.63        46.26        16.31         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E 
       15.65        19.30        64.57        59.18        11.70         8.68 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A922 
       49.25        20.81         1.71         7.36        44.25         8.61 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-ZA-A8F6 
       55.43         6.58         5.72        40.08         4.21 

  DEL PEAK  8(3P26.1) MUTATED DEL PEAK  8(3P26.1) WILD-TYPE 
                         0.07                          0.07 
  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 
                        11.31                         11.70 
[1] "0.1 - 115.7 (11.3)" "0.1 - 122.3 (11.7)"
[1] "hr=" "1.1"
D44V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  8(3P26.1) MUTATED         0        4       15        8         8
  DEL PEAK  8(3P26.1) WILD-TYPE       2        9       24       23        28
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  8(3P26.1) MUTATED          14         0         29         18
  DEL PEAK  8(3P26.1) WILD-TYPE        35         3         48         37
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  8(3P26.1) MUTATED           11       10
  DEL PEAK  8(3P26.1) WILD-TYPE         26       27
D44V3, multiclass
            clus
vv           DEL PEAK  8(3P26.1) MUTATED DEL PEAK  8(3P26.1) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             4                             9
  STAGE IB                            15                            24
  STAGE II                             8                            23
  STAGE IIA                            8                            28
  STAGE IIB                           14                            35
  STAGE III                            0                             3
  STAGE IIIA                          29                            48
  STAGE IIIB                          18                            37
  STAGE IIIC                          11                            26
  STAGE IV                            10                            27
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  8(3P26.1) MUTATED     7  27  52  32
  DEL PEAK  8(3P26.1) WILD-TYPE  14  60 121  72
D44V4, multiclass
    clus
vv   DEL PEAK  8(3P26.1) MUTATED DEL PEAK  8(3P26.1) WILD-TYPE
  T1                           7                            14
  T2                          27                            60
  T3                          52                           121
  T4                          32                            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"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK  8(3P26.1) MUTATED   31 33 33 21
  DEL PEAK  8(3P26.1) WILD-TYPE 91 74 42 58
D44V5, multiclass
    clus
vv   DEL PEAK  8(3P26.1) MUTATED DEL PEAK  8(3P26.1) WILD-TYPE
  N0                          31                            91
  N1                          33                            74
  N2                          33                            42
  N3                          21                            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"
                               vv
clus                             M0  M1  MX
  DEL PEAK  8(3P26.1) MUTATED   106   8   7
  DEL PEAK  8(3P26.1) WILD-TYPE 247  16  11
D44V6, multiclass
    clus
vv   DEL PEAK  8(3P26.1) MUTATED DEL PEAK  8(3P26.1) WILD-TYPE
  M0                         106                           247
  M1                           8                            16
  MX                           7                            11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P26.1) MUTATED    42  79
  DEL PEAK  8(3P26.1) WILD-TYPE 109 165
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P26.1) MUTATED     42   79
  DEL PEAK  8(3P26.1) WILD-TYPE  109  165
        clus
vv       DEL PEAK  8(3P26.1) MUTATED DEL PEAK  8(3P26.1) WILD-TYPE
  FEMALE                          42                           109
  MALE                            79                           165
[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                                    50
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  8(3P26.1) MUTATED                                                       46
  DEL PEAK  8(3P26.1) WILD-TYPE                                                    111
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  8(3P26.1) MUTATED                                                                  31
  DEL PEAK  8(3P26.1) WILD-TYPE                                                                38
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  8(3P26.1) MUTATED                                                 20
  DEL PEAK  8(3P26.1) WILD-TYPE                                               44
                               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                                          1
  DEL PEAK  8(3P26.1) WILD-TYPE                                        8
D44V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  8(3P26.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     46
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          31
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    1
                                                                   clus
vv                                                                  DEL PEAK  8(3P26.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      111
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             44
  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"
D44V9, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P26.1) MUTATED     2 119
  DEL PEAK  8(3P26.1) WILD-TYPE   4 270
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P26.1) MUTATED      2  119
  DEL PEAK  8(3P26.1) WILD-TYPE    4  270
     clus
vv    DEL PEAK  8(3P26.1) MUTATED DEL PEAK  8(3P26.1) WILD-TYPE
  NO                            2                             4
  YES                         119                           270
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  8(3P26.1) MUTATED   101   3   8   5
  DEL PEAK  8(3P26.1) WILD-TYPE 217  13  10  20
D44V10, multiclass
    clus
vv   DEL PEAK  8(3P26.1) MUTATED DEL PEAK  8(3P26.1) WILD-TYPE
  R0                         101                           217
  R1                           3                            13
  R2                           8                            10
  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                         1
  DEL PEAK  8(3P26.1) WILD-TYPE    63                         5
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  8(3P26.1) MUTATED                                           1    75
  DEL PEAK  8(3P26.1) WILD-TYPE                                         0   168
D44V12, multiclass
                                           clus
vv                                          DEL PEAK  8(3P26.1) MUTATED
  ASIAN                                                              25
  BLACK OR AFRICAN AMERICAN                                           1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              75
                                           clus
vv                                          DEL PEAK  8(3P26.1) WILD-TYPE
  ASIAN                                                                63
  BLACK OR AFRICAN AMERICAN                                             5
  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"

Clustering(45) Variable = DEL PEAK  9(3P14.2) MUTATION ANALYSIS
D45V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(3P14.2) MUTATED    81  49
  DEL PEAK  9(3P14.2) WILD-TYPE 161  73
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                          130                           234 
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                           49                            73 
$`DEL PEAK  9(3P14.2) MUTATED`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6705 
        5.62         6.61        10.13         7.00         0.62        13.84 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 
       31.20        32.94        35.24        15.42        28.01         0.16 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 
        0.95         0.69        18.71        17.49         1.32         0.69 
TCGA-BR-8289 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8686 
        0.26         5.39         0.72         9.21        20.22        15.68 
TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY 
        0.62         1.15         0.66        22.26         0.92        12.89 
TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI 
        0.72         0.53        13.51        20.65         1.15        13.64 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 
        3.25        13.15        13.18         0.07         0.07         0.07 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A487 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 
        0.13         0.13         0.13        20.02         3.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 
        7.99         8.05        54.08         4.01        14.01        47.05 
TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 
       12.03        18.97         1.02         1.02        12.03        15.02 
TCGA-CG-5730 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 
        4.01        12.36        20.55        18.84        18.54         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-A4YT 
       17.19         4.14        15.22        12.79        12.33        14.27 
TCGA-D7-A4YY TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A74A TCGA-EQ-5647 
       13.78        11.31        11.44         9.76         7.40         0.62 
TCGA-EQ-8122 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF 
        7.79        19.53         3.02        17.06         0.56         1.55 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        12.59        14.17        11.41        12.10 
TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
       12.30         3.25        22.75        25.81        11.77         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-IN-7806 
        0.10         6.25         2.10        17.69         8.88        21.21 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38         5.19         1.41         6.44         6.74         6.87 
TCGA-IN-A7NT TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A663 TCGA-RD-A7C1 
        5.56         5.56        60.56        28.90         4.31        16.67 
TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8P5 
       37.91         8.94         5.79         5.46        13.25         7.73 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PY TCGA-VQ-A91X TCGA-VQ-A922 
        2.70        17.85         9.27        14.33         8.58         8.61 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-AA6B TCGA-ZQ-A9CR 
       55.43         4.54        29.98         0.79 

$`DEL PEAK  9(3P14.2) WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       11.70         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        13.12 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 
       13.68        39.12         0.82        32.78        13.22        16.14 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-7196 TCGA-BR-7197 
        1.25         8.98        21.11        30.90        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7958 
       24.76        23.93         0.69        18.54        12.43        12.76 
TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.82        12.26         0.49        20.55         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       12.95        16.31         1.55         1.48         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       19.50         0.36         0.26        22.19         2.96         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       13.74         4.31        14.04         3.32         0.36        19.17 
TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 
       14.79         0.69         0.26        15.85         3.72         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         2.14        13.45         0.20         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 
        0.49        11.54        15.81        16.44         0.59        10.68 
TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 
       12.56         3.02        13.41        13.51         0.79        14.17 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL 
       12.82         0.66        19.36         0.46        20.42        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8528 
        5.13         2.83         0.30         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A486 
        0.13         0.16         0.10         0.10         0.10         6.35 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        0.13         0.13         0.13         0.07         0.10         0.10 
TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4460 
        0.10        27.02         1.02        29.98        19.07        21.99 
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-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-D7-5578 TCGA-D7-5579 
       65.10        55.04        21.07         7.99        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 
       19.13        18.61        17.85        15.98        10.55        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         0.23         6.97 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 
       21.14        20.91        16.44         5.92        15.16        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74B 
       13.71        11.24         2.96        15.65         4.34         7.13 
TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
       16.24         6.58        14.47        72.23        21.27         8.12 
TCGA-FP-7735 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A8CX 
        0.39        22.29        59.54         5.03        13.58         0.23 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       18.08         1.51        14.27        10.62         0.76        24.30 
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-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 
       10.19         0.26        12.95        19.36        12.30         9.67 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ 
        8.81        27.42         3.45        18.81         3.39         5.36 
TCGA-IN-A6RN TCGA-IN-A7NU TCGA-IP-7968 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS 
       13.08         1.81         2.53         3.72        19.73        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        8.61         4.67       122.30        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       71.38        57.44        35.61        16.87         0.92        37.74 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       13.02        31.10        21.73        22.36        23.77        19.07 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       33.63        46.26        16.31         1.87        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       19.30        23.57        64.57        59.18        28.70        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y 
        8.68        49.25        20.81         1.71         7.36         9.73 
TCGA-VQ-A91Z TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6J TCGA-ZA-A8F6 
       44.25         6.58         5.72        40.08        21.11         4.21 

  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                        60.56                        122.30 
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                        9.095                        12.365 
[1] "0.1 - 60.6 (9.1)"   "0.1 - 122.3 (12.4)"
[1] "hr=" "1.4"
D45V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  9(3P14.2) MUTATED         0        5       13       12        11
  DEL PEAK  9(3P14.2) WILD-TYPE       2        8       26       19        25
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  9(3P14.2) MUTATED          19         0         36         18
  DEL PEAK  9(3P14.2) WILD-TYPE        30         3         41         37
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  9(3P14.2) MUTATED           10       11
  DEL PEAK  9(3P14.2) WILD-TYPE         27       26
D45V3, multiclass
            clus
vv           DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             5                             8
  STAGE IB                            13                            26
  STAGE II                            12                            19
  STAGE IIA                           11                            25
  STAGE IIB                           19                            30
  STAGE III                            0                             3
  STAGE IIIA                          36                            41
  STAGE IIIB                          18                            37
  STAGE IIIC                          10                            27
  STAGE IV                            11                            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  9(3P14.2) MUTATED     9  32  61  33
  DEL PEAK  9(3P14.2) WILD-TYPE  12  55 112  71
D45V4, multiclass
    clus
vv   DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  T1                           9                            12
  T2                          32                            55
  T3                          61                           112
  T4                          33                            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  9(3P14.2) MUTATED   38 42 33 22
  DEL PEAK  9(3P14.2) WILD-TYPE 84 65 42 57
D45V5, multiclass
    clus
vv   DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  N0                          38                            84
  N1                          42                            65
  N2                          33                            42
  N3                          22                            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"
                               vv
clus                             M0  M1  MX
  DEL PEAK  9(3P14.2) MUTATED   120   9   7
  DEL PEAK  9(3P14.2) WILD-TYPE 233  15  11
D45V6, multiclass
    clus
vv   DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  M0                         120                           233
  M1                           9                            15
  MX                           7                            11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P14.2) MUTATED    52  84
  DEL PEAK  9(3P14.2) WILD-TYPE  99 160
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P14.2) MUTATED     52   84
  DEL PEAK  9(3P14.2) WILD-TYPE   99  160
        clus
vv       DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  FEMALE                          52                            99
  MALE                            84                           160
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK  9(3P14.2) MUTATED                                      17
  DEL PEAK  9(3P14.2) WILD-TYPE                                    48
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  9(3P14.2) MUTATED                                                       50
  DEL PEAK  9(3P14.2) WILD-TYPE                                                    107
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  9(3P14.2) MUTATED                                                                  30
  DEL PEAK  9(3P14.2) WILD-TYPE                                                                39
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  9(3P14.2) MUTATED                                                 28
  DEL PEAK  9(3P14.2) WILD-TYPE                                               36
                               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                                          3
  DEL PEAK  9(3P14.2) WILD-TYPE                                        6
D45V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  9(3P14.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      17
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     50
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          30
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           28
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    3
                                                                   clus
vv                                                                  DEL PEAK  9(3P14.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      107
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     17
  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"
D45V9, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P14.2) MUTATED     2 134
  DEL PEAK  9(3P14.2) WILD-TYPE   4 255
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P14.2) MUTATED      2  134
  DEL PEAK  9(3P14.2) WILD-TYPE    4  255
     clus
vv    DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  NO                            2                             4
  YES                         134                           255
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  9(3P14.2) MUTATED   120   2   7   3
  DEL PEAK  9(3P14.2) WILD-TYPE 198  14  11  22
D45V10, multiclass
    clus
vv   DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  R0                         120                           198
  R1                           2                            14
  R2                           7                            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"
D45V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  9(3P14.2) MUTATED      34                         0
  DEL PEAK  9(3P14.2) WILD-TYPE    54                         6
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  9(3P14.2) MUTATED                                           0    79
  DEL PEAK  9(3P14.2) WILD-TYPE                                         1   164
D45V12, multiclass
                                           clus
vv                                          DEL PEAK  9(3P14.2) MUTATED
  ASIAN                                                              34
  BLACK OR AFRICAN AMERICAN                                           0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              79
                                           clus
vv                                          DEL PEAK  9(3P14.2) WILD-TYPE
  ASIAN                                                                54
  BLACK OR AFRICAN AMERICAN                                             6
  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"

Clustering(46) Variable = DEL PEAK 10(3Q26.31) MUTATION ANALYSIS
D46V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 10(3Q26.31) MUTATED    27  10
  DEL PEAK 10(3Q26.31) WILD-TYPE 215 112
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                            37                            327 
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                            10                            112 
$`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         1.15        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         0.13        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         7.79 
TCGA-FP-A4BF TCGA-HU-8249 TCGA-HU-A4GF TCGA-HU-A4GU TCGA-IN-7806 TCGA-KB-A6F5 
        1.55        14.17        25.81         6.25        21.21         5.56 
TCGA-KB-A93H TCGA-MX-A663 TCGA-RD-A7C1 TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A91X 
       28.90         4.31        16.67         5.46        13.25         8.58 
TCGA-VQ-AA6B 
       29.98 

$`DEL PEAK 10(3Q26.31) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         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-6458 TCGA-BR-6563 
       15.95        13.12        10.13        13.68         7.00        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62        32.78        13.84        13.22        16.14 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.25         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 
       12.82         9.21        24.76        23.93        28.01         0.69 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
        0.16        18.54        12.43         0.95         0.69        12.76 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49         0.82         1.32        12.26         0.49        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        0.72         0.26        12.95         0.26        16.31         1.55 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
        1.48         7.40         6.18        19.50         0.36         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19         2.96         0.95        13.74         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 
        3.32         0.36        19.17        14.79         0.69         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         0.72         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         2.14        13.45         0.20         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         0.59        15.68         0.62 
TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       12.56         0.66         3.02        22.26         0.92        13.41 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       13.51         0.79        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL 
       19.36         0.46        20.65        20.42        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-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-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-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        6.35         0.13         0.13         0.13         0.07         0.10 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10         0.10        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4444 
        1.02         7.99         8.05         4.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 
       19.07        12.03        21.99         9.01         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         1.02         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-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        55.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.36        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.61        17.85         5.95         4.14        15.22        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-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19         0.23         6.97        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-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.24         9.76        15.65         4.34         7.40         7.13 
TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62        16.24         6.58        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
        8.12         0.39        19.53         3.02        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HF-A5NB 
       59.54         5.03        13.58         0.56         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-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-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        17.69        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88         8.81        27.42         3.45        18.81         3.39 
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-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F7 
        6.74         6.87         5.56         1.81         2.53        60.56 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV 
        3.72        19.73        11.05         8.61         4.67       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-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        16.87         5.79         0.92        37.74 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       13.02        31.10        21.73        22.36        23.77         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       19.07        33.63        46.26        16.31         2.70        17.85 
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        19.30        23.57 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        59.18        28.70        11.70         8.68 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z 
       49.25        20.81         1.71         7.36         9.73        44.25 
TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 
        8.61        55.43         4.54         6.58         5.72        40.08 
TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11         4.21         0.79 

  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                          0.13                           0.07 
  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 
                         12.66                          11.57 
[1] "0.1 - 54.1 (12.7)"  "0.1 - 122.3 (11.6)"
[1] "hr=" "1.2"
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       2       12       34       29        32
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 10(3Q26.31) MUTATED           6         0         10          8
  DEL PEAK 10(3Q26.31) WILD-TYPE        43         3         67         47
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 10(3Q26.31) MUTATED            2        1
  DEL PEAK 10(3Q26.31) WILD-TYPE         35       36
D46V3, multiclass
            clus
vv           DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              1                             12
  STAGE IB                              5                             34
  STAGE II                              2                             29
  STAGE IIA                             4                             32
  STAGE IIB                             6                             43
  STAGE III                             0                              3
  STAGE IIIA                           10                             67
  STAGE IIIB                            8                             47
  STAGE IIIC                            2                             35
  STAGE IV                              1                             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 10(3Q26.31) MUTATED     1   6  25   8
  DEL PEAK 10(3Q26.31) WILD-TYPE  20  81 148  96
D46V4, multiclass
    clus
vv   DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  T1                            1                             20
  T2                            6                             81
  T3                           25                            148
  T4                            8                             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 10(3Q26.31) MUTATED    13   8  12   6
  DEL PEAK 10(3Q26.31) WILD-TYPE 109  99  63  73
D46V5, multiclass
    clus
vv   DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  N0                           13                            109
  N1                            8                             99
  N2                           12                             63
  N3                            6                             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                              M0  M1  MX
  DEL PEAK 10(3Q26.31) MUTATED    38   0   3
  DEL PEAK 10(3Q26.31) WILD-TYPE 315  24  15
D46V6, multiclass
    clus
vv   DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  M0                           38                            315
  M1                            0                             24
  MX                            3                             15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                                cls
clus                               0   1
  DEL PEAK 10(3Q26.31) MUTATED    15  26
  DEL PEAK 10(3Q26.31) WILD-TYPE 136 218
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q26.31) MUTATED     15   26
  DEL PEAK 10(3Q26.31) WILD-TYPE  136  218
        clus
vv       DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  FEMALE                           15                            136
  MALE                             26                            218
[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                                    61
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 10(3Q26.31) MUTATED                                                       16
  DEL PEAK 10(3Q26.31) WILD-TYPE                                                    141
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 10(3Q26.31) MUTATED                                                                  11
  DEL PEAK 10(3Q26.31) WILD-TYPE                                                                58
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 10(3Q26.31) MUTATED                                                  8
  DEL PEAK 10(3Q26.31) WILD-TYPE                                               56
                                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                                          1
  DEL PEAK 10(3Q26.31) WILD-TYPE                                        8
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)                           11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     1
                                                                   clus
vv                                                                  DEL PEAK 10(3Q26.31) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         61
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       141
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             58
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              56
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      20
  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"
D46V9, binary
                                cls
clus                               0   1
  DEL PEAK 10(3Q26.31) MUTATED     1  40
  DEL PEAK 10(3Q26.31) WILD-TYPE   5 349
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q26.31) MUTATED      1   40
  DEL PEAK 10(3Q26.31) WILD-TYPE    5  349
     clus
vv    DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  NO                             1                              5
  YES                           40                            349
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 10(3Q26.31) MUTATED    36   1   0   2
  DEL PEAK 10(3Q26.31) WILD-TYPE 282  15  18  23
D46V10, multiclass
    clus
vv   DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  R0                           36                            282
  R1                            1                             15
  R2                            0                             18
  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                         0
  DEL PEAK 10(3Q26.31) WILD-TYPE    80                         6
                                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      28
  DEL PEAK 10(3Q26.31) WILD-TYPE   215
D46V12, multiclass
                                           clus
vv                                          DEL PEAK 10(3Q26.31) MUTATED
  ASIAN                                                                8
  BLACK OR AFRICAN AMERICAN                                            0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               28
                                           clus
vv                                          DEL PEAK 10(3Q26.31) WILD-TYPE
  ASIAN                                                                 80
  BLACK OR AFRICAN AMERICAN                                              6
  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"

Clustering(47) Variable = DEL PEAK 11(4P16.3) MUTATION ANALYSIS
D47V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(4P16.3) MUTATED    93  47
  DEL PEAK 11(4P16.3) WILD-TYPE 149  75
  DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE 
                          140                           224 
  DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE 
                           47                            75 
$`DEL PEAK 11(4P16.3) MUTATED`
TCGA-BR-4183 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-6803 
        6.61         7.43        18.35        10.13         0.62        31.20 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 
        9.21        24.76        15.42        28.01         0.69        18.54 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8080 TCGA-BR-8286 
        0.95         0.69        18.71        17.49         0.49        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8364 
        0.26        16.31         1.55         1.48         7.40        22.19 
TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 
        2.96        14.04        14.79         3.72         5.39         9.21 
TCGA-BR-8486 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 
       20.22         0.49        11.54         0.59        15.68        10.68 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 
        0.66        22.26         0.92         0.72         0.66        13.51 
TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 
        0.46        13.64         0.30         0.07         0.07         0.07 
TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 
        0.13         0.10         0.13         0.13         0.13         0.13 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        0.13         0.10        20.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 
        4.01        47.05        19.07        12.03        18.97         7.07 
TCGA-CG-5725 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6527 
       15.02        19.13        20.55        18.84        17.19         4.14 
TCGA-D7-6528 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8578 
       15.22        11.31        24.72        19.50         0.23        21.14 
TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-6875 
       16.44        11.31         2.96         7.40         7.79        72.23 
TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HJ-7597 
        8.12         3.02        17.06         1.55        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GD 
        1.51         5.92        12.59        14.17        12.10        22.75 
TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
       25.81         8.98         6.25         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RJ 
       17.69         9.67        27.42        21.21        18.81         5.36 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG 
        1.41         6.44         2.53         5.56        60.56         3.72 
TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 
        4.31        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        31.10        21.73 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PU 
       23.77         7.73        46.26         2.70         1.87        23.57 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       59.18        28.70         8.58         9.73        44.25         8.61 
TCGA-VQ-A925 TCGA-VQ-AA6B 
        4.54        29.98 

$`DEL PEAK 11(4P16.3) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4201 TCGA-BR-4267 
        5.62        11.70         6.97         4.64        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        13.12        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        7.00        39.12         0.82        32.78        13.84        13.22 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 
       16.14         1.25         8.98        21.11        30.90        32.94 
TCGA-BR-7196 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7958 
       12.82        35.24        23.93         0.16        12.43        12.76 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
        0.82         1.32         0.69        12.26        20.55         0.72 
TCGA-BR-8285 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 
        0.26         6.18        19.50         0.36         0.26         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 
       13.74         4.31         3.32         0.36        19.17         0.69 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        0.26        15.85         0.72         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 
        2.14        13.45         0.20         7.53        15.81        16.44 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
        0.62        12.56         1.15         3.02        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 
       12.89         0.79        14.17         0.53        12.82        19.36 
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-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8528 
        3.25        13.15        13.18         0.07         0.07         0.10 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A4MG 
        0.16         0.10         0.10         6.35         0.13         0.07 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10         0.10         3.02        27.02        15.95         1.02 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4472 TCGA-CG-4475 
       14.01        29.98        21.99         9.01        12.00        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97         1.02         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-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 
       11.93        18.54        18.61        17.85         5.95        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 
       12.79        10.55        12.33        16.80        17.19         6.97 
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-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A748 
       13.71        11.24        11.44         9.76        15.65         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 
        7.13         0.62        16.24         6.58        14.47        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        0.39        19.53        22.29        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A8CX TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
        0.56         0.23        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-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       11.77        21.37        29.98         0.10         6.51        10.19 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8663 
       19.36        12.30         8.88         8.81         3.45         3.39 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT 
       18.38         5.19        13.08         6.74         6.87         5.56 
TCGA-IN-A7NU TCGA-KB-A93H TCGA-MX-A5UJ TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV 
        1.81        28.90        19.73         8.61         4.67       122.30 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-VQ-A8DL 
       40.64       116.38        71.38        57.44        16.87         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DZ TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       37.74        13.02        22.36        19.07        33.63        16.31 
TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX 
       17.85         9.27        23.41        15.65        19.30        64.57 
TCGA-VQ-A8PY TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U 
       14.33        11.70         8.68        49.25        20.81         1.71 
TCGA-VQ-A91W TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6J 
        7.36        55.43         6.58         5.72        40.08        21.11 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        4.21         0.79 

  DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE 
                         0.07                          0.07 
  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 
                        9.700                        12.145 
[1] "0.1 - 115.7 (9.7)"  "0.1 - 122.3 (12.1)"
[1] "hr=" "1.1"
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       2        9       27       18        18
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 11(4P16.3) MUTATED          15         0         36         20
  DEL PEAK 11(4P16.3) WILD-TYPE        34         3         41         35
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 11(4P16.3) MUTATED           15       11
  DEL PEAK 11(4P16.3) WILD-TYPE         22       26
D47V3, multiclass
            clus
vv           DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             4                             9
  STAGE IB                            12                            27
  STAGE II                            13                            18
  STAGE IIA                           18                            18
  STAGE IIB                           15                            34
  STAGE III                            0                             3
  STAGE IIIA                          36                            41
  STAGE IIIB                          20                            35
  STAGE IIIC                          15                            22
  STAGE IV                            11                            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 11(4P16.3) MUTATED    6 27 79 34
  DEL PEAK 11(4P16.3) WILD-TYPE 15 60 94 70
D47V4, multiclass
    clus
vv   DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE
  T1                           6                            15
  T2                          27                            60
  T3                          79                            94
  T4                          34                            70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 11(4P16.3) MUTATED   43 44 32 28
  DEL PEAK 11(4P16.3) WILD-TYPE 79 63 43 51
D47V5, multiclass
    clus
vv   DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE
  N0                          43                            79
  N1                          44                            63
  N2                          32                            43
  N3                          28                            51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK 11(4P16.3) MUTATED   140   5   6
  DEL PEAK 11(4P16.3) WILD-TYPE 213  19  12
D47V6, multiclass
    clus
vv   DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE
  M0                         140                           213
  M1                           5                            19
  MX                           6                            12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(4P16.3) MUTATED    53  98
  DEL PEAK 11(4P16.3) WILD-TYPE  98 146
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P16.3) MUTATED     53   98
  DEL PEAK 11(4P16.3) WILD-TYPE   98  146
        clus
vv       DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE
  FEMALE                          53                            98
  MALE                            98                           146
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 11(4P16.3) MUTATED                                      22
  DEL PEAK 11(4P16.3) WILD-TYPE                                    43
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 11(4P16.3) MUTATED                                                       55
  DEL PEAK 11(4P16.3) WILD-TYPE                                                    102
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 11(4P16.3) MUTATED                                                                  24
  DEL PEAK 11(4P16.3) WILD-TYPE                                                                45
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 11(4P16.3) MUTATED                                                 32
  DEL PEAK 11(4P16.3) WILD-TYPE                                               32
                               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                                          5
  DEL PEAK 11(4P16.3) WILD-TYPE                                        4
D47V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 11(4P16.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      22
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     55
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          24
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    5
                                                                   clus
vv                                                                  DEL PEAK 11(4P16.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        43
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      102
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            45
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     11
  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"
D47V9, binary
                               cls
clus                              0   1
  DEL PEAK 11(4P16.3) MUTATED     2 149
  DEL PEAK 11(4P16.3) WILD-TYPE   4 240
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P16.3) MUTATED      2  149
  DEL PEAK 11(4P16.3) WILD-TYPE    4  240
     clus
vv    DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE
  NO                            2                             4
  YES                         149                           240
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 11(4P16.3) MUTATED   123   7   4   9
  DEL PEAK 11(4P16.3) WILD-TYPE 195   9  14  16
D47V10, multiclass
    clus
vv   DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE
  R0                         123                           195
  R1                           7                             9
  R2                           4                            14
  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                         1
  DEL PEAK 11(4P16.3) WILD-TYPE    50                         5
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 11(4P16.3) MUTATED                                           0    93
  DEL PEAK 11(4P16.3) WILD-TYPE                                         1   150
D47V12, multiclass
                                           clus
vv                                          DEL PEAK 11(4P16.3) MUTATED
  ASIAN                                                              38
  BLACK OR AFRICAN AMERICAN                                           1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              93
                                           clus
vv                                          DEL PEAK 11(4P16.3) WILD-TYPE
  ASIAN                                                                50
  BLACK OR AFRICAN AMERICAN                                             5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               150
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = DEL PEAK 12(4Q22.1) MUTATION ANALYSIS
D48V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(4Q22.1) MUTATED   107  53
  DEL PEAK 12(4Q22.1) WILD-TYPE 135  69
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                          160                           204 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                           53                            69 
$`DEL PEAK 12(4Q22.1) MUTATED`
TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6801 
        6.61        18.35        10.13         7.00         0.62        21.11 
TCGA-BR-6803 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 
       31.20        28.01         0.69         0.69        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        0.82         0.69         0.49        12.95         0.26        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 
        1.55         1.48        19.50        22.19         2.96        14.04 
TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       14.79         3.72         5.39         0.72         9.21        20.22 
TCGA-BR-8589 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ 
       15.81        11.54         0.59        10.68         0.66        22.26 
TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QI 
        0.92         0.72         0.66        13.51         1.15        13.64 
TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 
        5.13         3.25        13.15         0.30         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 
        0.07         0.07         0.10         0.16         0.10         0.13 
TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        0.13         0.13         0.13         0.13         0.07         0.10 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       20.02         3.02         7.99         8.05        54.08         4.01 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       47.05        19.07        12.03        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5720 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 
       30.97         0.99        12.03        79.07         4.01        55.04 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6526 
       12.36        12.66        11.93        19.13        20.55        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8573 
        4.14        15.22        15.98        10.55        11.31        19.50 
TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 
        0.23        16.44        11.31         7.40         0.62         7.79 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 
       72.23         8.12         0.39        19.53         3.02        17.06 
TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 
       13.58         1.55         0.23         1.51         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4GD TCGA-HU-A4GP 
       14.17        12.10         0.76         5.59        22.75         8.98 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
        6.25         0.26         2.10        12.95        17.69        12.30 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ 
        9.67        27.42        21.21        18.81         3.39         5.36 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IP-7968 TCGA-MX-A663 
        1.41         6.44         6.74         5.56         2.53         4.31 
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-A8E2 TCGA-VQ-A8E3 
       35.61        37.74        13.25        13.02        31.10        21.73 
TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PY TCGA-VQ-A8PZ 
        7.73        46.26         2.70         9.27        14.33        59.18 
TCGA-VQ-A91A TCGA-VQ-A91Q TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A925 
       28.70        20.81         8.58         9.73        44.25         4.54 
TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J 
        5.72        40.08        29.98        21.11 

$`DEL PEAK 12(4Q22.1) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
        5.62        11.70         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        13.12 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.68        39.12         0.82        32.78        13.84        13.22 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 
       16.14         1.25         8.98        30.90        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7722 
        9.21        24.76        35.24        23.93        15.42         0.16 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8060 TCGA-BR-8078 
       18.54        12.43         0.95        12.76         1.32        12.26 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 
       20.55         0.72         0.26         7.40         6.18         0.36 
TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
        0.26         0.95        13.74         4.31         3.32         0.36 
TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8588 
       19.17         0.69         0.26        15.85         1.12        12.79 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        2.14        13.45         0.20         7.53         0.49        15.81 
TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 
       16.44        15.68         0.62        12.56         1.15         3.02 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51        12.89         0.79        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL 
       12.82        19.36         0.46        20.65        20.42        11.57 
TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8536 
        2.83        13.18         0.07         0.13         0.10         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 
        6.35         0.13         0.10         0.10        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4472 
        1.02        14.01        29.98        21.99         9.01        12.00 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.97         1.02         1.02         6.02         0.99       105.07 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-6520 
       15.02        28.96        65.10        21.07         7.99        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6817 TCGA-D7-6822 
       18.54        18.61        17.85         5.95        12.79        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       24.72        16.80        17.19         6.97        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-A6F2 TCGA-D7-A748 
       11.24        11.44         9.76         2.96        15.65         4.34 
TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7998 
        7.13        16.24         6.58        14.47        21.27        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 
       59.54         5.03         0.56        18.08        26.47        14.27 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       11.41        10.62        24.30        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
        3.25        25.81        11.77        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 
        6.51        10.19        19.36         8.88         8.81         3.45 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NU TCGA-KB-A6F5 
       18.38         5.19        13.08         6.87         1.81         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BW TCGA-RD-A8MV 
       60.56        28.90         3.72        19.73         4.67       122.30 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EB 
       40.64       116.38        71.38        57.44        16.87         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
        0.92         5.46        22.36        23.77        19.07        33.63 
TCGA-VQ-A8PD TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       16.31        17.85         1.87        23.41        15.65        19.30 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91U 
       23.57        64.57        11.70         8.68        49.25         1.71 
TCGA-VQ-A91W TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        7.36         8.61        55.43         6.58         4.21         0.79 

  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                         0.07                          0.07 
  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 
                        9.470                        12.495 
[1] "0.1 - 115.7 (9.5)"  "0.1 - 122.3 (12.5)"
[1] "hr=" "1.1"
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       2        9       26       14        18
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 12(4Q22.1) MUTATED          21         1         38         22
  DEL PEAK 12(4Q22.1) WILD-TYPE        28         2         39         33
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 12(4Q22.1) MUTATED           16       17
  DEL PEAK 12(4Q22.1) WILD-TYPE         21       20
D48V3, multiclass
            clus
vv           DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             4                             9
  STAGE IB                            13                            26
  STAGE II                            17                            14
  STAGE IIA                           18                            18
  STAGE IIB                           21                            28
  STAGE III                            1                             2
  STAGE IIIA                          38                            39
  STAGE IIIB                          22                            33
  STAGE IIIC                          16                            21
  STAGE IV                            17                            20
[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 86 40
  DEL PEAK 12(4Q22.1) WILD-TYPE 16 50 87 64
D48V4, multiclass
    clus
vv   DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  T1                           5                            16
  T2                          37                            50
  T3                          86                            87
  T4                          40                            64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 12(4Q22.1) MUTATED   48 49 38 34
  DEL PEAK 12(4Q22.1) WILD-TYPE 74 58 37 45
D48V5, multiclass
    clus
vv   DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  N0                          48                            74
  N1                          49                            58
  N2                          38                            37
  N3                          34                            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"
                               vv
clus                             M0  M1  MX
  DEL PEAK 12(4Q22.1) MUTATED   156   9   8
  DEL PEAK 12(4Q22.1) WILD-TYPE 197  15  10
D48V6, multiclass
    clus
vv   DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  M0                         156                           197
  M1                           9                            15
  MX                           8                            10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q22.1) MUTATED    64 109
  DEL PEAK 12(4Q22.1) WILD-TYPE  87 135
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED     64  109
  DEL PEAK 12(4Q22.1) WILD-TYPE   87  135
        clus
vv       DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  FEMALE                          64                            87
  MALE                           109                           135
[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                                    42
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 12(4Q22.1) MUTATED                                                       65
  DEL PEAK 12(4Q22.1) WILD-TYPE                                                     92
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 12(4Q22.1) MUTATED                                                                  32
  DEL PEAK 12(4Q22.1) WILD-TYPE                                                                37
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 12(4Q22.1) MUTATED                                                 32
  DEL PEAK 12(4Q22.1) WILD-TYPE                                               32
                               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                                          6
  DEL PEAK 12(4Q22.1) WILD-TYPE                                        3
D48V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 12(4Q22.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      23
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     65
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          32
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    6
                                                                   clus
vv                                                                  DEL PEAK 12(4Q22.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        42
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       92
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      3
[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     4 169
  DEL PEAK 12(4Q22.1) WILD-TYPE   2 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED      4  169
  DEL PEAK 12(4Q22.1) WILD-TYPE    2  220
     clus
vv    DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  NO                            4                             2
  YES                         169                           220
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 12(4Q22.1) MUTATED   137   8  10   8
  DEL PEAK 12(4Q22.1) WILD-TYPE 181   8   8  17
D48V10, multiclass
    clus
vv   DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  R0                         137                           181
  R1                           8                             8
  R2                          10                             8
  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                         4
  DEL PEAK 12(4Q22.1) WILD-TYPE    45                         2
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 12(4Q22.1) MUTATED                                           1   100
  DEL PEAK 12(4Q22.1) WILD-TYPE                                         0   143
D48V12, multiclass
                                           clus
vv                                          DEL PEAK 12(4Q22.1) MUTATED
  ASIAN                                                              43
  BLACK OR AFRICAN AMERICAN                                           4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             100
                                           clus
vv                                          DEL PEAK 12(4Q22.1) WILD-TYPE
  ASIAN                                                                45
  BLACK OR AFRICAN AMERICAN                                             2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               143
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(49) Variable = DEL PEAK 13(4Q34.3) MUTATION ANALYSIS
D49V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(4Q34.3) MUTATED   112  50
  DEL PEAK 13(4Q34.3) WILD-TYPE 130  72
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                          162                           202 
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                           50                            72 
$`DEL PEAK 13(4Q34.3) MUTATED`
TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6709 
       18.35        10.13         7.00         0.62        13.84         1.25 
TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7723 
       31.20         9.21        35.24        15.42         0.69        18.54 
TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
       12.43         0.69        18.71        17.49         0.82         0.69 
TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.49         0.26        16.31         1.55         1.48         7.40 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8384 
       19.50        22.19         2.96        14.04        14.79         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8677 TCGA-BR-8678 
        5.39         0.72         9.21        20.22         0.49        11.54 
TCGA-BR-8683 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 
        0.59         0.66        22.26         0.92         0.72         0.66 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 
       13.51        20.65         1.15        13.64         3.25        13.15 
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-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A489 
        0.10         0.16         0.10         0.13         0.13         0.13 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4436 
        0.13         0.13         0.10        20.02        27.02         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-4465 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 
        9.01        18.97        22.98        30.97         6.97         1.02 
TCGA-CG-5725 TCGA-CG-5727 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6525 TCGA-D7-6526 
       15.02        79.07        12.66        19.13         5.95        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 
        4.14        15.22        15.98        12.79        11.31        12.33 
TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6EX 
       19.50         0.23        14.27        16.44        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       11.44         2.96         7.40         0.62         7.79        16.24 
TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-A4BF 
        8.12        19.53         3.02        17.06        13.58         1.55 
TCGA-FP-A8CX TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 
        0.23         1.51         5.92        12.59        12.10         0.76 
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-A6RJ TCGA-IN-A6RL 
       17.69        12.30         9.67        27.42         5.36         5.19 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU 
       13.08         1.41         6.44         6.74         5.56         1.81 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MV 
        2.53        60.56         4.31        11.05        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV 
       37.91         8.94        35.61         0.92        37.74        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PU 
       13.02        31.10        21.73         7.73        46.26        23.57 
TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y 
       64.57        59.18        28.70         1.71         8.58         9.73 
TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       44.25         4.54        40.08        29.98        21.11         0.79 

$`DEL PEAK 13(4Q34.3) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         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-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6706 
       13.12        13.68        39.12         0.82        32.78        13.22 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 
       16.14         8.98        21.11        30.90        32.94        12.82 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7958 
       24.76        23.93        28.01         0.16         0.95        12.76 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        1.32        12.26        20.55         0.72         0.26        12.95 
TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        6.18         0.36         0.26         0.95        13.74         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 
        3.32         0.36        19.17         0.69         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         2.14        13.45         0.20 
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         0.62        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       12.56         1.15         3.02        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 
        0.79        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         6.35         0.13         0.07         0.10 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 
        0.10         3.02        15.95         1.02        14.01        29.98 
TCGA-CG-4460 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 
       21.99         7.07        12.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6519 
       55.04        21.07         7.99        12.36        11.93        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6818 TCGA-D7-8570 
       18.84        18.54        18.61        17.85        10.55        24.72 
TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YV 
       16.80        17.19         6.97        21.14        20.91         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EZ TCGA-D7-A6F2 
       15.16        13.78        14.76        13.71         9.76        15.65 
TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        4.34         7.13         6.58        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HF-A5NB 
        0.39        22.29        59.54         5.03         0.56        18.08 
TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-A4G2 
       26.47        14.27        14.17        11.41        10.62        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-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       11.77        21.37        29.98         0.10         6.51        10.19 
TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       19.36         8.88         8.81        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RS TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A5UG 
        3.39        18.38         6.87         5.56        28.90         3.72 
TCGA-MX-A5UJ TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       19.73         8.61         4.67        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8P2 
       71.38        57.44        16.87         5.79         5.46        22.36 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       23.77        19.07        33.63        16.31         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PY 
        1.87         9.27        23.41        15.65        19.30        14.33 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91W TCGA-VQ-A922 
       11.70         8.68        49.25        20.81         7.36         8.61 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-ZA-A8F6 
       55.43         6.58         5.72         4.21 

  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                         0.07                          0.07 
  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 
                         9.44                         12.33 
[1] "0.1 - 122.3 (9.4)"  "0.1 - 116.4 (12.3)"
[1] "hr=" "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        18
  DEL PEAK 13(4Q34.3) WILD-TYPE       2        9       24       11        18
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 13(4Q34.3) MUTATED          18         1         37         24
  DEL PEAK 13(4Q34.3) WILD-TYPE        31         2         40         31
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 13(4Q34.3) MUTATED           20       10
  DEL PEAK 13(4Q34.3) WILD-TYPE         17       27
D49V3, multiclass
            clus
vv           DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             4                             9
  STAGE IB                            15                            24
  STAGE II                            20                            11
  STAGE IIA                           18                            18
  STAGE IIB                           18                            31
  STAGE III                            1                             2
  STAGE IIIA                          37                            40
  STAGE IIIB                          24                            31
  STAGE IIIC                          20                            17
  STAGE IV                            10                            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 13(4Q34.3) MUTATED    8 35 81 44
  DEL PEAK 13(4Q34.3) WILD-TYPE 13 52 92 60
D49V4, multiclass
    clus
vv   DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  T1                           8                            13
  T2                          35                            52
  T3                          81                            92
  T4                          44                            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"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 13(4Q34.3) MUTATED   53 46 33 37
  DEL PEAK 13(4Q34.3) WILD-TYPE 69 61 42 42
D49V5, multiclass
    clus
vv   DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  N0                          53                            69
  N1                          46                            61
  N2                          33                            42
  N3                          37                            42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK 13(4Q34.3) MUTATED   157   7   9
  DEL PEAK 13(4Q34.3) WILD-TYPE 196  17   9
D49V6, multiclass
    clus
vv   DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  M0                         157                           196
  M1                           7                            17
  MX                           9                             9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                               cls
clus                              0   1
  DEL PEAK 13(4Q34.3) MUTATED    70 103
  DEL PEAK 13(4Q34.3) WILD-TYPE  81 141
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q34.3) MUTATED     70  103
  DEL PEAK 13(4Q34.3) WILD-TYPE   81  141
        clus
vv       DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  FEMALE                          70                            81
  MALE                           103                           141
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 13(4Q34.3) MUTATED                                      20
  DEL PEAK 13(4Q34.3) WILD-TYPE                                    45
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 13(4Q34.3) MUTATED                                                       65
  DEL PEAK 13(4Q34.3) WILD-TYPE                                                     92
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 13(4Q34.3) MUTATED                                                                  37
  DEL PEAK 13(4Q34.3) WILD-TYPE                                                                32
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 13(4Q34.3) MUTATED                                                 33
  DEL PEAK 13(4Q34.3) WILD-TYPE                                               31
                               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                                          5
  DEL PEAK 13(4Q34.3) WILD-TYPE                                        4
D49V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 13(4Q34.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      20
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     65
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          37
  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                                                                  DEL PEAK 13(4Q34.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        45
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       92
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            32
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             31
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     4
  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"
D49V9, binary
                               cls
clus                              0   1
  DEL PEAK 13(4Q34.3) MUTATED     4 169
  DEL PEAK 13(4Q34.3) WILD-TYPE   2 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q34.3) MUTATED      4  169
  DEL PEAK 13(4Q34.3) WILD-TYPE    2  220
     clus
vv    DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  NO                            4                             2
  YES                         169                           220
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 13(4Q34.3) MUTATED   146   6   6   6
  DEL PEAK 13(4Q34.3) WILD-TYPE 172  10  12  19
D49V10, multiclass
    clus
vv   DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  R0                         146                           172
  R1                           6                            10
  R2                           6                            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"
D49V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 13(4Q34.3) MUTATED      42                         2
  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   105
  DEL PEAK 13(4Q34.3) WILD-TYPE                                         1   138
D49V12, multiclass
                                           clus
vv                                          DEL PEAK 13(4Q34.3) MUTATED
  ASIAN                                                              42
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             105
                                           clus
vv                                          DEL PEAK 13(4Q34.3) WILD-TYPE
  ASIAN                                                                46
  BLACK OR AFRICAN AMERICAN                                             4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               138
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(50) Variable = DEL PEAK 14(5Q12.1) MUTATION ANALYSIS
D50V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(5Q12.1) MUTATED    91  47
  DEL PEAK 14(5Q12.1) WILD-TYPE 151  75
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                          138                           226 
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                           47                            75 
$`DEL PEAK 14(5Q12.1) MUTATED`
TCGA-BR-4183 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7704 TCGA-BR-7715 
        6.61         7.00         0.62         1.25        35.24        15.42 
TCGA-BR-7716 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 
       28.01         0.95        12.76        18.71         1.32         0.69 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8483 
       12.95         0.26         1.55        14.04        14.79         5.39 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 
        9.21        20.22        11.54         0.59         0.62        10.68 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4PE 
        1.15         0.66        22.26         0.92         0.72        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 
        1.15        13.64        13.15        13.18         0.30         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8535 
        0.07         0.07         0.07         0.10         0.13         0.13 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4304 
        6.35         0.13         0.13         0.13         0.10        27.02 
TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        7.99         4.01        14.01        47.05        19.07        12.03 
TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5725 TCGA-CG-5732 
       18.97        22.98        30.97         1.02        15.02        55.04 
TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       11.93        18.84         5.95        17.19         4.14        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-A6EV 
       15.98        12.79        11.31        12.33        24.72        11.24 
TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 
       11.31         2.96        15.65         7.40         0.62         7.79 
TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       72.23        19.53        17.06        13.58         0.56         1.55 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4G3 
        1.51         5.92        12.59        14.17         0.76         5.59 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H0 
        3.25        22.75        25.81        11.77         6.25         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
       12.95        17.69         9.67        27.42        21.21        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
        3.39        18.38         5.19        13.08         6.44         6.74 
TCGA-IN-A7NT TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A663 TCGA-RD-A8MW 
        5.56         2.53        60.56        28.90         4.31        37.91 
TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
      115.69         8.94         5.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       31.10         7.73        46.26         2.70        17.85         1.87 
TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91U TCGA-VQ-A91Y TCGA-VQ-A91Z 
       23.57        14.33        28.70         1.71         9.73        44.25 
TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6J TCGA-ZQ-A9CR 
        8.61         4.54         5.72        40.08        21.11         0.79 

$`DEL PEAK 14(5Q12.1) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
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-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       13.12        10.13        13.68        39.12         0.82        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       13.84        13.22        16.14         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-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-8058 
        0.69         0.16        18.54        12.43         0.69        17.49 
TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.82        12.26         0.49        20.55         0.72         0.26 
TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       16.31         1.48         7.40         6.18        19.50         0.36 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19         2.96         0.95        13.74         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 
        3.32         0.36        19.17         0.69         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        3.72         0.72         1.12        12.79        15.81         2.14 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       13.45         0.20         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         3.02        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.79        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         0.13         0.07         0.10         0.10        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-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5719 
       21.99         9.01         7.07        12.00         6.97         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-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-D7-6518 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-D7-6818 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       10.55        16.80        19.50        17.19         0.23         6.97 
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-A6EY TCGA-D7-A6EZ TCGA-D7-A748 
       13.78        14.76        13.71        11.44         9.76         4.34 
TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        7.13        16.24         6.58        14.47        21.27         8.12 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A8CX 
        0.39         3.02        22.29        59.54         5.03         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       18.08        26.47        14.27        11.41        12.10        10.62 
TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.30        12.30        11.84        24.20        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 
        8.98         0.10         6.51        10.19         0.26        19.36 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-A6RJ TCGA-IN-A6RO 
       12.30         8.88         8.81         3.45         5.36         1.41 
TCGA-IN-A6RS TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS 
        6.87         1.81         5.56         3.72        19.73        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 
        8.61         4.67        16.67       122.30        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       71.38        57.44        35.61        16.87         0.92        37.74 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       21.73        22.36        23.77        19.07        33.63        16.31 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ 
        9.27        23.41        15.65        19.30        64.57        59.18 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91W TCGA-VQ-A91X 
       11.70         8.68        49.25        20.81         7.36         8.58 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-AA6B TCGA-ZA-A8F6 
       55.43         6.58        29.98         4.21 

  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                         0.07                          0.07 
  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 
                       10.205                        12.065 
[1] "0.1 - 115.7 (10.2)" "0.1 - 122.3 (12.1)"
[1] "hr=" "1.1"
D50V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 14(5Q12.1) MUTATED         0        4       14       11        11
  DEL PEAK 14(5Q12.1) WILD-TYPE       2        9       25       20        25
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 14(5Q12.1) MUTATED          23         0         38         20
  DEL PEAK 14(5Q12.1) WILD-TYPE        26         3         39         35
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 14(5Q12.1) MUTATED           11       11
  DEL PEAK 14(5Q12.1) WILD-TYPE         26       26
D50V3, multiclass
            clus
vv           DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             4                             9
  STAGE IB                            14                            25
  STAGE II                            11                            20
  STAGE IIA                           11                            25
  STAGE IIB                           23                            26
  STAGE III                            0                             3
  STAGE IIIA                          38                            39
  STAGE IIIB                          20                            35
  STAGE IIIC                          11                            26
  STAGE IV                            11                            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 14(5Q12.1) MUTATED     8  35  70  31
  DEL PEAK 14(5Q12.1) WILD-TYPE  13  52 103  73
D50V4, multiclass
    clus
vv   DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  T1                           8                            13
  T2                          35                            52
  T3                          70                           103
  T4                          31                            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 14(5Q12.1) MUTATED   39 42 36 27
  DEL PEAK 14(5Q12.1) WILD-TYPE 83 65 39 52
D50V5, multiclass
    clus
vv   DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  N0                          39                            83
  N1                          42                            65
  N2                          36                            39
  N3                          27                            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"
                               vv
clus                             M0  M1  MX
  DEL PEAK 14(5Q12.1) MUTATED   135   6   6
  DEL PEAK 14(5Q12.1) WILD-TYPE 218  18  12
D50V6, multiclass
    clus
vv   DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  M0                         135                           218
  M1                           6                            18
  MX                           6                            12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q12.1) MUTATED    54  93
  DEL PEAK 14(5Q12.1) WILD-TYPE  97 151
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q12.1) MUTATED     54   93
  DEL PEAK 14(5Q12.1) WILD-TYPE   97  151
        clus
vv       DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  FEMALE                          54                            97
  MALE                            93                           151
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 14(5Q12.1) MUTATED                                      10
  DEL PEAK 14(5Q12.1) WILD-TYPE                                    55
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 14(5Q12.1) MUTATED                                                       56
  DEL PEAK 14(5Q12.1) WILD-TYPE                                                    101
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 14(5Q12.1) MUTATED                                                                  26
  DEL PEAK 14(5Q12.1) WILD-TYPE                                                                43
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 14(5Q12.1) MUTATED                                                 36
  DEL PEAK 14(5Q12.1) WILD-TYPE                                               28
                               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                                        5
D50V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 14(5Q12.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      10
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     56
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          26
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           36
  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                                                        55
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      101
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            43
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             28
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     11
  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"
D50V9, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q12.1) MUTATED     3 144
  DEL PEAK 14(5Q12.1) WILD-TYPE   3 245
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q12.1) MUTATED      3  144
  DEL PEAK 14(5Q12.1) WILD-TYPE    3  245
     clus
vv    DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  NO                            3                             3
  YES                         144                           245
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 14(5Q12.1) MUTATED   121   8   6   5
  DEL PEAK 14(5Q12.1) WILD-TYPE 197   8  12  20
D50V10, multiclass
    clus
vv   DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  R0                         121                           197
  R1                           8                             8
  R2                           6                            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"
D50V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 14(5Q12.1) MUTATED      38                         3
  DEL PEAK 14(5Q12.1) WILD-TYPE    50                         3
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 14(5Q12.1) MUTATED                                           0    88
  DEL PEAK 14(5Q12.1) WILD-TYPE                                         1   155
D50V12, multiclass
                                           clus
vv                                          DEL PEAK 14(5Q12.1) MUTATED
  ASIAN                                                              38
  BLACK OR AFRICAN AMERICAN                                           3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              88
                                           clus
vv                                          DEL PEAK 14(5Q12.1) WILD-TYPE
  ASIAN                                                                50
  BLACK OR AFRICAN AMERICAN                                             3
  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"

Clustering(51) Variable = DEL PEAK 15(5Q23.2) MUTATION ANALYSIS
D51V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(5Q23.2) MUTATED    85  43
  DEL PEAK 15(5Q23.2) WILD-TYPE 157  79
  DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE 
                          128                           236 
  DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE 
                           43                            79 
$`DEL PEAK 15(5Q23.2) MUTATED`
TCGA-BR-4183 TCGA-BR-4267 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7704 
        6.61         6.18         7.00         0.62         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8060 
       15.42        28.01         0.95        12.76        18.71         1.32 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8373 
       12.95         0.26         1.55         4.31        14.04        14.79 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8687 
        5.39         9.21        20.22        11.54         0.59         0.62 
TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4PD 
       10.68         0.66        22.26         0.92         0.72        20.65 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 
       20.42        13.64        13.15        13.18         0.30         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A489 
        0.07         0.07         0.10         0.13         0.13         0.13 
TCGA-CD-A4MH TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        0.10        27.02         7.99        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5718 
       29.98        47.05        19.07        18.97        30.97         1.02 
TCGA-CG-5725 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
       15.02        11.93        18.84        17.19         4.14        15.98 
TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-A4YT TCGA-D7-A6EV 
       12.79        12.33        24.72        19.50        14.27        11.24 
TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 
       11.31         2.96        15.65         7.79        16.24        72.23 
TCGA-FP-7829 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8238 TCGA-HU-8243 
       19.53        13.58         0.56         1.55         1.51         5.92 
TCGA-HU-8245 TCGA-HU-8610 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.59         0.76         3.25        22.75        25.81        11.77 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 
        8.98         6.25         2.10        12.95        17.69         9.67 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN 
       27.42        21.21        18.81        18.38         5.19        13.08 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IP-7968 TCGA-KB-A6F7 
        1.41         6.44         6.74         5.56         2.53        60.56 
TCGA-KB-A93H TCGA-MX-A663 TCGA-RD-A7BT TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 
       28.90         4.31         8.61        37.91       115.69         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        5.79         0.92         5.46        13.25        13.02        31.10 
TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PU TCGA-VQ-A91A 
        7.73        46.26         2.70        17.85        23.57        28.70 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 
       20.81         1.71         9.73        44.25         8.61         4.54 
TCGA-VQ-AA68 TCGA-ZQ-A9CR 
       40.08         0.79 

$`DEL PEAK 15(5Q23.2) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         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        13.12 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
       10.13        13.68        39.12         0.82        32.78        13.84 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       13.22        16.14         1.25         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 
       31.20        32.94        12.82        24.76        23.93         0.69 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8059 
        0.16        18.54        12.43         0.69        17.49         0.82 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        12.26         0.49        20.55         0.72         0.26 
TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       16.31         1.48         7.40         6.18        19.50         0.36 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8370 
        0.26        22.19         2.96         0.95        13.74         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        0.36        19.17         0.69         0.26        15.85         3.72 
TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        0.72         1.12        12.79        15.81         2.14        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 
        0.20         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         1.15         3.02        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.79        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         6.35         0.13         0.13         0.13 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 
        0.07         0.10         0.10        20.02         3.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4469 
        1.02         8.05        12.03        21.99         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-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        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        55.04        21.07         7.99        12.36        12.66 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        20.55        18.54        18.61        17.85         5.95 
TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 
       15.22        10.55        11.31        16.80        17.19         0.23 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
        6.97        21.14        20.91        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 
       13.78        14.76        13.71        11.44         9.76         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 
        7.40         7.13         0.62         6.58        14.47        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        8.12         0.39         3.02        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8249 
        5.03         0.23        18.08        26.47        14.27        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       11.41        12.10        10.62        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.84        24.20        21.37        29.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB 
       10.19         0.26        19.36        12.30         8.88         8.81 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RS TCGA-IN-A7NU TCGA-KB-A6F5 
        3.45         3.39         5.36         6.87         1.81         5.56 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        3.72        19.73        11.05         4.67        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-VQ-A8DT TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.74        21.73        22.36        23.77        19.07        33.63 
TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       16.31         1.87         9.27        23.41        15.65        19.30 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       64.57        14.33        59.18        11.70         8.68        49.25 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6B 
        7.36         8.58        55.43         6.58         5.72        29.98 
TCGA-VQ-AA6J TCGA-ZA-A8F6 
       21.11         4.21 

  DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE 
                         0.07                          0.07 
  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 
                       11.425                        11.700 
[1] "0.1 - 115.7 (11.4)" "0.1 - 122.3 (11.7)"
[1] "hr=" "1"  
D51V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 15(5Q23.2) MUTATED         0        6       15       10        12
  DEL PEAK 15(5Q23.2) WILD-TYPE       2        7       24       21        24
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 15(5Q23.2) MUTATED          18         0         36         15
  DEL PEAK 15(5Q23.2) WILD-TYPE        31         3         41         40
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 15(5Q23.2) MUTATED           11        8
  DEL PEAK 15(5Q23.2) WILD-TYPE         26       29
D51V3, multiclass
            clus
vv           DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             6                             7
  STAGE IB                            15                            24
  STAGE II                            10                            21
  STAGE IIA                           12                            24
  STAGE IIB                           18                            31
  STAGE III                            0                             3
  STAGE IIIA                          36                            41
  STAGE IIIB                          15                            40
  STAGE IIIC                          11                            26
  STAGE IV                             8                            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 15(5Q23.2) MUTATED     9  30  64  28
  DEL PEAK 15(5Q23.2) WILD-TYPE  12  57 109  76
D51V4, multiclass
    clus
vv   DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE
  T1                           9                            12
  T2                          30                            57
  T3                          64                           109
  T4                          28                            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 15(5Q23.2) MUTATED   43 37 29 23
  DEL PEAK 15(5Q23.2) WILD-TYPE 79 70 46 56
D51V5, multiclass
    clus
vv   DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE
  N0                          43                            79
  N1                          37                            70
  N2                          29                            46
  N3                          23                            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"
                               vv
clus                             M0  M1  MX
  DEL PEAK 15(5Q23.2) MUTATED   123   4   6
  DEL PEAK 15(5Q23.2) WILD-TYPE 230  20  12
D51V6, multiclass
    clus
vv   DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE
  M0                         123                           230
  M1                           4                            20
  MX                           6                            12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q23.2) MUTATED    48  85
  DEL PEAK 15(5Q23.2) WILD-TYPE 103 159
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q23.2) MUTATED     48   85
  DEL PEAK 15(5Q23.2) WILD-TYPE  103  159
        clus
vv       DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE
  FEMALE                          48                           103
  MALE                            85                           159
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 15(5Q23.2) MUTATED                                       8
  DEL PEAK 15(5Q23.2) WILD-TYPE                                    57
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 15(5Q23.2) MUTATED                                                       53
  DEL PEAK 15(5Q23.2) WILD-TYPE                                                    104
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 15(5Q23.2) MUTATED                                                                  25
  DEL PEAK 15(5Q23.2) WILD-TYPE                                                                44
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 15(5Q23.2) MUTATED                                                 34
  DEL PEAK 15(5Q23.2) WILD-TYPE                                               30
                               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                                          3
  DEL PEAK 15(5Q23.2) WILD-TYPE                                        6
D51V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 15(5Q23.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     53
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          25
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    3
                                                                   clus
vv                                                                  DEL PEAK 15(5Q23.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        57
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      104
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            44
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             30
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     5
  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"
D51V9, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q23.2) MUTATED     2 131
  DEL PEAK 15(5Q23.2) WILD-TYPE   4 258
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q23.2) MUTATED      2  131
  DEL PEAK 15(5Q23.2) WILD-TYPE    4  258
     clus
vv    DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE
  NO                            2                             4
  YES                         131                           258
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 15(5Q23.2) MUTATED   113   6   6   4
  DEL PEAK 15(5Q23.2) WILD-TYPE 205  10  12  21
D51V10, multiclass
    clus
vv   DEL PEAK 15(5Q23.2) MUTATED DEL PEAK 15(5Q23.2) WILD-TYPE
  R0                         113                           205
  R1                           6                            10
  R2                           6                            12
  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                         2
  DEL PEAK 15(5Q23.2) WILD-TYPE    55                         4
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 15(5Q23.2) MUTATED                                           1    80
  DEL PEAK 15(5Q23.2) WILD-TYPE                                         0   163
D51V12, multiclass
                                           clus
vv                                          DEL PEAK 15(5Q23.2) MUTATED
  ASIAN                                                              33
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              80
                                           clus
vv                                          DEL PEAK 15(5Q23.2) WILD-TYPE
  ASIAN                                                                55
  BLACK OR AFRICAN AMERICAN                                             4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               163
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = DEL PEAK 16(6P25.3) MUTATION ANALYSIS
D52V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 16(6P25.3) MUTATED    63  32
  DEL PEAK 16(6P25.3) WILD-TYPE 179  90
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                           95                           269 
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                           32                            90 
$`DEL PEAK 16(6P25.3) MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6709 TCGA-BR-6803 
        5.62         6.97        10.13         7.00         1.25        31.20 
TCGA-BR-7716 TCGA-BR-7901 TCGA-BR-8077 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8485 
       28.01         0.95         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         0.59         0.62        22.26         0.92 
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         0.13 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CG-4437 TCGA-CG-4466 TCGA-CG-5719 TCGA-CG-5724 
        0.13         0.13         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        55.04        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         5.95        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 
        8.12        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-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N1 
        6.74         1.81         5.56        16.67       122.30       115.69 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       57.44         8.94         0.92         5.46        23.77         7.73 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A91Q 
        2.70        17.85         1.87        23.57        14.33        20.81 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-ZQ-A9CR 
       44.25         8.61         5.72        40.08         0.79 

$`DEL PEAK 16(6P25.3) WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       11.70         6.61         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        13.12 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.68        39.12         0.82         0.62        32.78        13.84 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 
       13.22        16.14         8.98        21.11        30.90        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-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 
        0.69         0.16        18.54        12.43         0.69        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49         0.82         1.32        12.26         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       20.55         0.72         0.26        12.95         0.26        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        1.55         1.48         7.40         0.36         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
        2.96         0.95        13.74         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 
        0.36        19.17        14.79         0.69         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         0.72         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        2.14        13.45         0.20         7.53         0.49        15.81 
TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       16.44        15.68        10.68        12.56         1.15         0.66 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
        3.02        13.41        13.51         0.79        14.17         0.53 
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-5801 TCGA-CD-5803 
       11.57         5.13         2.83         3.25        13.18         0.07 
TCGA-CD-8524 TCGA-CD-8526 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-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        0.13         0.10         6.35         0.13         0.07         0.10 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10         0.10        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02         7.99        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4469 
       47.05        19.07        12.03        21.99         9.01         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 
       12.00        22.98        30.97         6.97         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 
        6.02         0.99       105.07        15.02        28.96         4.01 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6522 TCGA-D7-6524 
       21.07         7.99        12.36        11.93        18.61        17.85 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 
       17.19         4.14        12.79        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         0.23         6.97        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-A6EZ TCGA-D7-A6F0 TCGA-D7-A748 
       14.76        13.71        11.24         9.76         2.96         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 
        7.13         0.62         7.79         6.58        14.47        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
        0.39        19.53         3.02        22.29        59.54         5.03 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
        0.56         1.55         0.23         1.51        14.27        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 
       14.17        11.41        10.62         0.76        24.30        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-A4H0 TCGA-HU-A4H3 
        0.10         6.51        10.19         0.26         2.10        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       17.69        12.30         8.88         8.81        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS 
       18.81         3.39        18.38        13.08         6.44         6.87 
TCGA-IN-A7NT TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56         2.53        60.56        28.90         3.72        19.73 
TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 
        4.31        11.05         8.61         4.67        37.91        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DT 
      116.38        71.38        35.61        16.87         5.79        37.74 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P8 
       13.25        13.02        31.10        21.73        22.36        19.07 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       33.63        46.26        16.31         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       19.30        64.57        59.18        28.70        11.70         8.68 
TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A924 
       49.25         1.71         7.36         8.58         9.73        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 
        4.54         6.58        29.98        21.11         4.21 

  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                         0.07                          0.07 
  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 
                        11.31                         11.84 
[1] "0.1 - 122.3 (11.3)" "0.1 - 116.4 (11.8)"
[1] "hr=" "1.1"
D52V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 16(6P25.3) MUTATED         0        4        9        6        10
  DEL PEAK 16(6P25.3) WILD-TYPE       2        9       30       25        26
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 16(6P25.3) MUTATED          12         0         24         13
  DEL PEAK 16(6P25.3) WILD-TYPE        37         3         53         42
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 16(6P25.3) MUTATED            9        9
  DEL PEAK 16(6P25.3) WILD-TYPE         28       28
D52V3, multiclass
            clus
vv           DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             4                             9
  STAGE IB                             9                            30
  STAGE II                             6                            25
  STAGE IIA                           10                            26
  STAGE IIB                           12                            37
  STAGE III                            0                             3
  STAGE IIIA                          24                            53
  STAGE IIIB                          13                            42
  STAGE IIIC                           9                            28
  STAGE IV                             9                            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 16(6P25.3) MUTATED     4  24  48  23
  DEL PEAK 16(6P25.3) WILD-TYPE  17  63 125  81
D52V4, multiclass
    clus
vv   DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  T1                           4                            17
  T2                          24                            63
  T3                          48                           125
  T4                          23                            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 16(6P25.3) MUTATED   30 26 21 19
  DEL PEAK 16(6P25.3) WILD-TYPE 92 81 54 60
D52V5, multiclass
    clus
vv   DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  N0                          30                            92
  N1                          26                            81
  N2                          21                            54
  N3                          19                            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"
                               vv
clus                             M0  M1  MX
  DEL PEAK 16(6P25.3) MUTATED    90   3   8
  DEL PEAK 16(6P25.3) WILD-TYPE 263  21  10
D52V6, multiclass
    clus
vv   DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  M0                          90                           263
  M1                           3                            21
  MX                           8                            10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                               cls
clus                              0   1
  DEL PEAK 16(6P25.3) MUTATED    40  61
  DEL PEAK 16(6P25.3) WILD-TYPE 111 183
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6P25.3) MUTATED     40   61
  DEL PEAK 16(6P25.3) WILD-TYPE  111  183
        clus
vv       DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  FEMALE                          40                           111
  MALE                            61                           183
[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                                    52
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 16(6P25.3) MUTATED                                                       36
  DEL PEAK 16(6P25.3) WILD-TYPE                                                    121
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 16(6P25.3) MUTATED                                                                  15
  DEL PEAK 16(6P25.3) WILD-TYPE                                                                54
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 16(6P25.3) MUTATED                                                 29
  DEL PEAK 16(6P25.3) WILD-TYPE                                               35
                               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                                        7
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)                          15
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           29
  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                                                        52
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      121
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            54
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     17
  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"
D52V9, binary
                               cls
clus                              0   1
  DEL PEAK 16(6P25.3) MUTATED     1 100
  DEL PEAK 16(6P25.3) WILD-TYPE   5 289
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6P25.3) MUTATED      1  100
  DEL PEAK 16(6P25.3) WILD-TYPE    5  289
     clus
vv    DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  NO                            1                             5
  YES                         100                           289
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 16(6P25.3) MUTATED    82   7   2   6
  DEL PEAK 16(6P25.3) WILD-TYPE 236   9  16  19
D52V10, multiclass
    clus
vv   DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  R0                          82                           236
  R1                           7                             9
  R2                           2                            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"
D52V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 16(6P25.3) MUTATED      24                         1
  DEL PEAK 16(6P25.3) WILD-TYPE    64                         5
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 16(6P25.3) MUTATED                                           0    63
  DEL PEAK 16(6P25.3) WILD-TYPE                                         1   180
D52V12, multiclass
                                           clus
vv                                          DEL PEAK 16(6P25.3) MUTATED
  ASIAN                                                              24
  BLACK OR AFRICAN AMERICAN                                           1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              63
                                           clus
vv                                          DEL PEAK 16(6P25.3) WILD-TYPE
  ASIAN                                                                64
  BLACK OR AFRICAN AMERICAN                                             5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(53) Variable = DEL PEAK 17(6Q14.1) MUTATION ANALYSIS
D53V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 17(6Q14.1) MUTATED    49  21
  DEL PEAK 17(6Q14.1) WILD-TYPE 193 101
  DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE 
                           70                           294 
  DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE 
                           21                           101 
$`DEL PEAK 17(6Q14.1) MUTATED`
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-7716 TCGA-BR-7722 
       18.35         6.18        10.13         0.62        28.01         0.16 
TCGA-BR-8080 TCGA-BR-8486 TCGA-BR-A4CQ TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.49        20.22        22.26         0.53        13.51        20.65 
TCGA-BR-A4PF TCGA-CD-5803 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 
        1.15         0.07         0.16         0.10         0.13         6.35 
TCGA-CD-A48A TCGA-CG-4301 TCGA-CG-4437 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 
        0.13         3.02         8.05        29.98        47.05        12.03 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 TCGA-D7-5578 TCGA-D7-6520 
        1.02         1.02        12.03        15.02        12.66        18.84 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-8570 TCGA-D7-8576 TCGA-D7-A4YY 
       18.54         5.95         4.14        24.72         6.97        13.78 
TCGA-D7-A6EX TCGA-D7-A74A TCGA-EQ-A4SO TCGA-F1-A72C TCGA-FP-8099 TCGA-FP-8211 
       11.31         7.40        16.24         8.12        17.06        13.58 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4H5 
        0.56        26.47        22.75        11.77         8.98        12.30 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
       27.42        21.21         5.19        13.08         1.41         6.44 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N5 
        6.87         5.56         1.81        16.67       122.30        57.44 
TCGA-VQ-A8P5 TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91Q TCGA-VQ-A925 
        7.73        23.57        14.33        28.70        20.81         4.54 
TCGA-VQ-AA68 TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       40.08        21.11         4.21         0.79 

$`DEL PEAK 17(6Q14.1) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
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        13.12 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
       13.68         7.00        39.12         0.82        32.78        13.84 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       13.22        16.14         1.25         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-7717 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       23.93        15.42         0.69        18.54        12.43         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        0.69        12.76        18.71        17.49         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69        12.26        20.55         0.72         0.26        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        0.26        16.31         1.55         1.48         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       19.50         0.36         0.26        22.19         2.96         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       13.74         4.31        14.04         3.32         0.36        19.17 
TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       14.79         0.69         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 
        0.72         9.21         1.12        12.79        15.81         2.14 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         0.20         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         0.59        15.68         0.62        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        1.15         0.66         3.02         0.92        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         0.79         0.72        14.17        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       19.36         0.46        20.42        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 
        0.07         0.07         0.07         0.10         0.13         0.10 
TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG 
        0.13         0.10         0.13         0.13         0.13         0.07 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 
        0.10         0.10         0.10        20.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 
        1.02         7.99        54.08         4.01        14.01        19.07 
TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
       21.99         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        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6522 
        7.99        12.36        11.93        19.13        20.55        18.61 
TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.85        17.19        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        12.33        16.80        19.50        17.19         0.23 
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-A6F0 
       14.76        13.71        11.24        11.44         9.76         2.96 
TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 
       15.65         4.34         7.13         0.62         7.79         6.58 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         0.39        19.53         3.02 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB 
       22.29        59.54         5.03         1.55         0.23        18.08 
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-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-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        17.69         9.67         8.88         8.81 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RR 
        3.45        18.81         3.39        18.38         5.36         6.74 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        60.56        28.90         3.72        19.73 
TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 
        4.31        11.05         8.61         4.67        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      115.69       116.38        71.38         8.94        35.61        16.87 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        37.74         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       31.10        21.73        22.36        23.77        19.07        33.63 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
       46.26        16.31         2.70        17.85         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91D 
       23.41        15.65        19.30        64.57        59.18        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
        8.68        49.25         1.71         7.36         8.58         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6B 
       44.25         8.61        55.43         6.58         5.72        29.98 

  DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE 
                         0.07                          0.07 
  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 
                       11.540                        11.635 
[1] "0.1 - 122.3 (11.5)" "0.1 - 116.4 (11.6)"
[1] "hr=" "1.1"
D53V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 17(6Q14.1) MUTATED         0        5        7        7         6
  DEL PEAK 17(6Q14.1) WILD-TYPE       2        8       32       24        30
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 17(6Q14.1) MUTATED           8         0         17         11
  DEL PEAK 17(6Q14.1) WILD-TYPE        41         3         60         44
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 17(6Q14.1) MUTATED            7        4
  DEL PEAK 17(6Q14.1) WILD-TYPE         30       33
D53V3, multiclass
            clus
vv           DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             5                             8
  STAGE IB                             7                            32
  STAGE II                             7                            24
  STAGE IIA                            6                            30
  STAGE IIB                            8                            41
  STAGE III                            0                             3
  STAGE IIIA                          17                            60
  STAGE IIIB                          11                            44
  STAGE IIIC                           7                            30
  STAGE IV                             4                            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 17(6Q14.1) MUTATED     7  18  35  14
  DEL PEAK 17(6Q14.1) WILD-TYPE  14  69 138  90
D53V4, multiclass
    clus
vv   DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE
  T1                           7                            14
  T2                          18                            69
  T3                          35                           138
  T4                          14                            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 17(6Q14.1) MUTATED   23 22 15 14
  DEL PEAK 17(6Q14.1) WILD-TYPE 99 85 60 65
D53V5, multiclass
    clus
vv   DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE
  N0                          23                            99
  N1                          22                            85
  N2                          15                            60
  N3                          14                            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                             M0  M1  MX
  DEL PEAK 17(6Q14.1) MUTATED    64   3   9
  DEL PEAK 17(6Q14.1) WILD-TYPE 289  21   9
D53V6, multiclass
    clus
vv   DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE
  M0                          64                           289
  M1                           3                            21
  MX                           9                             9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                               cls
clus                              0   1
  DEL PEAK 17(6Q14.1) MUTATED    22  54
  DEL PEAK 17(6Q14.1) WILD-TYPE 129 190
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(6Q14.1) MUTATED     22   54
  DEL PEAK 17(6Q14.1) WILD-TYPE  129  190
        clus
vv       DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE
  FEMALE                          22                           129
  MALE                            54                           190
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 17(6Q14.1) MUTATED                                       9
  DEL PEAK 17(6Q14.1) WILD-TYPE                                    56
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 17(6Q14.1) MUTATED                                                       35
  DEL PEAK 17(6Q14.1) WILD-TYPE                                                    122
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 17(6Q14.1) MUTATED                                                                  10
  DEL PEAK 17(6Q14.1) WILD-TYPE                                                                59
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 17(6Q14.1) MUTATED                                                 15
  DEL PEAK 17(6Q14.1) WILD-TYPE                                               49
                               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                                        8
D53V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 17(6Q14.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     35
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          10
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           15
  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                                                        56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      122
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            59
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             49
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     17
  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"
D53V9, binary
                               cls
clus                              0   1
  DEL PEAK 17(6Q14.1) MUTATED     1  75
  DEL PEAK 17(6Q14.1) WILD-TYPE   5 314
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(6Q14.1) MUTATED      1   75
  DEL PEAK 17(6Q14.1) WILD-TYPE    5  314
     clus
vv    DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE
  NO                            1                             5
  YES                          75                           314
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 17(6Q14.1) MUTATED    64   1   3   5
  DEL PEAK 17(6Q14.1) WILD-TYPE 254  15  15  20
D53V10, multiclass
    clus
vv   DEL PEAK 17(6Q14.1) MUTATED DEL PEAK 17(6Q14.1) WILD-TYPE
  R0                          64                           254
  R1                           1                            15
  R2                           3                            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"
D53V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 17(6Q14.1) MUTATED      15                         1
  DEL PEAK 17(6Q14.1) WILD-TYPE    73                         5
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 17(6Q14.1) MUTATED                                           0    48
  DEL PEAK 17(6Q14.1) WILD-TYPE                                         1   195
D53V12, multiclass
                                           clus
vv                                          DEL PEAK 17(6Q14.1) MUTATED
  ASIAN                                                              15
  BLACK OR AFRICAN AMERICAN                                           1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              48
                                           clus
vv                                          DEL PEAK 17(6Q14.1) WILD-TYPE
  ASIAN                                                                73
  BLACK OR AFRICAN AMERICAN                                             5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               195
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(54) Variable = DEL PEAK 18(6Q24.3) MUTATION ANALYSIS
D54V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 18(6Q24.3) MUTATED    38  23
  DEL PEAK 18(6Q24.3) WILD-TYPE 204  99
  DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE 
                           61                           303 
  DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE 
                           23                            99 
$`DEL PEAK 18(6Q24.3) MUTATED`
TCGA-BR-4267 TCGA-BR-6565 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-8077 TCGA-BR-8080 
        6.18         0.62        28.01         0.16         0.69         0.49 
TCGA-BR-8360 TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5803 
        6.18         0.72        13.51         1.15        13.64         0.07 
TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CG-4440 
        0.16         0.10         0.13         0.13         6.35         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5725 
       14.01        29.98        12.03        12.00        22.98        15.02 
TCGA-D7-5578 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8573 
       12.66        18.54         5.95        12.79        24.72        19.50 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A TCGA-F1-A72C 
        0.23         6.97        11.31        15.65         7.40         8.12 
TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 TCGA-HJ-7597 TCGA-HU-A4GU TCGA-HU-A4H4 
       17.06        13.58         0.56        26.47         6.25        17.69 
TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NT TCGA-KB-A93H TCGA-MX-A663 TCGA-RD-A7BT 
        5.19         6.44         5.56        28.90         4.31         8.61 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       16.67       122.30        57.44         8.94        31.10        21.73 
TCGA-VQ-A8PC TCGA-VQ-A8PY TCGA-VQ-A91Q TCGA-VQ-A925 TCGA-VQ-AA68 TCGA-VQ-AA6J 
       46.26        14.33        20.81         4.54        40.08        21.11 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK 18(6Q24.3) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         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-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.12        10.13        13.68         7.00        39.12         0.82 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        13.84        13.22        16.14         1.25         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-7723 
       24.76        35.24        23.93        15.42         0.69        18.54 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         0.95         0.69        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.82         1.32        12.26        20.55         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         0.26        16.31         1.55         1.48         7.40 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       19.50         0.36         0.26        22.19         2.96         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       13.74         4.31        14.04         3.32         0.36        19.17 
TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       14.79         0.69         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 
        0.72         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 
        2.14        13.45         0.20         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         0.59        15.68         0.62        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56         1.15         0.66         3.02        22.26         0.92 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51        12.89         0.79        14.17         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-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-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         0.10         0.13         0.13         0.13 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
        0.13         0.07         0.10         0.10         0.10        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-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 
       54.08        47.05        19.07        21.99         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         1.02         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        55.04        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-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 
       17.19         4.14        15.22        15.98        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-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A748 TCGA-D7-A74B 
       11.24        11.44         9.76         2.96         4.34         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        0.62         7.79        16.24         6.58        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
       21.27         0.39        19.53         3.02        22.29        59.54 
TCGA-FP-8210 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 
        5.03         1.55         0.23        18.08         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-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        19.36        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-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NU 
        5.36        13.08         1.41         6.74         6.87         1.81 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS 
        2.53         5.56        60.56         3.72        19.73        11.05 
TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
        4.67        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        16.87         5.79         0.92        37.74         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       13.25        13.02        22.36        23.77         7.73        19.07 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
       33.63        16.31         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        19.30        23.57        64.57        59.18 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91W 
       28.70        11.70         8.68        49.25         1.71         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 
        8.58         9.73        44.25         8.61        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-AA6B TCGA-ZA-A8F6 
        5.72        29.98         4.21 

  DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE 
                         0.07                          0.07 
  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 
                        11.31                         11.70 
[1] "0.1 - 122.3 (11.3)" "0.1 - 116.4 (11.7)"
[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       2       12       34       26        28
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 18(6Q24.3) MUTATED           8         0         19          9
  DEL PEAK 18(6Q24.3) WILD-TYPE        41         3         58         46
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 18(6Q24.3) MUTATED            5        4
  DEL PEAK 18(6Q24.3) WILD-TYPE         32       33
D54V3, multiclass
            clus
vv           DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             1                            12
  STAGE IB                             5                            34
  STAGE II                             5                            26
  STAGE IIA                            8                            28
  STAGE IIB                            8                            41
  STAGE III                            0                             3
  STAGE IIIA                          19                            58
  STAGE IIIB                           9                            46
  STAGE IIIC                           5                            32
  STAGE IV                             4                            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 18(6Q24.3) MUTATED     2  14  39  10
  DEL PEAK 18(6Q24.3) WILD-TYPE  19  73 134  94
D54V4, multiclass
    clus
vv   DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE
  T1                           2                            19
  T2                          14                            73
  T3                          39                           134
  T4                          10                            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
  DEL PEAK 18(6Q24.3) MUTATED    19  18  16  12
  DEL PEAK 18(6Q24.3) WILD-TYPE 103  89  59  67
D54V5, multiclass
    clus
vv   DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE
  N0                          19                           103
  N1                          18                            89
  N2                          16                            59
  N3                          12                            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"
                               vv
clus                             M0  M1  MX
  DEL PEAK 18(6Q24.3) MUTATED    61   1   5
  DEL PEAK 18(6Q24.3) WILD-TYPE 292  23  13
D54V6, multiclass
    clus
vv   DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE
  M0                          61                           292
  M1                           1                            23
  MX                           5                            13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                               cls
clus                              0   1
  DEL PEAK 18(6Q24.3) MUTATED    18  49
  DEL PEAK 18(6Q24.3) WILD-TYPE 133 195
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(6Q24.3) MUTATED     18   49
  DEL PEAK 18(6Q24.3) WILD-TYPE  133  195
        clus
vv       DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE
  FEMALE                          18                           133
  MALE                            49                           195
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 18(6Q24.3) MUTATED                                       6
  DEL PEAK 18(6Q24.3) WILD-TYPE                                    59
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 18(6Q24.3) MUTATED                                                       25
  DEL PEAK 18(6Q24.3) WILD-TYPE                                                    132
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 18(6Q24.3) MUTATED                                                                  12
  DEL PEAK 18(6Q24.3) WILD-TYPE                                                                57
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 18(6Q24.3) MUTATED                                                 17
  DEL PEAK 18(6Q24.3) WILD-TYPE                                               47
                               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                                        7
D54V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 18(6Q24.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     25
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          12
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           17
  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                                                        59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            57
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             47
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     8
  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"
D54V9, binary
                               cls
clus                              0   1
  DEL PEAK 18(6Q24.3) MUTATED     2  65
  DEL PEAK 18(6Q24.3) WILD-TYPE   4 324
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(6Q24.3) MUTATED      2   65
  DEL PEAK 18(6Q24.3) WILD-TYPE    4  324
     clus
vv    DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE
  NO                            2                             4
  YES                          65                           324
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 18(6Q24.3) MUTATED    56   2   3   4
  DEL PEAK 18(6Q24.3) WILD-TYPE 262  14  15  21
D54V10, multiclass
    clus
vv   DEL PEAK 18(6Q24.3) MUTATED DEL PEAK 18(6Q24.3) WILD-TYPE
  R0                          56                           262
  R1                           2                            14
  R2                           3                            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"
D54V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 18(6Q24.3) MUTATED      13                         1
  DEL PEAK 18(6Q24.3) WILD-TYPE    75                         5
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 18(6Q24.3) MUTATED                                           1    42
  DEL PEAK 18(6Q24.3) WILD-TYPE                                         0   201
D54V12, multiclass
                                           clus
vv                                          DEL PEAK 18(6Q24.3) MUTATED
  ASIAN                                                              13
  BLACK OR AFRICAN AMERICAN                                           1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              42
                                           clus
vv                                          DEL PEAK 18(6Q24.3) WILD-TYPE
  ASIAN                                                                75
  BLACK OR AFRICAN AMERICAN                                             5
  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"

Clustering(55) Variable = DEL PEAK 19(6Q26) MUTATION ANALYSIS
D55V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 19(6Q26) MUTATED    51  32
  DEL PEAK 19(6Q26) WILD-TYPE 191  90
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                         83                         281 
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                         32                          90 
$`DEL PEAK 19(6Q26) MUTATED`
TCGA-BR-4183 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7716 TCGA-BR-7717 
        6.61         7.00         0.62         1.25        28.01         0.69 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7958 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8680 
        0.16        18.54        12.76         0.69         0.49        15.81 
TCGA-BR-A4IY TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-CD-5800 TCGA-CD-5803 
       12.89        13.51        20.42         1.15        13.15         0.07 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 
        0.13         0.16         0.10         0.13         0.13         6.35 
TCGA-CD-A487 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4443 
        0.13         3.02        15.95         8.05         4.01        29.98 
TCGA-CG-4455 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5724 
       12.03         7.07        12.00         6.97         1.02        12.03 
TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6525 
       15.02        55.04        12.66        20.55        18.54         5.95 
TCGA-D7-6526 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A6EX 
       17.19        24.72        19.50         0.23         6.97        11.31 
TCGA-D7-A6EY TCGA-D7-A6F2 TCGA-D7-A74A TCGA-F1-A72C TCGA-FP-8099 TCGA-FP-8211 
       11.44        15.65         7.40         8.12        17.06        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-A4G3 TCGA-HU-A4GU 
        0.56         1.55         0.23        26.47         5.59         6.25 
TCGA-HU-A4H4 TCGA-HU-A4HD TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU 
       17.69        27.42         5.19         6.44         5.56         1.81 
TCGA-MX-A663 TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-VQ-A8DL 
        4.31        16.67       122.30        57.44         8.94         0.92 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PY TCGA-VQ-A91Q 
       13.02        31.10         7.73        46.26        14.33        20.81 
TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-AA68 TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       44.25         4.54        40.08        21.11         0.79 

$`DEL PEAK 19(6Q26) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
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-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       13.12        10.13        13.68        39.12         0.82        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       13.84        13.22        16.14         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-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 
       23.93        15.42        12.43         0.95         0.69        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       17.49         0.82         1.32        12.26        20.55         0.72 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.26        12.95         0.26        16.31         1.55         1.48 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        19.50         0.36         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
        2.96         0.95        13.74         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 
        0.36        19.17        14.79         0.69         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         0.72         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         2.14        13.45         0.20         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        16.44         0.59        15.68         0.62 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56         1.15         0.66         3.02        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.92        13.41        13.51         0.79         0.72        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-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 
       13.64        11.57         5.13         2.83         3.25        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-8531 TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        0.10         0.10         0.13         0.13         0.13         0.07 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4306 
        0.10         0.10         0.10        20.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 
        7.99        54.08        14.01        47.05        19.07        21.99 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5720 
        9.01        18.97        22.98        30.97         1.02         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-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 
        4.01        21.07         7.99        12.36        11.93        19.13 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.84        18.61        17.85         4.14        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8574 
       12.79        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-A6EZ TCGA-D7-A6F0 
       13.78        14.76        13.71        11.24         9.76         2.96 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 
        4.34         7.13         0.62         7.79        16.24         6.58 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         0.39        19.53         3.02 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 
       22.29        59.54         5.03        18.08         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-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30        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-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-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       19.36        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-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        1.41         6.74         6.87         2.53         5.56        60.56 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
       28.90         3.72        19.73        11.05         8.61         4.67 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 
       37.91        40.64       115.69       116.38        71.38        35.61 
TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E3 
       16.87         5.79        37.74         5.46        13.25        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PJ 
       22.36        23.77        19.07        33.63        16.31         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        19.30 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       23.57        64.57        59.18        28.70        11.70         8.68 
TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 
       49.25         1.71         7.36         8.58         9.73         8.61 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6B TCGA-ZA-A8F6 
       55.43         6.58         5.72        29.98         4.21 

  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                       0.07                        0.07 
  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 
                       8.12                       11.84 
[1] "0.1 - 122.3 (8.1)"  "0.1 - 116.4 (11.8)"
[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       2       12       34       22        29
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 19(6Q26) MUTATED          10         0         20         15
  DEL PEAK 19(6Q26) WILD-TYPE        39         3         57         40
                             vv
clus                          STAGE IIIC STAGE IV
  DEL PEAK 19(6Q26) MUTATED            7       13
  DEL PEAK 19(6Q26) WILD-TYPE         30       24
D55V3, multiclass
            clus
vv           DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  STAGE I                            0                           2
  STAGE IA                           1                          12
  STAGE IB                           5                          34
  STAGE II                           9                          22
  STAGE IIA                          7                          29
  STAGE IIB                         10                          39
  STAGE III                          0                           3
  STAGE IIIA                        20                          57
  STAGE IIIB                        15                          40
  STAGE IIIC                         7                          30
  STAGE IV                          13                          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 19(6Q26) MUTATED     2  19  49  18
  DEL PEAK 19(6Q26) WILD-TYPE  19  68 124  86
D55V4, multiclass
    clus
vv   DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  T1                         2                          19
  T2                        19                          68
  T3                        49                         124
  T4                        18                          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 19(6Q26) MUTATED   23 25 20 20
  DEL PEAK 19(6Q26) WILD-TYPE 99 82 55 59
D55V5, multiclass
    clus
vv   DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  N0                        23                          99
  N1                        25                          82
  N2                        20                          55
  N3                        20                          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"
                             vv
clus                           M0  M1  MX
  DEL PEAK 19(6Q26) MUTATED    76   7   6
  DEL PEAK 19(6Q26) WILD-TYPE 277  17  12
D55V6, multiclass
    clus
vv   DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  M0                        76                         277
  M1                         7                          17
  MX                         6                          12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                             cls
clus                            0   1
  DEL PEAK 19(6Q26) MUTATED    29  60
  DEL PEAK 19(6Q26) WILD-TYPE 122 184
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(6Q26) MUTATED     29   60
  DEL PEAK 19(6Q26) WILD-TYPE  122  184
        clus
vv       DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  FEMALE                        29                         122
  MALE                          60                         184
[1] 2 2
[1] FALSE
                             vv
clus                          STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 19(6Q26) MUTATED                                       9
  DEL PEAK 19(6Q26) WILD-TYPE                                    56
                             vv
clus                          STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 19(6Q26) MUTATED                                                       33
  DEL PEAK 19(6Q26) WILD-TYPE                                                    124
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 19(6Q26) MUTATED                                                                  13
  DEL PEAK 19(6Q26) WILD-TYPE                                                                56
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 19(6Q26) MUTATED                                                 22
  DEL PEAK 19(6Q26) WILD-TYPE                                               42
                             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                                        4
D55V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 19(6Q26) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                   33
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                         22
  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                                                      56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          56
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           42
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   7
  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"
D55V9, binary
                             cls
clus                            0   1
  DEL PEAK 19(6Q26) MUTATED     2  87
  DEL PEAK 19(6Q26) WILD-TYPE   4 302
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(6Q26) MUTATED      2   87
  DEL PEAK 19(6Q26) WILD-TYPE    4  302
     clus
vv    DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  NO                          2                           4
  YES                        87                         302
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 19(6Q26) MUTATED    72   6   5   3
  DEL PEAK 19(6Q26) WILD-TYPE 246  10  13  22
D55V10, multiclass
    clus
vv   DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  R0                        72                         246
  R1                         6                          10
  R2                         5                          13
  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                         2
  DEL PEAK 19(6Q26) WILD-TYPE    70                         4
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 19(6Q26) MUTATED                                           0    52
  DEL PEAK 19(6Q26) WILD-TYPE                                         1   191
D55V12, multiclass
                                           clus
vv                                          DEL PEAK 19(6Q26) MUTATED
  ASIAN                                                            18
  BLACK OR AFRICAN AMERICAN                                         2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         0
  WHITE                                                            52
                                           clus
vv                                          DEL PEAK 19(6Q26) WILD-TYPE
  ASIAN                                                              70
  BLACK OR AFRICAN AMERICAN                                           4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             191
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(56) Variable = DEL PEAK 20(7Q31.1) MUTATION ANALYSIS
D56V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 20(7Q31.1) MUTATED    40  16
  DEL PEAK 20(7Q31.1) WILD-TYPE 202 106
  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                           56                           308 
  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                           16                           106 
$`DEL PEAK 20(7Q31.1) MUTATED`
TCGA-BR-6564 TCGA-BR-6706 TCGA-BR-7723 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8369 
        0.82        13.22        18.54         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         0.66         0.92         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         6.35         0.13         0.13         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         0.23        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        17.69 
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-IP-7968 TCGA-KB-A93H TCGA-RD-A7BT TCGA-RD-A8MW TCGA-RD-A8N6 
       13.08         2.53        28.90         8.61        37.91         8.94 
TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A91Q 
       35.61         5.46        13.02        23.77         7.73        20.81 
TCGA-VQ-A928 TCGA-VQ-AA68 
        5.72        40.08 

$`DEL PEAK 20(7Q31.1) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         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-6458 TCGA-BR-6563 
       15.95        13.12        10.13        13.68         7.00        39.12 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        0.62        32.78        13.84        16.14         1.25         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         0.69 
TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
        0.16        12.43         0.95         0.69        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       17.49         0.82         1.32         0.69        12.26         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       20.55         0.72         0.26        12.95         0.26        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        1.55         1.48         7.40         0.36         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
        2.96         0.95        13.74         4.31         3.32         0.36 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       19.17        14.79         0.69         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         0.72         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         2.14        13.45         0.20         7.53         0.49 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         0.59        15.68         0.62        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV 
       12.56         1.15         3.02        22.26        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         0.79         0.72        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-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-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-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.13         0.13         0.07         0.10         0.10         0.10 
TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4440 
       20.02        27.02        15.95         1.02         7.99         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 
       14.01        29.98        47.05        21.99         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         1.02         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-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        55.04        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-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85         5.95        17.19         4.14 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       15.22        12.79        10.55        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         6.97        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44         5.92        13.78        14.76        13.71        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A 
       11.44         9.76         2.96        15.65         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 
        7.13         0.62         7.79        16.24         6.58        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         8.12         0.39         3.02        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         1.55         0.23        18.08 
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-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-A4GF TCGA-HU-A4GJ 
       12.30        11.84        24.20         3.25        25.81        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-A4H3 TCGA-HU-A4H5 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
        2.10        19.36        12.30         8.81        21.21         3.45 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
        5.36         5.19         1.41         6.44         6.74         6.87 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56         1.81         5.56        60.56         3.72        19.73 
TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 
        4.31        11.05         4.67        16.67       122.30        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EB 
      115.69       116.38        71.38        57.44        16.87         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 
        0.92        37.74        13.25        31.10        21.73        22.36 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       19.07        33.63        46.26        16.31         2.70        17.85 
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        19.30        23.57 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        59.18        28.70        11.70         8.68 
TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       49.25         1.71         7.36         8.58         9.73        44.25 
TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-AA6B TCGA-VQ-AA6J 
        8.61        55.43         4.54         6.58        29.98        21.11 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        4.21         0.79 

  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                         0.07                          0.07 
  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 
                       11.885                        11.505 
[1] "0.1 - 72.2 (11.9)"  "0.1 - 122.3 (11.5)"
[1] "hr=" "1.2"
D56V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 20(7Q31.1) MUTATED         0        2        3        7         6
  DEL PEAK 20(7Q31.1) WILD-TYPE       2       11       36       24        30
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 20(7Q31.1) MUTATED          12         0         13          6
  DEL PEAK 20(7Q31.1) WILD-TYPE        37         3         64         49
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 20(7Q31.1) MUTATED            4        7
  DEL PEAK 20(7Q31.1) WILD-TYPE         33       30
D56V3, multiclass
            clus
vv           DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             2                            11
  STAGE IB                             3                            36
  STAGE II                             7                            24
  STAGE IIA                            6                            30
  STAGE IIB                           12                            37
  STAGE III                            0                             3
  STAGE IIIA                          13                            64
  STAGE IIIB                           6                            49
  STAGE IIIC                           4                            33
  STAGE IV                             7                            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 20(7Q31.1) MUTATED     4  13  33  10
  DEL PEAK 20(7Q31.1) WILD-TYPE  17  74 140  94
D56V4, multiclass
    clus
vv   DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  T1                           4                            17
  T2                          13                            74
  T3                          33                           140
  T4                          10                            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
  DEL PEAK 20(7Q31.1) MUTATED    12  22  16  10
  DEL PEAK 20(7Q31.1) WILD-TYPE 110  85  59  69
D56V5, multiclass
    clus
vv   DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  N0                          12                           110
  N1                          22                            85
  N2                          16                            59
  N3                          10                            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                             M0  M1  MX
  DEL PEAK 20(7Q31.1) MUTATED    57   2   2
  DEL PEAK 20(7Q31.1) WILD-TYPE 296  22  16
D56V6, multiclass
    clus
vv   DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  M0                          57                           296
  M1                           2                            22
  MX                           2                            16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                               cls
clus                              0   1
  DEL PEAK 20(7Q31.1) MUTATED    18  43
  DEL PEAK 20(7Q31.1) WILD-TYPE 133 201
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(7Q31.1) MUTATED     18   43
  DEL PEAK 20(7Q31.1) WILD-TYPE  133  201
        clus
vv       DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  FEMALE                          18                           133
  MALE                            43                           201
[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                                    59
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 20(7Q31.1) MUTATED                                                       22
  DEL PEAK 20(7Q31.1) WILD-TYPE                                                    135
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 20(7Q31.1) MUTATED                                                                  10
  DEL PEAK 20(7Q31.1) WILD-TYPE                                                                59
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 20(7Q31.1) MUTATED                                                 16
  DEL PEAK 20(7Q31.1) WILD-TYPE                                               48
                               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                                          1
  DEL PEAK 20(7Q31.1) WILD-TYPE                                        8
D56V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 20(7Q31.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     22
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          10
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    1
                                                                   clus
vv                                                                  DEL PEAK 20(7Q31.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      135
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            59
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             48
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     18
  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"
D56V9, binary
                               cls
clus                              0   1
  DEL PEAK 20(7Q31.1) MUTATED     1  60
  DEL PEAK 20(7Q31.1) WILD-TYPE   5 329
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(7Q31.1) MUTATED      1   60
  DEL PEAK 20(7Q31.1) WILD-TYPE    5  329
     clus
vv    DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  NO                            1                             5
  YES                          60                           329
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 20(7Q31.1) MUTATED    52   1   3   2
  DEL PEAK 20(7Q31.1) WILD-TYPE 266  15  15  23
D56V10, multiclass
    clus
vv   DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  R0                          52                           266
  R1                           1                            15
  R2                           3                            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"
D56V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 20(7Q31.1) MUTATED      17                         2
  DEL PEAK 20(7Q31.1) WILD-TYPE    71                         4
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 20(7Q31.1) MUTATED                                           1    32
  DEL PEAK 20(7Q31.1) WILD-TYPE                                         0   211
D56V12, multiclass
                                           clus
vv                                          DEL PEAK 20(7Q31.1) MUTATED
  ASIAN                                                              17
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              32
                                           clus
vv                                          DEL PEAK 20(7Q31.1) WILD-TYPE
  ASIAN                                                                71
  BLACK OR AFRICAN AMERICAN                                             4
  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"

Clustering(57) Variable = DEL PEAK 21(7Q36.3) MUTATION ANALYSIS
D57V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 21(7Q36.3) MUTATED    53  24
  DEL PEAK 21(7Q36.3) WILD-TYPE 189  98
  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                           77                           287 
  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                           24                            98 
$`DEL PEAK 21(7Q36.3) MUTATED`
TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-7704 TCGA-BR-7723 TCGA-BR-7901 
       10.13         7.00         0.82        35.24        18.54         0.95 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8296 TCGA-BR-8369 TCGA-BR-8485 TCGA-BR-8678 
        1.32         0.69         1.48        14.04         9.21        11.54 
TCGA-BR-A4CS TCGA-BR-A4PF TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8528 
        0.92         1.15         0.30         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C 
        0.13         0.13         6.35         0.13         0.13         0.13 
TCGA-CG-4301 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4472 
        3.02         8.05        54.08        19.07        12.03        12.00 
TCGA-CG-4475 TCGA-CG-5724 TCGA-D7-6519 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 
       22.98        12.03        20.55         5.95        17.19        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8575 TCGA-D7-A6EV TCGA-D7-A6EX 
       12.79        10.55        11.31         0.23        11.24        11.31 
TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-A4SO TCGA-FP-7829 TCGA-FP-8631 TCGA-HU-8243 
        2.96         7.40        16.24        19.53         0.56         5.92 
TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 
       22.75        11.77         6.25        12.95        17.69         9.67 
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-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT TCGA-KB-A93H TCGA-RD-A8MW 
       13.08         6.44         6.74         5.56        28.90        37.91 
TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PJ 
       35.61         5.46        13.02        23.77         7.73         2.70 
TCGA-VQ-A8PK TCGA-VQ-A91Q TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-ZQ-A9CR 
       17.85        20.81         5.72        40.08         0.79 

$`DEL PEAK 21(7Q36.3) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         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-6565 TCGA-BR-6566 
       15.95        13.12        13.68        39.12         0.62        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       13.84        13.22        16.14         1.25         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-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 
       23.93        15.42        28.01         0.69         0.16        12.43 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 
        0.69        12.76        18.71        17.49         0.82        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.49        20.55         0.72         0.26        12.95         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       16.31         1.55         7.40         6.18        19.50         0.36 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19         2.96         0.95        13.74         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 
        3.32         0.36        19.17        14.79         0.69         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 
       15.85         3.72         5.39         0.72        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         2.14        13.45         0.20         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         0.59        15.68         0.62 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56         1.15         0.66         3.02        22.26 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         0.79         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-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8526 TCGA-CD-8527 
        3.25        13.15        13.18         0.07         0.07         0.07 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A48A 
        0.16         0.10         0.10         0.13         0.10         0.13 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 
        0.07         0.10         0.10         0.10        20.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       15.95         1.02         7.99         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       47.05        21.99         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         1.02         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 
       55.04        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-D7-6527 
       19.13        18.84        18.54        18.61        17.85         4.14 
TCGA-D7-6528 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       15.22        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 
        6.97        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-A6F2 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 
       15.65         4.34         7.13         0.62         7.79         6.58 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 
       14.47        72.23        21.27         8.12         0.39         3.02 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF 
       22.29        17.06        59.54         5.03        13.58         1.55 
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-A4GF 
        5.59        12.30        11.84        24.20         3.25        25.81 
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-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-A6RL TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NU TCGA-IP-7968 
       21.21         5.19         1.41         6.87         1.81         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS 
        5.56        60.56         3.72        19.73         4.31        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 
        8.61         4.67        16.67       122.30        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EB 
      116.38        71.38        57.44         8.94        16.87         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 
        0.92        37.74        13.25        31.10        21.73        22.36 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PO 
       19.07        33.63        46.26        16.31         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        19.30        23.57        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91U 
       59.18        28.70        11.70         8.68        49.25         1.71 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 
        7.36         8.58         9.73        44.25         8.61        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 
        4.54         6.58        29.98        21.11         4.21 

  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                        54.08                        122.30 
  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                         9.21                         12.30 
[1] "0.1 - 54.1 (9.2)"   "0.1 - 122.3 (12.3)"
[1] "hr=" "1.1"
D57V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 21(7Q36.3) MUTATED         0        1        4        8         4
  DEL PEAK 21(7Q36.3) WILD-TYPE       2       12       35       23        32
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 21(7Q36.3) MUTATED          17         1         19         10
  DEL PEAK 21(7Q36.3) WILD-TYPE        32         2         58         45
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 21(7Q36.3) MUTATED            8        9
  DEL PEAK 21(7Q36.3) WILD-TYPE         29       28
D57V3, multiclass
            clus
vv           DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             1                            12
  STAGE IB                             4                            35
  STAGE II                             8                            23
  STAGE IIA                            4                            32
  STAGE IIB                           17                            32
  STAGE III                            1                             2
  STAGE IIIA                          19                            58
  STAGE IIIB                          10                            45
  STAGE IIIC                           8                            29
  STAGE IV                             9                            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 21(7Q36.3) MUTATED     5  17  42  17
  DEL PEAK 21(7Q36.3) WILD-TYPE  16  70 131  87
D57V4, multiclass
    clus
vv   DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  T1                           5                            16
  T2                          17                            70
  T3                          42                           131
  T4                          17                            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 21(7Q36.3) MUTATED    15  28  20  18
  DEL PEAK 21(7Q36.3) WILD-TYPE 107  79  55  61
D57V5, multiclass
    clus
vv   DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  N0                          15                           107
  N1                          28                            79
  N2                          20                            55
  N3                          18                            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                             M0  M1  MX
  DEL PEAK 21(7Q36.3) MUTATED    74   6   3
  DEL PEAK 21(7Q36.3) WILD-TYPE 279  18  15
D57V6, multiclass
    clus
vv   DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  M0                          74                           279
  M1                           6                            18
  MX                           3                            15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                               cls
clus                              0   1
  DEL PEAK 21(7Q36.3) MUTATED    31  52
  DEL PEAK 21(7Q36.3) WILD-TYPE 120 192
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q36.3) MUTATED     31   52
  DEL PEAK 21(7Q36.3) WILD-TYPE  120  192
        clus
vv       DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  FEMALE                          31                           120
  MALE                            52                           192
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 21(7Q36.3) MUTATED                                      11
  DEL PEAK 21(7Q36.3) WILD-TYPE                                    54
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 21(7Q36.3) MUTATED                                                       32
  DEL PEAK 21(7Q36.3) WILD-TYPE                                                    125
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 21(7Q36.3) MUTATED                                                                  11
  DEL PEAK 21(7Q36.3) WILD-TYPE                                                                58
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 21(7Q36.3) MUTATED                                                 20
  DEL PEAK 21(7Q36.3) WILD-TYPE                                               44
                               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                                          1
  DEL PEAK 21(7Q36.3) WILD-TYPE                                        8
D57V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 21(7Q36.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      11
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     32
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    1
                                                                   clus
vv                                                                  DEL PEAK 21(7Q36.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        54
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            58
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             44
  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"
D57V9, binary
                               cls
clus                              0   1
  DEL PEAK 21(7Q36.3) MUTATED     3  80
  DEL PEAK 21(7Q36.3) WILD-TYPE   3 309
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q36.3) MUTATED      3   80
  DEL PEAK 21(7Q36.3) WILD-TYPE    3  309
     clus
vv    DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  NO                            3                             3
  YES                          80                           309
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 21(7Q36.3) MUTATED    69   1   4   3
  DEL PEAK 21(7Q36.3) WILD-TYPE 249  15  14  22
D57V10, multiclass
    clus
vv   DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  R0                          69                           249
  R1                           1                            15
  R2                           4                            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"
D57V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 21(7Q36.3) MUTATED      21                         1
  DEL PEAK 21(7Q36.3) WILD-TYPE    67                         5
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 21(7Q36.3) MUTATED                                           0    50
  DEL PEAK 21(7Q36.3) WILD-TYPE                                         1   193
D57V12, multiclass
                                           clus
vv                                          DEL PEAK 21(7Q36.3) MUTATED
  ASIAN                                                              21
  BLACK OR AFRICAN AMERICAN                                           1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              50
                                           clus
vv                                          DEL PEAK 21(7Q36.3) WILD-TYPE
  ASIAN                                                                67
  BLACK OR AFRICAN AMERICAN                                             5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  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"

Clustering(58) Variable = DEL PEAK 22(8P23.3) MUTATION ANALYSIS
D58V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 22(8P23.3) MUTATED    63  36
  DEL PEAK 22(8P23.3) WILD-TYPE 179  86
  DEL PEAK 22(8P23.3) MUTATED DEL PEAK 22(8P23.3) WILD-TYPE 
                           99                           265 
  DEL PEAK 22(8P23.3) MUTATED DEL PEAK 22(8P23.3) WILD-TYPE 
                           36                            86 
$`DEL PEAK 22(8P23.3) MUTATED`
TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6709 
       18.35        10.13        13.68         0.62        13.84         1.25 
TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7958 TCGA-BR-8077 
        9.21        15.42        28.01        18.54        12.76         0.69 
TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8361 TCGA-BR-8362 
        0.49        12.95         0.26         1.48        19.50         0.36 
TCGA-BR-8485 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 
        9.21        15.81        16.44         0.59         0.62        10.68 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J8 
        1.15         0.66         0.92        12.89         0.72        13.51 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8526 
       20.65         1.15        13.64        13.15         0.30         0.07 
TCGA-CD-8527 TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        0.07         0.13         6.35         0.13         0.13         0.10 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 
        3.02        27.02         7.99        54.08         4.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5725 
       47.05        19.07        22.98         1.02        12.03        15.02 
TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6526 
        4.01        55.04        12.66        19.13        18.54        17.19 
TCGA-D7-6528 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-A4YU TCGA-D7-A6F2 TCGA-D7-A74A 
       15.22        11.31        24.72        16.44        15.65         7.40 
TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6875 TCGA-FP-8099 TCGA-HU-8243 TCGA-HU-8245 
        0.62         6.58        72.23        17.06         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4GU TCGA-HU-A4HD TCGA-IN-8663 
       14.17         0.76        22.75         6.25        27.42         3.39 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IP-7968 TCGA-KB-A6F5 TCGA-RD-A7BT 
        1.41         6.44         6.74         2.53         5.56         8.61 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8E2 TCGA-VQ-A8P5 
      122.30        37.91         8.94         5.79        31.10         7.73 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A91A TCGA-VQ-A91U TCGA-VQ-A91Z TCGA-VQ-A925 
       17.85         1.87        28.70         1.71        44.25         4.54 
TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J 
       40.08        29.98        21.11 

$`DEL PEAK 22(8P23.3) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         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-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6706 
       13.12         7.00        39.12         0.82        32.78        13.22 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       16.14         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 
       12.82        24.76        35.24        23.93         0.69         0.16 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       12.43         0.95         0.69        18.71        17.49         0.82 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 
        1.32        12.26        20.55         0.72         0.26        16.31 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        1.55         7.40         6.18         0.26        22.19         2.96 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        13.74         4.31        14.04         3.32         0.36 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       19.17        14.79         0.69         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        5.39         0.72        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-8678 
        2.14        13.45         0.20         7.53         0.49        11.54 
TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV 
       15.68        12.56         3.02        22.26        13.41        13.51 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.79        14.17         0.53        12.82         0.66        19.36 
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-5801 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 
       13.18         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 
        0.16         0.10         0.10         0.13         0.10         0.13 
TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4305 
        0.13         0.07         0.10         0.10        20.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 
        1.02         8.05        14.01        12.03        21.99         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 
       18.97         7.07        12.00        30.97         6.97         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-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-D7-6519 
       65.10        21.07         7.99        12.36        11.93        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 
       18.84        18.61        17.85         5.95         4.14        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       12.79        10.55        12.33        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
        0.23         6.97        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-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         7.79 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        21.27         8.12         0.39        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
        3.02        22.29        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-8244 
        1.55         0.23        18.08        26.47         1.51        14.27 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       11.41        12.10        10.62        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-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        17.69        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI 
        8.88         8.81        21.21         3.45        18.81        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU 
        5.36         5.19        13.08         6.87         5.56         1.81 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS 
       60.56        28.90         3.72        19.73         4.31        11.05 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
        4.67        16.67        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       57.44        35.61        16.87         0.92        37.74         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       13.25        13.02        21.73        22.36        23.77        19.07 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP 
       33.63        46.26        16.31         2.70         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        19.30        23.57        64.57        14.33        59.18 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91W TCGA-VQ-A91X 
       11.70         8.68        49.25        20.81         7.36         8.58 
TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-ZA-A8F6 
        9.73         8.61        55.43         6.58         5.72         4.21 
TCGA-ZQ-A9CR 
        0.79 

  DEL PEAK 22(8P23.3) MUTATED DEL PEAK 22(8P23.3) WILD-TYPE 
                         0.07                          0.07 
  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 
                        10.68                         11.70 
[1] "0.1 - 122.3 (10.7)" "0.1 - 116.4 (11.7)"
[1] "hr=" "1.2"
D58V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 22(8P23.3) MUTATED         1        4        5        8         9
  DEL PEAK 22(8P23.3) WILD-TYPE       1        9       34       23        27
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 22(8P23.3) MUTATED          12         0         20         20
  DEL PEAK 22(8P23.3) WILD-TYPE        37         3         57         35
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 22(8P23.3) MUTATED           12       12
  DEL PEAK 22(8P23.3) WILD-TYPE         25       25
D58V3, multiclass
            clus
vv           DEL PEAK 22(8P23.3) MUTATED DEL PEAK 22(8P23.3) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             4                             9
  STAGE IB                             5                            34
  STAGE II                             8                            23
  STAGE IIA                            9                            27
  STAGE IIB                           12                            37
  STAGE III                            0                             3
  STAGE IIIA                          20                            57
  STAGE IIIB                          20                            35
  STAGE IIIC                          12                            25
  STAGE IV                            12                            25
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 22(8P23.3) MUTATED     5  19  52  28
  DEL PEAK 22(8P23.3) WILD-TYPE  16  68 121  76
D58V4, multiclass
    clus
vv   DEL PEAK 22(8P23.3) MUTATED DEL PEAK 22(8P23.3) WILD-TYPE
  T1                           5                            16
  T2                          19                            68
  T3                          52                           121
  T4                          28                            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 22(8P23.3) MUTATED   28 23 25 28
  DEL PEAK 22(8P23.3) WILD-TYPE 94 84 50 51
D58V5, multiclass
    clus
vv   DEL PEAK 22(8P23.3) MUTATED DEL PEAK 22(8P23.3) WILD-TYPE
  N0                          28                            94
  N1                          23                            84
  N2                          25                            50
  N3                          28                            51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK 22(8P23.3) MUTATED    96   7   3
  DEL PEAK 22(8P23.3) WILD-TYPE 257  17  15
D58V6, multiclass
    clus
vv   DEL PEAK 22(8P23.3) MUTATED DEL PEAK 22(8P23.3) WILD-TYPE
  M0                          96                           257
  M1                           7                            17
  MX                           3                            15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                               cls
clus                              0   1
  DEL PEAK 22(8P23.3) MUTATED    32  74
  DEL PEAK 22(8P23.3) WILD-TYPE 119 170
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(8P23.3) MUTATED     32   74
  DEL PEAK 22(8P23.3) WILD-TYPE  119  170
        clus
vv       DEL PEAK 22(8P23.3) MUTATED DEL PEAK 22(8P23.3) WILD-TYPE
  FEMALE                          32                           119
  MALE                            74                           170
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 22(8P23.3) MUTATED                                       6
  DEL PEAK 22(8P23.3) WILD-TYPE                                    59
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 22(8P23.3) MUTATED                                                       47
  DEL PEAK 22(8P23.3) WILD-TYPE                                                    110
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 22(8P23.3) MUTATED                                                                  22
  DEL PEAK 22(8P23.3) WILD-TYPE                                                                47
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 22(8P23.3) MUTATED                                                 21
  DEL PEAK 22(8P23.3) WILD-TYPE                                               43
                               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                                          1
  DEL PEAK 22(8P23.3) WILD-TYPE                                        8
D58V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 22(8P23.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     47
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          22
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    1
                                                                   clus
vv                                                                  DEL PEAK 22(8P23.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      110
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            47
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             43
  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"
D58V9, binary
                               cls
clus                              0   1
  DEL PEAK 22(8P23.3) MUTATED     2 104
  DEL PEAK 22(8P23.3) WILD-TYPE   4 285
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(8P23.3) MUTATED      2  104
  DEL PEAK 22(8P23.3) WILD-TYPE    4  285
     clus
vv    DEL PEAK 22(8P23.3) MUTATED DEL PEAK 22(8P23.3) WILD-TYPE
  NO                            2                             4
  YES                         104                           285
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 22(8P23.3) MUTATED    86   5   7   3
  DEL PEAK 22(8P23.3) WILD-TYPE 232  11  11  22
D58V10, multiclass
    clus
vv   DEL PEAK 22(8P23.3) MUTATED DEL PEAK 22(8P23.3) WILD-TYPE
  R0                          86                           232
  R1                           5                            11
  R2                           7                            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"
D58V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 22(8P23.3) MUTATED      26                         3
  DEL PEAK 22(8P23.3) WILD-TYPE    62                         3
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 22(8P23.3) MUTATED                                           1    58
  DEL PEAK 22(8P23.3) WILD-TYPE                                         0   185
D58V12, multiclass
                                           clus
vv                                          DEL PEAK 22(8P23.3) MUTATED
  ASIAN                                                              26
  BLACK OR AFRICAN AMERICAN                                           3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              58
                                           clus
vv                                          DEL PEAK 22(8P23.3) WILD-TYPE
  ASIAN                                                                62
  BLACK OR AFRICAN AMERICAN                                             3
  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"

Clustering(59) Variable = DEL PEAK 23(9P23) MUTATION ANALYSIS
D59V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 23(9P23) MUTATED   102  49
  DEL PEAK 23(9P23) WILD-TYPE 140  73
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                        151                         213 
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                         49                          73 
$`DEL PEAK 23(9P23) MUTATED`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        5.62         6.61        18.35        10.13        13.68         7.00 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 
       16.14         1.25        31.20         9.21        35.24        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7959 
       28.01         0.69         0.16        18.54         0.95        18.71 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8284 TCGA-BR-8289 TCGA-BR-8291 
       17.49         1.32         0.69         0.72         0.26        16.31 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       22.19         2.96        14.04         5.39         0.72         9.21 
TCGA-BR-8486 TCGA-BR-8676 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       20.22         7.53        16.44         0.59        15.68         0.62 
TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 
        1.15        22.26         0.92         0.72         0.66        13.51 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5803 
       20.65         1.15        13.64         3.25        13.15         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 
        0.07         0.07         0.07         0.16         0.10         0.13 
TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CG-4301 TCGA-CG-4437 TCGA-CG-4438 
        6.35         0.13         0.13         3.02         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 
        4.01        29.98        47.05        19.07        12.03        18.97 
TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5730 
       12.00         1.02         1.02       105.07        12.03         4.01 
TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
       55.04        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-D7-6815 
       18.84        18.54         5.95        17.19         4.14        15.98 
TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       12.79        11.31        19.50         0.23         6.97        21.14 
TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A 
       16.44        11.24        11.31         2.96        15.65         7.40 
TCGA-EQ-8122 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 
        7.79         8.12        19.53         3.02        17.06         0.56 
TCGA-FP-A4BF TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-A4GF TCGA-HU-A4GH 
        1.55         1.51         5.92        12.59        25.81        11.77 
TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
        6.25        19.36         9.67        27.42        21.21        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38         5.36         5.19         1.41         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-KB-A6F5 TCGA-KB-A93H TCGA-RD-A7BT TCGA-RD-A7BW 
        6.87         5.56         5.56        28.90         8.61         4.67 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB 
       16.67       122.30        37.91       115.69         8.94         5.79 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       37.74        13.25        31.10         7.73         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91Q TCGA-VQ-A91U 
        1.87        23.57        64.57        14.33        20.81         1.71 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-AA68 TCGA-VQ-AA6J 
        8.58         9.73        44.25         8.61        40.08        21.11 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK 23(9P23) WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 
       11.70         6.97         4.64         7.43        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6563 
        9.57         6.61        34.68        15.95        13.12        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6710 
        0.82         0.62        32.78        13.84        13.22         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-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 
       12.43         0.69        12.76         0.82        12.26         0.49 
TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       20.55         0.26        12.95         1.55         1.48         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 
        6.18        19.50         0.36         0.26         0.95        13.74 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 
        4.31         3.32         0.36        19.17        14.79         0.69 
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 
        2.14        13.45         0.20         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         0.66         3.02        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 
       12.89         0.79        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         0.13         0.13         0.07         0.10         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
        0.10        20.02        27.02        15.95         1.02         7.99 
TCGA-CG-4441 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
       14.01        21.99         9.01         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5725 TCGA-CG-5726 
        6.97         0.99         6.02         0.99        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-6522 TCGA-D7-6524 
       79.07        65.10        21.07         7.99        18.61        17.85 
TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 
       15.22        10.55        12.33        24.72        16.80        17.19 
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-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 
       13.71        11.44         9.76         4.34         7.13         0.62 
TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
       16.24         6.58        14.47        72.23        21.27         0.39 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A8CX TCGA-HF-A5NB 
       22.29        59.54         5.03        13.58         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       26.47        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-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        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-A4H4 
        6.51        10.19         0.26         2.10        12.95        17.69 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RN 
       12.30         8.88         8.81         3.45         3.39        13.08 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        1.81         2.53        60.56         3.72        19.73         4.31 
TCGA-RD-A7BS TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
       11.05        40.64       116.38        71.38        57.44        35.61 
TCGA-RD-A8NB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8P2 
       16.87         0.92         5.46        13.02        21.73        22.36 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PO 
       23.77        19.07        33.63        46.26        16.31         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       23.41        15.65        19.30        59.18        28.70        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91W TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
        8.68        49.25         7.36        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-AA6B TCGA-ZA-A8F6 
        5.72        29.98         4.21 

  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                       0.07                        0.07 
  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 
                       9.73                       12.26 
[1] "0.1 - 122.3 (9.7)"  "0.1 - 116.4 (12.3)"
[1] "hr=" "1"  
D59V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 23(9P23) MUTATED         0        6       11       16        16
  DEL PEAK 23(9P23) WILD-TYPE       2        7       28       15        20
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 23(9P23) MUTATED          19         0         38         24
  DEL PEAK 23(9P23) WILD-TYPE        30         3         39         31
                             vv
clus                          STAGE IIIC STAGE IV
  DEL PEAK 23(9P23) MUTATED           13       16
  DEL PEAK 23(9P23) WILD-TYPE         24       21
D59V3, multiclass
            clus
vv           DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  STAGE I                            0                           2
  STAGE IA                           6                           7
  STAGE IB                          11                          28
  STAGE II                          16                          15
  STAGE IIA                         16                          20
  STAGE IIB                         19                          30
  STAGE III                          0                           3
  STAGE IIIA                        38                          39
  STAGE IIIB                        24                          31
  STAGE IIIC                        13                          24
  STAGE IV                          16                          21
[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    9 36 80 35
  DEL PEAK 23(9P23) WILD-TYPE 12 51 93 69
D59V4, multiclass
    clus
vv   DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  T1                         9                          12
  T2                        36                          51
  T3                        80                          93
  T4                        35                          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
  DEL PEAK 23(9P23) MUTATED   45 48 36 32
  DEL PEAK 23(9P23) WILD-TYPE 77 59 39 47
D59V5, multiclass
    clus
vv   DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  N0                        45                          77
  N1                        48                          59
  N2                        36                          39
  N3                        32                          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                           M0  M1  MX
  DEL PEAK 23(9P23) MUTATED   152   7   6
  DEL PEAK 23(9P23) WILD-TYPE 201  17  12
D59V6, multiclass
    clus
vv   DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  M0                       152                         201
  M1                         7                          17
  MX                         6                          12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, binary
                             cls
clus                            0   1
  DEL PEAK 23(9P23) MUTATED    62 103
  DEL PEAK 23(9P23) WILD-TYPE  89 141
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 23(9P23) MUTATED     62  103
  DEL PEAK 23(9P23) WILD-TYPE   89  141
        clus
vv       DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  FEMALE                        62                          89
  MALE                         103                         141
[1] 2 2
[1] FALSE
                             vv
clus                          STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 23(9P23) MUTATED                                      20
  DEL PEAK 23(9P23) WILD-TYPE                                    45
                             vv
clus                          STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 23(9P23) MUTATED                                                       63
  DEL PEAK 23(9P23) WILD-TYPE                                                     94
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 23(9P23) MUTATED                                                                  35
  DEL PEAK 23(9P23) WILD-TYPE                                                                34
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 23(9P23) MUTATED                                                 32
  DEL PEAK 23(9P23) WILD-TYPE                                               32
                             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                                          2
  DEL PEAK 23(9P23) WILD-TYPE                                        7
D59V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 23(9P23) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                    20
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                   63
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                         32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                  9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                 3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                  2
                                                                   clus
vv                                                                  DEL PEAK 23(9P23) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      45
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     94
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          34
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   12
  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"
D59V9, binary
                             cls
clus                            0   1
  DEL PEAK 23(9P23) MUTATED     3 162
  DEL PEAK 23(9P23) WILD-TYPE   3 227
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 23(9P23) MUTATED      3  162
  DEL PEAK 23(9P23) WILD-TYPE    3  227
     clus
vv    DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  NO                          3                           3
  YES                       162                         227
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 23(9P23) MUTATED   135   7   7   9
  DEL PEAK 23(9P23) WILD-TYPE 183   9  11  16
D59V10, multiclass
    clus
vv   DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  R0                       135                         183
  R1                         7                           9
  R2                         7                          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"
D59V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 23(9P23) MUTATED      33                         1
  DEL PEAK 23(9P23) WILD-TYPE    55                         5
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 23(9P23) MUTATED                                           1   105
  DEL PEAK 23(9P23) WILD-TYPE                                         0   138
D59V12, multiclass
                                           clus
vv                                          DEL PEAK 23(9P23) MUTATED
  ASIAN                                                            33
  BLACK OR AFRICAN AMERICAN                                         1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         1
  WHITE                                                           105
                                           clus
vv                                          DEL PEAK 23(9P23) WILD-TYPE
  ASIAN                                                              55
  BLACK OR AFRICAN AMERICAN                                           5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             138
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(60) Variable = DEL PEAK 24(9P21.3) MUTATION ANALYSIS
D60V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 24(9P21.3) MUTATED   103  52
  DEL PEAK 24(9P21.3) WILD-TYPE 139  70
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                          155                           209 
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                           52                            70 
$`DEL PEAK 24(9P21.3) MUTATED`
TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6709 
        6.61        18.35        10.13        13.68         7.00         1.25 
TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       31.20         9.21        35.24        15.42        28.01         0.69 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        0.16        18.54         0.95        18.71        17.49         0.82 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8291 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 
        1.32         0.69        16.31        22.19         2.96        14.04 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8677 TCGA-BR-8682 
        5.39         0.72         9.21        20.22         0.49        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS 
        0.59        15.68         0.62         1.15        22.26         0.92 
TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.72         0.66        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5803 TCGA-CD-8524 
       13.64         2.83         3.25        13.15         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 
        0.07         0.07         0.07         0.16         0.10         0.13 
TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4438 
        6.35         0.13         0.13         3.02        27.02        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-4466 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       18.97        12.00        30.97         1.02         1.02         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-5579 
       12.03        15.02         4.01        55.04        12.66        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         5.95        17.19         4.14 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       15.98        12.79        11.31         0.23         6.97        21.14 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A74A 
       14.27        16.44        11.24        11.31         2.96         7.40 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 
        7.79        72.23         8.12        17.06        13.58         0.56 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-A4G3 TCGA-HU-A4GH 
        1.51         5.92        14.27        12.59         5.59        11.77 
TCGA-HU-A4GU TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
        6.25        12.30         9.67        27.42        21.21        18.81 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT 
        5.36         5.19         1.41         6.74         6.87         5.56 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-RD-A7BT TCGA-RD-A7BW 
        2.53         5.56        60.56        28.90         8.61         4.67 
TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DT 
       16.67        37.91       115.69         8.94         5.79        37.74 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       13.25        13.02        31.10        21.73        23.77         7.73 
TCGA-VQ-A8PC TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A8PX 
       46.26         2.70        17.85         1.87        23.57        64.57 
TCGA-VQ-A8PY TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       14.33        20.81         1.71         8.58         9.73        44.25 
TCGA-VQ-A922 TCGA-VQ-AA68 TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        8.61        40.08        21.11         4.21         0.79 

$`DEL PEAK 24(9P21.3) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
        5.62        11.70         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        13.12 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12         0.82         0.62        32.78        13.84        13.22 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 
       16.14         8.98        21.11        30.90        32.94        12.82 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8078 
       24.76        23.93        12.43         0.69        12.76        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.49        20.55         0.72         0.26        12.95         0.26 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        1.55         1.48         7.40         6.18        19.50         0.36 
TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
        0.26         0.95        13.74         4.31         3.32         0.36 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       19.17        14.79         0.69         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         2.14        13.45         0.20 
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         0.66 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        3.02        13.41        13.51        12.89         0.79        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         0.13         0.13         0.07         0.10         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        0.10        20.02        15.95         1.02         7.99         8.05 
TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5721 
       21.99         9.01         7.07        22.98         6.97         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5733 
        0.99       105.07        28.96        79.07        65.10        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6528 
        7.99        12.36        19.13        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-D7-8579 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-A6F2 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 
       11.44         9.76        15.65         4.34         7.13         0.62 
TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24         6.58        14.47        21.27         0.39        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF TCGA-FP-A8CX 
        3.02        22.29        59.54         5.03         1.55         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       18.08        26.47        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30        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-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-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI 
       17.69         8.88         8.81         3.45         3.39        18.38 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NU TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
       13.08         6.44         1.81         3.72        19.73         4.31 
TCGA-RD-A7BS TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       11.05       122.30        40.64       116.38        71.38        57.44 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8P2 TCGA-VQ-A8P8 
       35.61        16.87         0.92         5.46        22.36        19.07 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       33.63        16.31         9.27        23.41        15.65        19.30 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91W 
       59.18        28.70        11.70         8.68        49.25         7.36 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6B 
       55.43         4.54         6.58         5.72        29.98 

  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                         0.07                          0.07 
  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 
                        11.24                         11.84 
[1] "0.1 - 115.7 (11.2)" "0.1 - 122.3 (11.8)"
[1] "hr=" "1"  
D60V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 24(9P21.3) MUTATED         0        8       17       16        14
  DEL PEAK 24(9P21.3) WILD-TYPE       2        5       22       15        22
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 24(9P21.3) MUTATED          20         1         36         24
  DEL PEAK 24(9P21.3) WILD-TYPE        29         2         41         31
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 24(9P21.3) MUTATED            9       16
  DEL PEAK 24(9P21.3) WILD-TYPE         28       21
D60V3, multiclass
            clus
vv           DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             8                             5
  STAGE IB                            17                            22
  STAGE II                            16                            15
  STAGE IIA                           14                            22
  STAGE IIB                           20                            29
  STAGE III                            1                             2
  STAGE IIIA                          36                            41
  STAGE IIIB                          24                            31
  STAGE IIIC                           9                            28
  STAGE IV                            16                            21
[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    9 41 78 33
  DEL PEAK 24(9P21.3) WILD-TYPE 12 46 95 71
D60V4, multiclass
    clus
vv   DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  T1                           9                            12
  T2                          41                            46
  T3                          78                            95
  T4                          33                            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 24(9P21.3) MUTATED   51 48 37 27
  DEL PEAK 24(9P21.3) WILD-TYPE 71 59 38 52
D60V5, multiclass
    clus
vv   DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  N0                          51                            71
  N1                          48                            59
  N2                          37                            38
  N3                          27                            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"
                               vv
clus                             M0  M1  MX
  DEL PEAK 24(9P21.3) MUTATED   150   7   8
  DEL PEAK 24(9P21.3) WILD-TYPE 203  17  10
D60V6, multiclass
    clus
vv   DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  M0                         150                           203
  M1                           7                            17
  MX                           8                            10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V7, binary
                               cls
clus                              0   1
  DEL PEAK 24(9P21.3) MUTATED    63 102
  DEL PEAK 24(9P21.3) WILD-TYPE  88 142
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 24(9P21.3) MUTATED     63  102
  DEL PEAK 24(9P21.3) WILD-TYPE   88  142
        clus
vv       DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  FEMALE                          63                            88
  MALE                           102                           142
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 24(9P21.3) MUTATED                                      16
  DEL PEAK 24(9P21.3) WILD-TYPE                                    49
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 24(9P21.3) MUTATED                                                       63
  DEL PEAK 24(9P21.3) WILD-TYPE                                                     94
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 24(9P21.3) MUTATED                                                                  37
  DEL PEAK 24(9P21.3) WILD-TYPE                                                                32
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 24(9P21.3) MUTATED                                                 32
  DEL PEAK 24(9P21.3) WILD-TYPE                                               32
                               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                                          3
  DEL PEAK 24(9P21.3) WILD-TYPE                                        6
D60V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 24(9P21.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      16
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     63
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    3
                                                                   clus
vv                                                                  DEL PEAK 24(9P21.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       94
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            32
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     12
  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"
D60V9, binary
                               cls
clus                              0   1
  DEL PEAK 24(9P21.3) MUTATED     3 162
  DEL PEAK 24(9P21.3) WILD-TYPE   3 227
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 24(9P21.3) MUTATED      3  162
  DEL PEAK 24(9P21.3) WILD-TYPE    3  227
     clus
vv    DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  NO                            3                             3
  YES                         162                           227
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 24(9P21.3) MUTATED   138   6   8   6
  DEL PEAK 24(9P21.3) WILD-TYPE 180  10  10  19
D60V10, multiclass
    clus
vv   DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  R0                         138                           180
  R1                           6                            10
  R2                           8                            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"
D60V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 24(9P21.3) MUTATED      34                         3
  DEL PEAK 24(9P21.3) WILD-TYPE    54                         3
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 24(9P21.3) MUTATED                                           1    98
  DEL PEAK 24(9P21.3) WILD-TYPE                                         0   145
D60V12, multiclass
                                           clus
vv                                          DEL PEAK 24(9P21.3) MUTATED
  ASIAN                                                              34
  BLACK OR AFRICAN AMERICAN                                           3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              98
                                           clus
vv                                          DEL PEAK 24(9P21.3) WILD-TYPE
  ASIAN                                                                54
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               145
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(61) Variable = DEL PEAK 25(9Q21.11) MUTATION ANALYSIS
D61V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(9Q21.11) MUTATED    59  29
  DEL PEAK 25(9Q21.11) WILD-TYPE 183  93
  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                            88                            276 
  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                            29                             93 
$`DEL PEAK 25(9Q21.11) MUTATED`
TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6803 TCGA-BR-7715 
        6.61        10.13        13.68         7.00        31.20        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8058 TCGA-BR-8286 
       28.01         0.69        18.54         0.95        17.49        12.95 
TCGA-BR-8291 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       16.31        22.19         2.96         5.39         0.72         9.21 
TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 
       16.44        15.68         0.62        22.26         0.92         0.72 
TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
       13.51         1.15        13.64         3.25        13.15         0.30 
TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-A486 
        0.07         0.07         0.07         0.10         0.13         6.35 
TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4304 TCGA-CG-4438 TCGA-CG-4455 
        0.13         0.13         0.10        27.02        54.08        12.03 
TCGA-CG-5724 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6527 
       12.03        20.55        18.84        18.54         5.95         4.14 
TCGA-D7-6815 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6F0 
       15.98         0.23         6.97        21.14        16.44         2.96 
TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-8099 TCGA-FP-8211 
        7.40         7.79        72.23         8.12        17.06        13.58 
TCGA-FP-8631 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GF TCGA-HU-A4GH 
        0.56         5.92        12.59        14.17        25.81        11.77 
TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H6 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RP 
        6.25         2.10         9.67        18.38         5.36         6.44 
TCGA-IN-A6RR TCGA-KB-A93H TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB 
        6.74        28.90        16.67        37.91         8.94         5.79 
TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A91Q TCGA-VQ-A91Y 
       13.25        31.10         2.70        17.85        20.81         9.73 
TCGA-VQ-A922 TCGA-VQ-AA68 TCGA-VQ-AA6J TCGA-ZQ-A9CR 
        8.61        40.08        21.11         0.79 

$`DEL PEAK 25(9Q21.11) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
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 
       13.12        39.12         0.82         0.62        32.78        13.84 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       13.22        16.14         1.25         8.98        21.11        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-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 
        0.16        12.43         0.69        12.76        18.71         0.82 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
        1.32         0.69        12.26         0.49        20.55         0.72 
TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        0.26         0.26         1.55         1.48         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       19.50         0.36         0.26         0.95        13.74         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 
       14.04         3.32         0.36        19.17        14.79         0.69 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        0.26        15.85         3.72        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         2.14        13.45         0.20         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       11.54        15.81         0.59        10.68        12.56         1.15 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        0.66         3.02        13.41        13.51        12.89         0.79 
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-5801 
       20.65        20.42        11.57         5.13         2.83        13.18 
TCGA-CD-8524 TCGA-CD-8526 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-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI 
        0.13         0.10         0.13         0.13         0.07         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
        0.10        20.02         3.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
        8.05         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
       21.99         9.01        18.97         7.07        12.00        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97         1.02         1.02         0.99         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-D7-5578 
        4.01        55.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6528 
       11.93        19.13        18.61        17.85        17.19        15.22 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX 
       19.50        17.19        20.91        14.27         5.92        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-A6EZ TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO 
        9.76        15.65         4.34         7.13         0.62        16.24 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
        6.58        14.47        21.27         0.39        19.53         3.02 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB 
       22.29        59.54         5.03         1.55         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-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-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        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        17.69 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       12.30         8.88         8.81        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RS 
       18.81         3.39         5.19        13.08         1.41         6.87 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG 
        5.56         1.81         2.53         5.56        60.56         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV 
       19.73         4.31        11.05         8.61         4.67       122.30 
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-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E3 
       16.87         0.92        37.74         5.46        13.02        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       22.36        23.77         7.73        19.07        33.63        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       16.31         1.87         9.27        23.41        15.65        19.30 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       23.57        64.57        14.33        59.18        28.70        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z 
        8.68        49.25         1.71         7.36         8.58        44.25 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6B TCGA-ZA-A8F6 
       55.43         4.54         6.58         5.72        29.98         4.21 

  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                          0.07                           0.07 
  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 
                          9.70                          11.77 
[1] "0.1 - 72.2 (9.7)"   "0.1 - 122.3 (11.8)"
[1] "hr=" "1.1"
D61V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 25(9Q21.11) MUTATED         0        2        8       10        13
  DEL PEAK 25(9Q21.11) WILD-TYPE       2       11       31       21        23
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 25(9Q21.11) MUTATED          12         0         18         12
  DEL PEAK 25(9Q21.11) WILD-TYPE        37         3         59         43
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 25(9Q21.11) MUTATED           11        7
  DEL PEAK 25(9Q21.11) WILD-TYPE         26       30
D61V3, multiclass
            clus
vv           DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              2                             11
  STAGE IB                              8                             31
  STAGE II                             10                             21
  STAGE IIA                            13                             23
  STAGE IIB                            12                             37
  STAGE III                             0                              3
  STAGE IIIA                           18                             59
  STAGE IIIB                           12                             43
  STAGE IIIC                           11                             26
  STAGE IV                              7                             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 25(9Q21.11) MUTATED     4  18  49  22
  DEL PEAK 25(9Q21.11) WILD-TYPE  17  69 124  82
D61V4, multiclass
    clus
vv   DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  T1                            4                             17
  T2                           18                             69
  T3                           49                            124
  T4                           22                             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
  DEL PEAK 25(9Q21.11) MUTATED   30 26 21 17
  DEL PEAK 25(9Q21.11) WILD-TYPE 92 81 54 62
D61V5, multiclass
    clus
vv   DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  N0                           30                             92
  N1                           26                             81
  N2                           21                             54
  N3                           17                             62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  DEL PEAK 25(9Q21.11) MUTATED    89   2   5
  DEL PEAK 25(9Q21.11) WILD-TYPE 264  22  13
D61V6, multiclass
    clus
vv   DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  M0                           89                            264
  M1                            2                             22
  MX                            5                             13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
                                cls
clus                               0   1
  DEL PEAK 25(9Q21.11) MUTATED    33  63
  DEL PEAK 25(9Q21.11) WILD-TYPE 118 181
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(9Q21.11) MUTATED     33   63
  DEL PEAK 25(9Q21.11) WILD-TYPE  118  181
        clus
vv       DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  FEMALE                           33                            118
  MALE                             63                            181
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 25(9Q21.11) MUTATED                                      12
  DEL PEAK 25(9Q21.11) WILD-TYPE                                    53
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 25(9Q21.11) MUTATED                                                       43
  DEL PEAK 25(9Q21.11) WILD-TYPE                                                    114
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 25(9Q21.11) MUTATED                                                                  13
  DEL PEAK 25(9Q21.11) WILD-TYPE                                                                56
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 25(9Q21.11) MUTATED                                                 20
  DEL PEAK 25(9Q21.11) WILD-TYPE                                               44
                                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                                          0
  DEL PEAK 25(9Q21.11) WILD-TYPE                                        9
D61V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 25(9Q21.11) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      43
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     0
                                                                   clus
vv                                                                  DEL PEAK 25(9Q21.11) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         53
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       114
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             56
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              44
  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"
D61V9, binary
                                cls
clus                               0   1
  DEL PEAK 25(9Q21.11) MUTATED     1  95
  DEL PEAK 25(9Q21.11) WILD-TYPE   5 294
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(9Q21.11) MUTATED      1   95
  DEL PEAK 25(9Q21.11) WILD-TYPE    5  294
     clus
vv    DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  NO                             1                              5
  YES                           95                            294
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 25(9Q21.11) MUTATED    77   3   3   5
  DEL PEAK 25(9Q21.11) WILD-TYPE 241  13  15  20
D61V10, multiclass
    clus
vv   DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  R0                           77                            241
  R1                            3                             13
  R2                            3                             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"
D61V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 25(9Q21.11) MUTATED      26                         2
  DEL PEAK 25(9Q21.11) WILD-TYPE    62                         4
                                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      59
  DEL PEAK 25(9Q21.11) WILD-TYPE   184
D61V12, multiclass
                                           clus
vv                                          DEL PEAK 25(9Q21.11) MUTATED
  ASIAN                                                               26
  BLACK OR AFRICAN AMERICAN                                            2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               59
                                           clus
vv                                          DEL PEAK 25(9Q21.11) WILD-TYPE
  ASIAN                                                                 62
  BLACK OR AFRICAN AMERICAN                                              4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  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"

Clustering(62) Variable = DEL PEAK 26(10P12.31) MUTATION ANALYSIS
D62V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 26(10P12.31) MUTATED    31  20
  DEL PEAK 26(10P12.31) WILD-TYPE 211 102
  DEL PEAK 26(10P12.31) MUTATED DEL PEAK 26(10P12.31) WILD-TYPE 
                             51                             313 
  DEL PEAK 26(10P12.31) MUTATED DEL PEAK 26(10P12.31) WILD-TYPE 
                             20                             102 
$`DEL PEAK 26(10P12.31) MUTATED`
TCGA-BR-4267 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-7901 TCGA-BR-8059 TCGA-BR-8060 
        6.18         7.00         0.82         0.95         0.82         1.32 
TCGA-BR-8291 TCGA-BR-8365 TCGA-BR-8372 TCGA-BR-8486 TCGA-BR-A452 TCGA-BR-A4IY 
       16.31         2.96        19.17        20.22         0.66        12.89 
TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8533 TCGA-CG-4301 TCGA-CG-4455 
        0.07         0.07         0.10         0.13         3.02        12.03 
TCGA-CG-4475 TCGA-CG-5732 TCGA-D7-6521 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 
       22.98        55.04        18.54        15.22        15.98        11.31 
TCGA-D7-8570 TCGA-D7-8575 TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-EQ-A4SO TCGA-FP-7829 
       24.72         0.23        11.24         2.96        16.24        19.53 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HU-8249 TCGA-HU-A4H5 TCGA-IN-8462 
        0.56         1.55         0.23        14.17        12.30        18.81 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB 
        1.41         6.44         6.74       115.69         8.94         5.79 
TCGA-VQ-A8DT TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A91Q TCGA-VQ-A922 TCGA-VQ-A925 
       37.74        13.02        31.10        20.81         8.61         4.54 
TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-ZQ-A9CR 
        5.72        40.08         0.79 

$`DEL PEAK 26(10P12.31) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         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-6565 TCGA-BR-6566 
       13.12        10.13        13.68        39.12         0.62        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       13.84        13.22        16.14         1.25         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-7722 
       35.24        23.93        15.42        28.01         0.69         0.16 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       18.54        12.43         0.69        12.76        18.71        17.49 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        12.26         0.49        20.55         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       12.95         0.26         1.55         1.48         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.36         0.26        22.19         0.95        13.74 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8380 
        4.31        14.04         3.32         0.36        14.79         0.69 
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         0.72         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         2.14        13.45         0.20 
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         0.59 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 
       15.68         0.62        10.68        12.56         1.15         3.02 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 
       22.26         0.92        13.41        13.51         0.79         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-8526 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-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         6.35         0.13         0.13 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.13         0.13         0.07         0.10         0.10         0.10 
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-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
       21.99         9.01        18.97         7.07        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97         1.02         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-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-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        20.55        18.84        18.61        17.85         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8572 
       17.19         4.14        12.79        10.55        12.33        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19         6.97        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-A6F2 TCGA-D7-A748 TCGA-D7-A74A 
       11.31        11.44         9.76        15.65         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        7.13         0.62         7.79         6.58        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         8.12         0.39         3.02        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       59.54         5.03        13.58        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-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        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        17.69         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-A6RS TCGA-IN-A7NT TCGA-IN-A7NU 
        5.36         5.19        13.08         6.87         5.56         1.81 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        60.56        28.90         3.72        19.73 
TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        4.31        11.05         8.61         4.67        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-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E3 TCGA-VQ-A8P2 
       16.87         0.92         5.46        13.25        21.73        22.36 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       23.77         7.73        19.07        33.63        46.26        16.31 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.70        17.85         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       19.30        23.57        64.57        14.33        59.18        28.70 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X 
       11.70         8.68        49.25         1.71         7.36         8.58 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-AA6B TCGA-VQ-AA6J 
        9.73        44.25        55.43         6.58        29.98        21.11 
TCGA-ZA-A8F6 
        4.21 

  DEL PEAK 26(10P12.31) MUTATED DEL PEAK 26(10P12.31) WILD-TYPE 
                           0.07                            0.07 
  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 
                           8.61                           11.84 
[1] "0.1 - 115.7 (8.6)"  "0.1 - 122.3 (11.8)"
[1] "hr=" "1.4"
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       2       11       35       28        35
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 26(10P12.31) MUTATED          11         1         14          5
  DEL PEAK 26(10P12.31) WILD-TYPE        38         2         63         50
                                 vv
clus                              STAGE IIIC STAGE IV
  DEL PEAK 26(10P12.31) MUTATED            6        7
  DEL PEAK 26(10P12.31) WILD-TYPE         31       30
D62V3, multiclass
            clus
vv           DEL PEAK 26(10P12.31) MUTATED DEL PEAK 26(10P12.31) WILD-TYPE
  STAGE I                                0                               2
  STAGE IA                               2                              11
  STAGE IB                               4                              35
  STAGE II                               3                              28
  STAGE IIA                              1                              35
  STAGE IIB                             11                              38
  STAGE III                              1                               2
  STAGE IIIA                            14                              63
  STAGE IIIB                             5                              50
  STAGE IIIC                             6                              31
  STAGE IV                               7                              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 26(10P12.31) MUTATED     3  15  23  13
  DEL PEAK 26(10P12.31) WILD-TYPE  18  72 150  91
D62V4, multiclass
    clus
vv   DEL PEAK 26(10P12.31) MUTATED DEL PEAK 26(10P12.31) WILD-TYPE
  T1                             3                              18
  T2                            15                              72
  T3                            23                             150
  T4                            13                              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
  DEL PEAK 26(10P12.31) MUTATED    10  17  14  13
  DEL PEAK 26(10P12.31) WILD-TYPE 112  90  61  66
D62V5, multiclass
    clus
vv   DEL PEAK 26(10P12.31) MUTATED DEL PEAK 26(10P12.31) WILD-TYPE
  N0                            10                             112
  N1                            17                              90
  N2                            14                              61
  N3                            13                              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"
                                 vv
clus                               M0  M1  MX
  DEL PEAK 26(10P12.31) MUTATED    51   2   4
  DEL PEAK 26(10P12.31) WILD-TYPE 302  22  14
D62V6, multiclass
    clus
vv   DEL PEAK 26(10P12.31) MUTATED DEL PEAK 26(10P12.31) WILD-TYPE
  M0                            51                             302
  M1                             2                              22
  MX                             4                              14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                                 cls
clus                                0   1
  DEL PEAK 26(10P12.31) MUTATED    21  36
  DEL PEAK 26(10P12.31) WILD-TYPE 130 208
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(10P12.31) MUTATED     21   36
  DEL PEAK 26(10P12.31) WILD-TYPE  130  208
        clus
vv       DEL PEAK 26(10P12.31) MUTATED DEL PEAK 26(10P12.31) WILD-TYPE
  FEMALE                            21                             130
  MALE                              36                             208
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 26(10P12.31) MUTATED                                       4
  DEL PEAK 26(10P12.31) WILD-TYPE                                    61
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 26(10P12.31) MUTATED                                                       22
  DEL PEAK 26(10P12.31) WILD-TYPE                                                    135
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 26(10P12.31) MUTATED                                                                   7
  DEL PEAK 26(10P12.31) WILD-TYPE                                                                62
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 26(10P12.31) MUTATED                                                 13
  DEL PEAK 26(10P12.31) WILD-TYPE                                               51
                                 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                                        6
D62V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 26(10P12.31) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       22
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             13
  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                                                          61
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        135
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              62
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               51
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       6
  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"
D62V9, binary
                                 cls
clus                                0   1
  DEL PEAK 26(10P12.31) MUTATED     1  56
  DEL PEAK 26(10P12.31) WILD-TYPE   5 333
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(10P12.31) MUTATED      1   56
  DEL PEAK 26(10P12.31) WILD-TYPE    5  333
     clus
vv    DEL PEAK 26(10P12.31) MUTATED DEL PEAK 26(10P12.31) WILD-TYPE
  NO                              1                               5
  YES                            56                             333
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 26(10P12.31) MUTATED    46   3   3   5
  DEL PEAK 26(10P12.31) WILD-TYPE 272  13  15  20
D62V10, multiclass
    clus
vv   DEL PEAK 26(10P12.31) MUTATED DEL PEAK 26(10P12.31) WILD-TYPE
  R0                            46                             272
  R1                             3                              13
  R2                             3                              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"
D62V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 26(10P12.31) MUTATED      10                         1
  DEL PEAK 26(10P12.31) WILD-TYPE    78                         5
                                 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      38
  DEL PEAK 26(10P12.31) WILD-TYPE   205
D62V12, multiclass
                                           clus
vv                                          DEL PEAK 26(10P12.31) MUTATED
  ASIAN                                                                10
  BLACK OR AFRICAN AMERICAN                                             1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                38
                                           clus
vv                                          DEL PEAK 26(10P12.31) WILD-TYPE
  ASIAN                                                                  78
  BLACK OR AFRICAN AMERICAN                                               5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 205
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(63) Variable = DEL PEAK 27(10Q22.3) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(10Q22.3) MUTATED    39  22
  DEL PEAK 27(10Q22.3) WILD-TYPE 203 100
  DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE 
                            61                            303 
  DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE 
                            22                            100 
$`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        18.54         0.95         1.32        16.31         2.96 
TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4QI TCGA-CD-5799 
        5.39        20.22         1.15        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         6.35         0.13         0.07 
TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4466 
        0.10         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         1.02         4.01        19.13        18.54         4.14 
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 
        7.79        19.53         1.55         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-KB-A93H TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ 
       28.90         8.94         5.79        37.74         5.46        13.02 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-AA68 
       17.85         1.87         1.71         8.58         9.73        40.08 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK 27(10Q22.3) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         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-6458 TCGA-BR-6563 
       15.95        13.12        10.13        13.68         7.00        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62        32.78        13.84        13.22        16.14 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.25         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-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
        0.69         0.16        12.43         0.69        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49         0.82         0.69        12.26         0.49        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 
        0.72         0.26        12.95         0.26         1.55         1.48 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        19.50         0.36         0.26        22.19 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        13.74         4.31        14.04         3.32         0.36 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       19.17        14.79         0.69         0.26        15.85         3.72 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        0.72         9.21         1.12        12.79        15.81         2.14 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         0.20         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         0.59        15.68         0.62        10.68        12.56 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        0.66         3.02         0.92        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        0.79         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-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-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-A487 TCGA-CD-A489 
        0.10         0.13         0.13         0.10         0.13         0.13 
TCGA-CD-A48C TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.13         0.10         0.10        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4444 
       15.95         1.02         8.05        54.08        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
       19.07        21.99         9.01         7.07        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.97         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-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        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 
       21.07         7.99        12.36        12.66        11.93        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6818 
       18.84        18.61        17.85         5.95        17.19        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-D7-8576 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YY 
        0.23         6.97        20.91        16.44         5.92        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-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
        2.96        15.65         4.34         7.40         7.13         0.62 
TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
       16.24         6.58        14.47        72.23        21.27         8.12 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        0.39         3.02        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-8244 
       13.58         0.56        18.08        26.47         1.51        14.27 
TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       12.59        11.41        10.62         0.76        24.30         5.59 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       11.84        24.20         3.25        22.75        25.81        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-A4H5 
        0.26         2.10        12.95        19.36        17.69        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-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38         5.36         5.19        13.08         6.44 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        6.87         5.56         1.81         2.53         5.56        60.56 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        3.72        19.73         4.31        11.05         8.61         4.67 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A8DL TCGA-VQ-A8DV 
       71.38        57.44        35.61        16.87         0.92        13.25 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       31.10        21.73        22.36        23.77         7.73        19.07 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP 
       33.63        46.26        16.31         2.70         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        19.30        23.57        64.57        14.33        59.18 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91W 
       28.70        11.70         8.68        49.25        20.81         7.36 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
       44.25         8.61        55.43         4.54         6.58         5.72 
TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 
       29.98        21.11         4.21 

  DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE 
                         40.08                         122.30 
  DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE 
                          8.94                          11.70 
[1] "0.1 - 40.1 (8.9)"   "0.1 - 122.3 (11.7)"
[1] "hr=" "1.3"
D63V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 27(10Q22.3) MUTATED         0        4        4        5         7
  DEL PEAK 27(10Q22.3) WILD-TYPE       2        9       35       26        29
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 27(10Q22.3) MUTATED          11         0         16          5
  DEL PEAK 27(10Q22.3) WILD-TYPE        38         3         61         50
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 27(10Q22.3) MUTATED            6        4
  DEL PEAK 27(10Q22.3) WILD-TYPE         31       33
D63V3, multiclass
            clus
vv           DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              4                              9
  STAGE IB                              4                             35
  STAGE II                              5                             26
  STAGE IIA                             7                             29
  STAGE IIB                            11                             38
  STAGE III                             0                              3
  STAGE IIIA                           16                             61
  STAGE IIIB                            5                             50
  STAGE IIIC                            6                             31
  STAGE IV                              4                             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 27(10Q22.3) MUTATED     4  18  30  10
  DEL PEAK 27(10Q22.3) WILD-TYPE  17  69 143  94
D63V4, multiclass
    clus
vv   DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE
  T1                            4                             17
  T2                           18                             69
  T3                           30                            143
  T4                           10                             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
  DEL PEAK 27(10Q22.3) MUTATED    17  19  11  16
  DEL PEAK 27(10Q22.3) WILD-TYPE 105  88  64  63
D63V5, multiclass
    clus
vv   DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE
  N0                           17                            105
  N1                           19                             88
  N2                           11                             64
  N3                           16                             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                              M0  M1  MX
  DEL PEAK 27(10Q22.3) MUTATED    60   3   3
  DEL PEAK 27(10Q22.3) WILD-TYPE 293  21  15
D63V6, multiclass
    clus
vv   DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE
  M0                           60                            293
  M1                            3                             21
  MX                            3                             15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(10Q22.3) MUTATED    22  44
  DEL PEAK 27(10Q22.3) WILD-TYPE 129 200
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10Q22.3) MUTATED     22   44
  DEL PEAK 27(10Q22.3) WILD-TYPE  129  200
        clus
vv       DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE
  FEMALE                           22                            129
  MALE                             44                            200
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 27(10Q22.3) MUTATED                                       4
  DEL PEAK 27(10Q22.3) WILD-TYPE                                    61
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 27(10Q22.3) MUTATED                                                       24
  DEL PEAK 27(10Q22.3) WILD-TYPE                                                    133
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 27(10Q22.3) MUTATED                                                                  15
  DEL PEAK 27(10Q22.3) WILD-TYPE                                                                54
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 27(10Q22.3) MUTATED                                                 13
  DEL PEAK 27(10Q22.3) WILD-TYPE                                               51
                                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                                        5
D63V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 27(10Q22.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      24
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           15
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            13
  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                                                         61
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             54
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              51
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      18
  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"
D63V9, binary
                                cls
clus                               0   1
  DEL PEAK 27(10Q22.3) MUTATED     1  65
  DEL PEAK 27(10Q22.3) WILD-TYPE   5 324
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10Q22.3) MUTATED      1   65
  DEL PEAK 27(10Q22.3) WILD-TYPE    5  324
     clus
vv    DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE
  NO                             1                              5
  YES                           65                            324
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 27(10Q22.3) MUTATED    49   2   4   4
  DEL PEAK 27(10Q22.3) WILD-TYPE 269  14  14  21
D63V10, multiclass
    clus
vv   DEL PEAK 27(10Q22.3) MUTATED DEL PEAK 27(10Q22.3) WILD-TYPE
  R0                           49                            269
  R1                            2                             14
  R2                            4                             14
  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                         1
  DEL PEAK 27(10Q22.3) WILD-TYPE    72                         5
                                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      40
  DEL PEAK 27(10Q22.3) WILD-TYPE   203
D63V12, multiclass
                                           clus
vv                                          DEL PEAK 27(10Q22.3) MUTATED
  ASIAN                                                               16
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               40
                                           clus
vv                                          DEL PEAK 27(10Q22.3) WILD-TYPE
  ASIAN                                                                 72
  BLACK OR AFRICAN AMERICAN                                              5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                203
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(64) Variable = DEL PEAK 28(10Q23.31) MUTATION ANALYSIS
D64V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 28(10Q23.31) MUTATED    59  33
  DEL PEAK 28(10Q23.31) WILD-TYPE 183  89
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                             92                             272 
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                             33                              89 
$`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        13.12        35.24        28.01 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8291 TCGA-BR-8295 
       18.54         0.95        17.49         1.32        16.31         1.55 
TCGA-BR-8365 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        2.96         4.31        14.04         5.39         0.72         9.21 
TCGA-BR-8486 TCGA-BR-8683 TCGA-BR-A4CQ TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5802 
       20.22         0.59        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         6.35         0.13 
TCGA-CD-A4MH TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        0.10        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         1.02        15.02 
TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6527 
        4.01        55.04        12.36        19.13        18.54         4.14 
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 
        7.79         0.39        19.53        13.58         0.56         1.55 
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-A7NU TCGA-KB-A93H TCGA-RD-A8N6 TCGA-SW-A7EB 
        6.44         6.74         1.81        28.90         8.94         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8PK TCGA-VQ-A8PM 
        0.92        37.74         5.46        13.02        17.85         1.87 
TCGA-VQ-A91A TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A928 
       28.70         1.71         8.58         9.73         8.61         5.72 
TCGA-VQ-AA68 TCGA-ZQ-A9CR 
       40.08         0.79 

$`DEL PEAK 28(10Q23.31) WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 
        5.62         6.97         4.64         7.43        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        34.68        15.95        10.13        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
        7.00        39.12         0.82         0.62        32.78        13.84 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       13.22        16.14         1.25         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-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 
       15.42         0.69         0.16        12.43         0.69        12.76 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       18.71         0.82         0.69        12.26         0.49        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8297 
        0.72         0.26        12.95         0.26         1.48         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 
        6.18        19.50         0.36         0.26        22.19         0.95 
TCGA-BR-8367 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 
       13.74         3.32         0.36        19.17        14.79         0.69 
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-8678 
        2.14        13.45         0.20         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         0.62        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        1.15         0.66         3.02         0.92        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         0.79         0.72        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-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 
        1.15        11.57         5.13         2.83        13.15        13.18 
TCGA-CD-5803 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-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C 
        0.13         0.13         0.10         0.13         0.13         0.13 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 
        0.07         0.10         0.10        20.02         3.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-4465 TCGA-CG-4469 
        1.02         8.05        54.08        19.07         9.01         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 
       12.00        22.98        30.97         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-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 
       65.10        21.07         7.99        12.66        11.93        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6818 
       18.84        18.61        17.85         5.95        17.19        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-D7-8576 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
        0.23         6.97        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-A6EZ TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
        9.76        15.65         4.34         7.40         7.13         0.62 
TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
       16.24         6.58        14.47        72.23        21.27         8.12 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-HF-A5NB 
        3.02        22.29        17.06        59.54         5.03        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 
       26.47         1.51        14.27        12.59        11.41        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-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        0.10        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       17.69         9.67         8.88         8.81        21.21         3.45 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NT 
        3.39         5.36         5.19        13.08         6.87         5.56 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        2.53         5.56        60.56         3.72        19.73         4.31 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         4.67        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-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       16.87        13.25        31.10        21.73        22.36        23.77 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ 
        7.73        19.07        33.63        46.26        16.31         2.70 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX 
        9.27        23.41        15.65        19.30        23.57        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q 
       14.33        59.18        11.70         8.68        49.25        20.81 
TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-AA6B 
        7.36        44.25        55.43         4.54         6.58        29.98 
TCGA-VQ-AA6J TCGA-ZA-A8F6 
       21.11         4.21 

  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                           0.07                            0.07 
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                          55.04                          122.30 
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                          9.075                          11.885 
[1] "0.1 - 55.0 (9.1)"   "0.1 - 122.3 (11.9)"
[1] "hr=" "1.3"
D64V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 28(10Q23.31) MUTATED         0        4       12        7         8
  DEL PEAK 28(10Q23.31) WILD-TYPE       2        9       27       24        28
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 28(10Q23.31) MUTATED          13         0         23          8
  DEL PEAK 28(10Q23.31) WILD-TYPE        36         3         54         47
                                 vv
clus                              STAGE IIIC STAGE IV
  DEL PEAK 28(10Q23.31) MUTATED            9        8
  DEL PEAK 28(10Q23.31) WILD-TYPE         28       29
D64V3, multiclass
            clus
vv           DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  STAGE I                                0                               2
  STAGE IA                               4                               9
  STAGE IB                              12                              27
  STAGE II                               7                              24
  STAGE IIA                              8                              28
  STAGE IIB                             13                              36
  STAGE III                              0                               3
  STAGE IIIA                            23                              54
  STAGE IIIB                             8                              47
  STAGE IIIC                             9                              28
  STAGE IV                               8                              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 28(10Q23.31) MUTATED     6  28  41  17
  DEL PEAK 28(10Q23.31) WILD-TYPE  15  59 132  87
D64V4, multiclass
    clus
vv   DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  T1                             6                              15
  T2                            28                              59
  T3                            41                             132
  T4                            17                              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 28(10Q23.31) MUTATED   29 26 16 23
  DEL PEAK 28(10Q23.31) WILD-TYPE 93 81 59 56
D64V5, multiclass
    clus
vv   DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  N0                            29                              93
  N1                            26                              81
  N2                            16                              59
  N3                            23                              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"
                                 vv
clus                               M0  M1  MX
  DEL PEAK 28(10Q23.31) MUTATED    87   4   6
  DEL PEAK 28(10Q23.31) WILD-TYPE 266  20  12
D64V6, multiclass
    clus
vv   DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  M0                            87                             266
  M1                             4                              20
  MX                             6                              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V7, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10Q23.31) MUTATED    36  61
  DEL PEAK 28(10Q23.31) WILD-TYPE 115 183
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10Q23.31) MUTATED     36   61
  DEL PEAK 28(10Q23.31) WILD-TYPE  115  183
        clus
vv       DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  FEMALE                            36                             115
  MALE                              61                             183
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 28(10Q23.31) MUTATED                                       6
  DEL PEAK 28(10Q23.31) WILD-TYPE                                    59
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 28(10Q23.31) MUTATED                                                       38
  DEL PEAK 28(10Q23.31) WILD-TYPE                                                    119
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 28(10Q23.31) MUTATED                                                                  22
  DEL PEAK 28(10Q23.31) WILD-TYPE                                                                47
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 28(10Q23.31) MUTATED                                                 19
  DEL PEAK 28(10Q23.31) WILD-TYPE                                               45
                                 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                                        5
D64V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 28(10Q23.31) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       38
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            22
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             19
  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                                                          59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        119
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              47
  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                                                        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"
D64V9, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10Q23.31) MUTATED     1  96
  DEL PEAK 28(10Q23.31) WILD-TYPE   5 293
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10Q23.31) MUTATED      1   96
  DEL PEAK 28(10Q23.31) WILD-TYPE    5  293
     clus
vv    DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  NO                              1                               5
  YES                            96                             293
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 28(10Q23.31) MUTATED    77   3   5   6
  DEL PEAK 28(10Q23.31) WILD-TYPE 241  13  13  19
D64V10, multiclass
    clus
vv   DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  R0                            77                             241
  R1                             3                              13
  R2                             5                              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"
D64V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 28(10Q23.31) MUTATED      21                         2
  DEL PEAK 28(10Q23.31) WILD-TYPE    67                         4
                                 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      59
  DEL PEAK 28(10Q23.31) WILD-TYPE   184
D64V12, multiclass
                                           clus
vv                                          DEL PEAK 28(10Q23.31) MUTATED
  ASIAN                                                                21
  BLACK OR AFRICAN AMERICAN                                             2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                59
                                           clus
vv                                          DEL PEAK 28(10Q23.31) WILD-TYPE
  ASIAN                                                                  67
  BLACK OR AFRICAN AMERICAN                                               4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  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"

Clustering(65) Variable = DEL PEAK 29(11P15.5) MUTATION ANALYSIS
D65V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(11P15.5) MUTATED    50  32
  DEL PEAK 29(11P15.5) WILD-TYPE 192  90
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                            82                            282 
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                            32                             90 
$`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         0.82        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        18.54         0.49         7.40 
TCGA-BR-8369 TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-CD-5799 TCGA-CD-5800 
       14.04         0.92         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         0.13        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        55.04        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         4.14        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         8.12 
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-RD-A7C1 TCGA-RD-A8MW 
        6.44         6.74         2.53        28.90        16.67        37.91 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        8.94        35.61        37.74         5.46        13.25        13.02 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PK TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A91E 
       23.77         7.73        17.85        23.57        14.33         8.68 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-AA68 
        9.73        44.25         4.54        40.08 

$`DEL PEAK 29(11P15.5) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 
        5.62        11.70         4.64         7.43        30.90         6.18 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.12        10.13        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        7.00        39.12         0.62        32.78        13.84        13.22 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       16.14         1.25         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 
       32.94        12.82         9.21        23.93         0.69         0.16 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         0.95         0.69        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
        0.82         1.32         0.69        12.26        20.55         0.72 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.26        12.95         0.26        16.31         1.55         1.48 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        19.50         0.36         0.26        22.19         2.96 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        13.74         4.31         3.32         0.36        19.17 
TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       14.79         0.69         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 
        0.72         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 
        2.14        13.45         0.20         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         0.59        15.68         0.62        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU 
       12.56         1.15         0.66         3.02        22.26        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 
       13.51        12.89         0.79        14.17        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-5801 TCGA-CD-5803 
       13.64        11.57         5.13         2.83        13.18         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-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.13         0.13         0.10         6.35         0.13         0.13 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
        0.13         0.07         0.10         0.10         0.10        20.02 
TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 
        4.01        14.01        12.03         9.01         7.07        12.00 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       22.98        30.97         1.02         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5733 
        0.99       105.07        28.96        79.07        65.10        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
        7.99        12.36        19.13        18.61        17.85         5.95 
TCGA-D7-6526 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       17.19        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 
       16.80        19.50        17.19         0.23         6.97        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-A6F2 
       11.24        11.31        11.44         9.76         2.96        15.65 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 
        4.34         7.13         7.79        16.24         6.58        14.47 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         0.39        19.53         3.02        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB 
       59.54         5.03         0.56         1.55         0.23        18.08 
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-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        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-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-HU-A4HD 
       19.36        17.69         9.67         8.88         8.81        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RJ TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NT 
       21.21         3.45         5.36         1.41         6.87         5.56 
TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        1.81         5.56        60.56         3.72        19.73         4.31 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 
       11.05         8.61         4.67       122.30        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL 
      116.38        71.38        57.44        16.87         5.79         0.92 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       31.10        21.73        22.36        19.07        33.63        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       16.31         2.70         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K 
       19.30        64.57        59.18        28.70        11.70        49.25 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A924 
       20.81         1.71         7.36         8.58         8.61        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        6.58         5.72        29.98        21.11         4.21         0.79 

  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                          0.07                           0.07 
  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 
                        13.115                         11.145 
[1] "0.1 - 72.2 (13.1)"  "0.1 - 122.3 (11.1)"
[1] "hr=" "1.1"
D65V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 29(11P15.5) MUTATED         0        3       10       11         5
  DEL PEAK 29(11P15.5) WILD-TYPE       2       10       29       20        31
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 29(11P15.5) MUTATED           7         0         21         10
  DEL PEAK 29(11P15.5) WILD-TYPE        42         3         56         45
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 29(11P15.5) MUTATED            9        7
  DEL PEAK 29(11P15.5) WILD-TYPE         28       30
D65V3, multiclass
            clus
vv           DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              3                             10
  STAGE IB                             10                             29
  STAGE II                             11                             20
  STAGE IIA                             5                             31
  STAGE IIB                             7                             42
  STAGE III                             0                              3
  STAGE IIIA                           21                             56
  STAGE IIIB                           10                             45
  STAGE IIIC                            9                             28
  STAGE IV                              7                             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 29(11P15.5) MUTATED     5  31  33  15
  DEL PEAK 29(11P15.5) WILD-TYPE  16  56 140  89
D65V4, multiclass
    clus
vv   DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  T1                            5                             16
  T2                           31                             56
  T3                           33                            140
  T4                           15                             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
  DEL PEAK 29(11P15.5) MUTATED   23 27 16 19
  DEL PEAK 29(11P15.5) WILD-TYPE 99 80 59 60
D65V5, multiclass
    clus
vv   DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  N0                           23                             99
  N1                           27                             80
  N2                           16                             59
  N3                           19                             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"
                                vv
clus                              M0  M1  MX
  DEL PEAK 29(11P15.5) MUTATED    78   5   4
  DEL PEAK 29(11P15.5) WILD-TYPE 275  19  14
D65V6, multiclass
    clus
vv   DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  M0                           78                            275
  M1                            5                             19
  MX                            4                             14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                                cls
clus                               0   1
  DEL PEAK 29(11P15.5) MUTATED    30  57
  DEL PEAK 29(11P15.5) WILD-TYPE 121 187
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(11P15.5) MUTATED     30   57
  DEL PEAK 29(11P15.5) WILD-TYPE  121  187
        clus
vv       DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  FEMALE                           30                            121
  MALE                             57                            187
[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                                    56
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 29(11P15.5) MUTATED                                                       31
  DEL PEAK 29(11P15.5) WILD-TYPE                                                    126
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 29(11P15.5) MUTATED                                                                  16
  DEL PEAK 29(11P15.5) WILD-TYPE                                                                53
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 29(11P15.5) MUTATED                                                 19
  DEL PEAK 29(11P15.5) WILD-TYPE                                               45
                                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                                          2
  DEL PEAK 29(11P15.5) WILD-TYPE                                        7
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)                           16
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
                                                                   clus
vv                                                                  DEL PEAK 29(11P15.5) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             53
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              45
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      3
  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"
D65V9, binary
                                cls
clus                               0   1
  DEL PEAK 29(11P15.5) MUTATED     1  86
  DEL PEAK 29(11P15.5) WILD-TYPE   5 303
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(11P15.5) MUTATED      1   86
  DEL PEAK 29(11P15.5) WILD-TYPE    5  303
     clus
vv    DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  NO                             1                              5
  YES                           86                            303
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 29(11P15.5) MUTATED    66   3   7   8
  DEL PEAK 29(11P15.5) WILD-TYPE 252  13  11  17
D65V10, multiclass
    clus
vv   DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  R0                           66                            252
  R1                            3                             13
  R2                            7                             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"
D65V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 29(11P15.5) MUTATED      17                         2
  DEL PEAK 29(11P15.5) WILD-TYPE    71                         4
                                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      55
  DEL PEAK 29(11P15.5) WILD-TYPE   188
D65V12, multiclass
                                           clus
vv                                          DEL PEAK 29(11P15.5) MUTATED
  ASIAN                                                               17
  BLACK OR AFRICAN AMERICAN                                            2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               55
                                           clus
vv                                          DEL PEAK 29(11P15.5) WILD-TYPE
  ASIAN                                                                 71
  BLACK OR AFRICAN AMERICAN                                              4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                188
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(66) Variable = DEL PEAK 30(11Q23.2) MUTATION ANALYSIS
D66V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(11Q23.2) MUTATED    47  32
  DEL PEAK 30(11Q23.2) WILD-TYPE 195  90
  DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE 
                            79                            285 
  DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE 
                            32                             90 
$`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        10.13         0.82 
TCGA-BR-6709 TCGA-BR-7722 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8289 
        1.25         0.16        17.49         1.32         0.49         0.26 
TCGA-BR-8297 TCGA-BR-8365 TCGA-BR-8486 TCGA-BR-8687 TCGA-BR-A4CQ TCGA-BR-A4CS 
        7.40         2.96        20.22         0.62        22.26         0.92 
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         0.13         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         1.02         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         4.14 
TCGA-D7-6815 TCGA-D7-8575 TCGA-D7-A4YT TCGA-D7-A6EZ TCGA-D7-A74A TCGA-EQ-5647 
       15.98         0.23        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 
        3.02        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-IP-7968 
       17.69         9.67         1.41         6.44         5.56         2.53 
TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8P5 
      115.69         8.94         0.92        37.74        13.25         7.73 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PU TCGA-VQ-A91A TCGA-VQ-A91Q TCGA-VQ-A91Z 
        2.70        17.85        23.57        28.70        20.81        44.25 
TCGA-VQ-A922 
        8.61 

$`DEL PEAK 30(11Q23.2) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
        5.62        11.70         6.61         4.64         7.43        30.90 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        6.61        34.68        15.95        13.12        13.68         7.00 
TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12         0.62        32.78        13.84        13.22        16.14 
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-7716 
        9.21        24.76        35.24        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
        0.69        18.54        12.43         0.95         0.69        12.76 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       18.71         0.82         0.69        12.26        20.55         0.72 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 
        0.26        12.95        16.31         1.55         1.48         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.36         0.26        22.19         0.95        13.74 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32         0.36        19.17        14.79 
TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
        0.69         0.26        15.85         3.72         5.39         0.72 
TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21         1.12        12.79        15.81         2.14        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        0.20         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
        0.59        15.68        10.68        12.56         1.15         0.66 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        3.02        13.41        13.51        12.89         0.79        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-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5803 
       20.42        11.57         5.13         2.83        13.18         0.07 
TCGA-CD-8524 TCGA-CD-8525 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-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.13         0.13         0.10         6.35         0.13         0.13 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
        0.13         0.07         0.10         0.10         0.10        20.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         7.99        54.08         4.01        14.01 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       47.05        19.07        21.99         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 
       12.00        22.98        30.97         6.97         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-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 
       55.04        21.07         7.99        12.36        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 
       18.84        18.61        17.85         5.95        17.19        15.22 
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-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU 
       19.50        17.19         6.97        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-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74B 
       11.31        11.44         2.96        15.65         4.34         7.13 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.79        16.24         6.58        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
        8.12         0.39        19.53        22.29        59.54         5.03 
TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
        1.55        18.08         1.51         5.92        14.27        12.59 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       11.41        12.10        10.62        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       11.84        24.20        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-A4H2 
        0.10         6.51         6.25        10.19         0.26        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       19.36        12.30         8.88         8.81        27.42        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-A6RR TCGA-IN-A6RS TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 
       13.08         6.74         6.87         1.81         5.56        60.56 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT 
       28.90         3.72        19.73         4.31        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 
        4.67        16.67       122.30        37.91        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DU 
       71.38        57.44        35.61        16.87         5.79         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       13.02        31.10        21.73        22.36        23.77        19.07 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       33.63        46.26        16.31         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D 
       15.65        19.30        64.57        14.33        59.18        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
        8.68        49.25         1.71         7.36         8.58         9.73 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B 
       55.43         4.54         6.58         5.72        40.08        29.98 
TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11         4.21         0.79 

  DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE 
                          0.07                           0.07 
  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 
                          7.73                          12.30 
[1] "0.1 - 115.7 (7.7)"  "0.1 - 122.3 (12.3)"
[1] "hr=" "1.7"
D66V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 30(11Q23.2) MUTATED         1        5        5       10         7
  DEL PEAK 30(11Q23.2) WILD-TYPE       1        8       34       21        29
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 30(11Q23.2) MUTATED           7         0         19         10
  DEL PEAK 30(11Q23.2) WILD-TYPE        42         3         58         45
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 30(11Q23.2) MUTATED            8       11
  DEL PEAK 30(11Q23.2) WILD-TYPE         29       26
D66V3, multiclass
            clus
vv           DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                              5                              8
  STAGE IB                              5                             34
  STAGE II                             10                             21
  STAGE IIA                             7                             29
  STAGE IIB                             7                             42
  STAGE III                             0                              3
  STAGE IIIA                           19                             58
  STAGE IIIB                           10                             45
  STAGE IIIC                            8                             29
  STAGE IV                             11                             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 30(11Q23.2) MUTATED     7  20  36  21
  DEL PEAK 30(11Q23.2) WILD-TYPE  14  67 137  83
D66V4, multiclass
    clus
vv   DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE
  T1                            7                             14
  T2                           20                             67
  T3                           36                            137
  T4                           21                             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 30(11Q23.2) MUTATED   23 21 22 18
  DEL PEAK 30(11Q23.2) WILD-TYPE 99 86 53 61
D66V5, multiclass
    clus
vv   DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE
  N0                           23                             99
  N1                           21                             86
  N2                           22                             53
  N3                           18                             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                              M0  M1  MX
  DEL PEAK 30(11Q23.2) MUTATED    69   8   8
  DEL PEAK 30(11Q23.2) WILD-TYPE 284  16  10
D66V6, multiclass
    clus
vv   DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE
  M0                           69                            284
  M1                            8                             16
  MX                            8                             10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(11Q23.2) MUTATED    29  56
  DEL PEAK 30(11Q23.2) WILD-TYPE 122 188
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11Q23.2) MUTATED     29   56
  DEL PEAK 30(11Q23.2) WILD-TYPE  122  188
        clus
vv       DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE
  FEMALE                           29                            122
  MALE                             56                            188
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 30(11Q23.2) MUTATED                                       9
  DEL PEAK 30(11Q23.2) WILD-TYPE                                    56
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 30(11Q23.2) MUTATED                                                       33
  DEL PEAK 30(11Q23.2) WILD-TYPE                                                    124
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 30(11Q23.2) MUTATED                                                                  15
  DEL PEAK 30(11Q23.2) WILD-TYPE                                                                54
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 30(11Q23.2) MUTATED                                                 18
  DEL PEAK 30(11Q23.2) WILD-TYPE                                               46
                                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                                          2
  DEL PEAK 30(11Q23.2) WILD-TYPE                                        7
D66V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 30(11Q23.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      33
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           15
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
                                                                   clus
vv                                                                  DEL PEAK 30(11Q23.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             54
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              46
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      15
  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"
D66V9, binary
                                cls
clus                               0   1
  DEL PEAK 30(11Q23.2) MUTATED     1  84
  DEL PEAK 30(11Q23.2) WILD-TYPE   5 305
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11Q23.2) MUTATED      1   84
  DEL PEAK 30(11Q23.2) WILD-TYPE    5  305
     clus
vv    DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE
  NO                             1                              5
  YES                           84                            305
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 30(11Q23.2) MUTATED    65   6   5   5
  DEL PEAK 30(11Q23.2) WILD-TYPE 253  10  13  20
D66V10, multiclass
    clus
vv   DEL PEAK 30(11Q23.2) MUTATED DEL PEAK 30(11Q23.2) WILD-TYPE
  R0                           65                            253
  R1                            6                             10
  R2                            5                             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"
D66V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 30(11Q23.2) MUTATED      19                         0
  DEL PEAK 30(11Q23.2) WILD-TYPE    69                         6
                                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      50
  DEL PEAK 30(11Q23.2) WILD-TYPE   193
D66V12, multiclass
                                           clus
vv                                          DEL PEAK 30(11Q23.2) MUTATED
  ASIAN                                                               19
  BLACK OR AFRICAN AMERICAN                                            0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               50
                                           clus
vv                                          DEL PEAK 30(11Q23.2) WILD-TYPE
  ASIAN                                                                 69
  BLACK OR AFRICAN AMERICAN                                              6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  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"

Clustering(67) Variable = DEL PEAK 31(12P13.1) MUTATION ANALYSIS
D67V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(12P13.1) MUTATED    34  27
  DEL PEAK 31(12P13.1) WILD-TYPE 208  95
  DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE 
                            61                            303 
  DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE 
                            27                             95 
$`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        10.13         7.00         1.25        35.24 
TCGA-BR-7715 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8289 TCGA-BR-8362 TCGA-BR-8369 
       15.42         0.95         1.32         0.26         0.36        14.04 
TCGA-BR-8483 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-A4CQ TCGA-CD-5800 TCGA-CD-8524 
        5.39        11.54         0.59        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         6.35         0.13         0.13         0.10 
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        55.04 
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         7.79        72.23        12.59        17.69        12.30 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A7NU TCGA-IP-7968 TCGA-RD-A8MW 
        3.39        18.38         5.19         1.81         2.53        37.91 
TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8P3 TCGA-VQ-A8PJ TCGA-VQ-A8PM 
       35.61         5.46        13.02        23.77         2.70         1.87 
TCGA-VQ-A8PY TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A928 
       14.33         1.71         8.58        44.25         8.61         5.72 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK 31(12P13.1) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         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        13.12 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.68        39.12         0.82         0.62        32.78        13.84 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       13.22        16.14         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-7957 TCGA-BR-7958 
        0.69         0.16        18.54        12.43         0.69        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49         0.82         0.69        12.26         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 
       20.55         0.72         0.26        12.95        16.31         1.55 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        1.48         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
        2.96         0.95        13.74         4.31         3.32         0.36 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       19.17        14.79         0.69         0.26        15.85         3.72 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        0.72         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-8680 
        2.14        13.45         0.20         7.53         0.49        15.81 
TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       16.44        15.68         0.62        10.68        12.56         1.15 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        0.66         3.02         0.92        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        0.79         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-5801 
       13.64        11.57         5.13         2.83         3.25        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 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-8536 TCGA-CD-A487 
        0.16         0.10         0.10         0.13         0.10         0.13 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 
        0.13         0.07         0.10         0.10        20.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 
       15.95         1.02         8.05        54.08         4.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03        21.99         9.01        18.97 
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         1.02         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-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-D7-6520 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-D7-6818 
       17.85         5.95        17.19         4.14        15.98        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         0.23 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
        6.97        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-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-A4SO 
        9.76         2.96        15.65         4.34         7.13        16.24 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        6.58        14.47        21.27         8.12         0.39        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        3.02        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         1.55         0.23        18.08        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        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-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
        2.10        12.95        19.36         9.67         8.88         8.81 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RN 
       27.42        21.21         3.45        18.81         5.36        13.08 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-KB-A6F5 
        1.41         6.44         6.74         6.87         5.56         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS 
       60.56        28.90         3.72        19.73         4.31        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 
        8.61         4.67        16.67       122.30        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EB 
      116.38        71.38        57.44         8.94        16.87         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 
        0.92        37.74        13.25        31.10        21.73        22.36 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PK 
        7.73        19.07        33.63        46.26        16.31        17.85 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX 
        9.27        23.41        15.65        19.30        23.57        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q 
       59.18        28.70        11.70         8.68        49.25        20.81 
TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-AA68 
        7.36         9.73        55.43         4.54         6.58        40.08 
TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 
       29.98        21.11         4.21 

  DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE 
                          0.07                           0.07 
  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 
                          7.79                          12.00 
[1] "0.1 - 72.2 (7.8)"   "0.1 - 122.3 (12.0)"
[1] "hr=" "1.7"
D67V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 31(12P13.1) MUTATED         0        1       10        5         6
  DEL PEAK 31(12P13.1) WILD-TYPE       2       12       29       26        30
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 31(12P13.1) MUTATED           7         0         15          8
  DEL PEAK 31(12P13.1) WILD-TYPE        42         3         62         47
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 31(12P13.1) MUTATED            3        9
  DEL PEAK 31(12P13.1) WILD-TYPE         34       28
D67V3, multiclass
            clus
vv           DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              1                             12
  STAGE IB                             10                             29
  STAGE II                              5                             26
  STAGE IIA                             6                             30
  STAGE IIB                             7                             42
  STAGE III                             0                              3
  STAGE IIIA                           15                             62
  STAGE IIIB                            8                             47
  STAGE IIIC                            3                             34
  STAGE IV                              9                             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 31(12P13.1) MUTATED     1  21  30  12
  DEL PEAK 31(12P13.1) WILD-TYPE  20  66 143  92
D67V4, multiclass
    clus
vv   DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE
  T1                            1                             20
  T2                           21                             66
  T3                           30                            143
  T4                           12                             92
[1] 4 2
[1] TRUE
[1] "dimension of 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    20  18  13  13
  DEL PEAK 31(12P13.1) WILD-TYPE 102  89  62  66
D67V5, multiclass
    clus
vv   DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE
  N0                           20                            102
  N1                           18                             89
  N2                           13                             62
  N3                           13                             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"
                                vv
clus                              M0  M1  MX
  DEL PEAK 31(12P13.1) MUTATED    57   5   4
  DEL PEAK 31(12P13.1) WILD-TYPE 296  19  14
D67V6, multiclass
    clus
vv   DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE
  M0                           57                            296
  M1                            5                             19
  MX                            4                             14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                                cls
clus                               0   1
  DEL PEAK 31(12P13.1) MUTATED    26  40
  DEL PEAK 31(12P13.1) WILD-TYPE 125 204
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(12P13.1) MUTATED     26   40
  DEL PEAK 31(12P13.1) WILD-TYPE  125  204
        clus
vv       DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE
  FEMALE                           26                            125
  MALE                             40                            204
[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                                    62
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 31(12P13.1) MUTATED                                                       30
  DEL PEAK 31(12P13.1) WILD-TYPE                                                    127
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 31(12P13.1) MUTATED                                                                  13
  DEL PEAK 31(12P13.1) WILD-TYPE                                                                56
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 31(12P13.1) MUTATED                                                 14
  DEL PEAK 31(12P13.1) WILD-TYPE                                               50
                                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                                        7
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)                           13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            14
  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                                                         62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             56
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              50
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      21
  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"
D67V9, binary
                                cls
clus                               0   1
  DEL PEAK 31(12P13.1) MUTATED     3  63
  DEL PEAK 31(12P13.1) WILD-TYPE   3 326
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(12P13.1) MUTATED      3   63
  DEL PEAK 31(12P13.1) WILD-TYPE    3  326
     clus
vv    DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE
  NO                             3                              3
  YES                           63                            326
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 31(12P13.1) MUTATED    50   2   4   5
  DEL PEAK 31(12P13.1) WILD-TYPE 268  14  14  20
D67V10, multiclass
    clus
vv   DEL PEAK 31(12P13.1) MUTATED DEL PEAK 31(12P13.1) WILD-TYPE
  R0                           50                            268
  R1                            2                             14
  R2                            4                             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"
D67V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 31(12P13.1) MUTATED      14                         2
  DEL PEAK 31(12P13.1) WILD-TYPE    74                         4
                                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      40
  DEL PEAK 31(12P13.1) WILD-TYPE   203
D67V12, multiclass
                                           clus
vv                                          DEL PEAK 31(12P13.1) MUTATED
  ASIAN                                                               14
  BLACK OR AFRICAN AMERICAN                                            2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               40
                                           clus
vv                                          DEL PEAK 31(12P13.1) WILD-TYPE
  ASIAN                                                                 74
  BLACK OR AFRICAN AMERICAN                                              4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                203
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(68) Variable = DEL PEAK 32(12Q12) MUTATION ANALYSIS
D68V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 32(12Q12) MUTATED    31  18
  DEL PEAK 32(12Q12) WILD-TYPE 211 104
  DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE 
                          49                          315 
  DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE 
                          18                          104 
$`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        10.13        24.76        35.24        15.42         0.69 
TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8483 TCGA-BR-8682 TCGA-BR-8683 
        0.95         1.32        12.95         5.39        16.44         0.59 
TCGA-BR-8687 TCGA-BR-A4J6 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5802 
        0.62         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 
        0.13         0.13         0.10        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         5.95        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 
        7.79         8.12        13.58        11.77        12.95        12.30 
TCGA-IN-7806 TCGA-KB-A93H TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DZ 
       21.21        28.90        35.61         5.79         5.46        13.02 
TCGA-VQ-A8PK TCGA-VQ-A8PU TCGA-VQ-A91Q TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-AA68 
       17.85        23.57        20.81        44.25         8.61        40.08 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK 32(12Q12) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         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-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.12        13.68         7.00        39.12         0.82         0.62 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        13.84        13.22        16.14         1.25         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-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 
       23.93        28.01         0.16        18.54        12.43         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        17.49         0.82         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 
        0.49        20.55         0.72         0.26         0.26        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        1.55         1.48         7.40         6.18        19.50         0.36 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19         2.96         0.95        13.74         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 
       14.04         3.32         0.36        19.17        14.79         0.69 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        0.26        15.85         3.72         0.72         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         2.14        13.45         0.20 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8690 
        7.53         0.49        11.54        15.81        15.68        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56         1.15         0.66         3.02        22.26         0.92 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         0.79         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-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       20.42        11.57         5.13         3.25        13.15        13.18 
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-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-A48C TCGA-CD-A4MG TCGA-CD-A4MI 
        0.10         6.35         0.13         0.13         0.07         0.10 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
        0.10         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-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-5720 
       22.98        30.97         6.97         1.02         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        55.04        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-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.85        17.19         4.14        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-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
        0.23         6.97        21.14        20.91        14.27        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-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.44         9.76         2.96         4.34         7.40         7.13 
TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
       16.24         6.58        14.47        72.23        21.27         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53         3.02        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         1.55         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-A4GJ TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
        2.10        19.36        17.69         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         6.87 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG 
        5.56         1.81         2.53         5.56        60.56         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
       19.73         4.31        11.05         8.61         4.67        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV 
       57.44         8.94        16.87         0.92        37.74        13.25 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       31.10        21.73        22.36        23.77         7.73        19.07 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO 
       33.63        46.26        16.31         2.70         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       23.41        15.65        19.30        64.57        14.33        59.18 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91W 
       28.70        11.70         8.68        49.25         1.71         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        8.58         9.73        55.43         4.54         6.58         5.72 
TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 
       29.98        21.11         4.21 

  DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE 
                        0.10                         0.07 
  DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE 
                       44.25                       122.30 
  DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE 
                       11.77                        11.57 
[1] "0.1 - 44.2 (11.8)"  "0.1 - 122.3 (11.6)"
[1] "hr=" "1.2"
D68V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 32(12Q12) MUTATED         0        2        6        5         7
  DEL PEAK 32(12Q12) WILD-TYPE       2       11       33       26        29
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 32(12Q12) MUTATED           8         0          6          7
  DEL PEAK 32(12Q12) WILD-TYPE        41         3         71         48
                              vv
clus                           STAGE IIIC STAGE IV
  DEL PEAK 32(12Q12) MUTATED            4        5
  DEL PEAK 32(12Q12) WILD-TYPE         33       32
D68V3, multiclass
            clus
vv           DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE
  STAGE I                             0                            2
  STAGE IA                            2                           11
  STAGE IB                            6                           33
  STAGE II                            5                           26
  STAGE IIA                           7                           29
  STAGE IIB                           8                           41
  STAGE III                           0                            3
  STAGE IIIA                          6                           71
  STAGE IIIB                          7                           48
  STAGE IIIC                          4                           33
  STAGE IV                            5                           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 32(12Q12) MUTATED     2  10  26  12
  DEL PEAK 32(12Q12) WILD-TYPE  19  77 147  92
D68V4, multiclass
    clus
vv   DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE
  T1                          2                           19
  T2                         10                           77
  T3                         26                          147
  T4                         12                           92
[1] 4 2
[1] TRUE
[1] "dimension of 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  12   9   9
  DEL PEAK 32(12Q12) WILD-TYPE 102  95  66  70
D68V5, multiclass
    clus
vv   DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE
  N0                         20                          102
  N1                         12                           95
  N2                          9                           66
  N3                          9                           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                            M0  M1  MX
  DEL PEAK 32(12Q12) MUTATED    46   2   3
  DEL PEAK 32(12Q12) WILD-TYPE 307  22  15
D68V6, multiclass
    clus
vv   DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE
  M0                         46                          307
  M1                          2                           22
  MX                          3                           15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V7, binary
                              cls
clus                             0   1
  DEL PEAK 32(12Q12) MUTATED    19  32
  DEL PEAK 32(12Q12) WILD-TYPE 132 212
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(12Q12) MUTATED     19   32
  DEL PEAK 32(12Q12) WILD-TYPE  132  212
        clus
vv       DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE
  FEMALE                         19                          132
  MALE                           32                          212
[1] 2 2
[1] FALSE
                              vv
clus                           STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 32(12Q12) MUTATED                                       6
  DEL PEAK 32(12Q12) WILD-TYPE                                    59
                              vv
clus                           STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 32(12Q12) MUTATED                                                       20
  DEL PEAK 32(12Q12) WILD-TYPE                                                    137
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 32(12Q12) MUTATED                                                                   6
  DEL PEAK 32(12Q12) WILD-TYPE                                                                63
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 32(12Q12) MUTATED                                                 13
  DEL PEAK 32(12Q12) WILD-TYPE                                               51
                              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                                          1
  DEL PEAK 32(12Q12) WILD-TYPE                                        8
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)                          6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                          13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                  2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   1
                                                                   clus
vv                                                                  DEL PEAK 32(12Q12) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     137
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           63
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            51
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    18
  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"
D68V9, binary
                              cls
clus                             0   1
  DEL PEAK 32(12Q12) MUTATED     0  51
  DEL PEAK 32(12Q12) WILD-TYPE   6 338
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(12Q12) MUTATED      0   51
  DEL PEAK 32(12Q12) WILD-TYPE    6  338
     clus
vv    DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE
  NO                           0                            6
  YES                         51                          338
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 32(12Q12) MUTATED    39   2   2   2
  DEL PEAK 32(12Q12) WILD-TYPE 279  14  16  23
D68V10, multiclass
    clus
vv   DEL PEAK 32(12Q12) MUTATED DEL PEAK 32(12Q12) WILD-TYPE
  R0                         39                          279
  R1                          2                           14
  R2                          2                           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"
D68V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 32(12Q12) MUTATED      13                         1
  DEL PEAK 32(12Q12) WILD-TYPE    75                         5
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 32(12Q12) MUTATED                                           0    31
  DEL PEAK 32(12Q12) WILD-TYPE                                         1   212
D68V12, multiclass
                                           clus
vv                                          DEL PEAK 32(12Q12) MUTATED
  ASIAN                                                             13
  BLACK OR AFRICAN AMERICAN                                          1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          0
  WHITE                                                             31
                                           clus
vv                                          DEL PEAK 32(12Q12) WILD-TYPE
  ASIAN                                                               75
  BLACK OR AFRICAN AMERICAN                                            5
  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"

Clustering(69) Variable = DEL PEAK 33(13Q12.11) MUTATION ANALYSIS
D69V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 33(13Q12.11) MUTATED    27  23
  DEL PEAK 33(13Q12.11) WILD-TYPE 215  99
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                             50                             314 
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                             23                              99 
$`DEL PEAK 33(13Q12.11) MUTATED`
TCGA-BR-4184 TCGA-BR-6456 TCGA-BR-6564 TCGA-BR-6709 TCGA-BR-7715 TCGA-BR-7716 
        6.97        10.13         0.82         1.25        15.42        28.01 
TCGA-BR-7959 TCGA-BR-8289 TCGA-BR-8297 TCGA-BR-8683 TCGA-BR-A4CS TCGA-BR-A4IY 
       18.71         0.26         7.40         0.59         0.92        12.89 
TCGA-BR-A4J6 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-A486 TCGA-CG-4444 TCGA-CG-4466 
        0.66         0.07         0.07         6.35        47.05        18.97 
TCGA-CG-4475 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5727 TCGA-D7-5579 TCGA-D7-6525 
       22.98        12.03        15.02        79.07        11.93         5.95 
TCGA-D7-6527 TCGA-D7-6818 TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A6F2 TCGA-FP-7916 
        4.14        10.55         0.23        16.44        15.65         3.02 
TCGA-HU-8243 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H2 
        5.92         3.25        25.81        11.77         6.25        12.95 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RR TCGA-RD-A7BS 
       18.81         3.39         5.36         5.19         6.74        11.05 
TCGA-RD-A8N1 TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8P5 TCGA-VQ-A8PM TCGA-VQ-A91A 
      115.69        13.25        13.02         7.73         1.87        28.70 
TCGA-VQ-A91Q TCGA-VQ-A925 
       20.81         4.54 

$`DEL PEAK 33(13Q12.11) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.61         4.64         7.43        18.35 
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-6565 TCGA-BR-6566 
       13.12        13.68         7.00        39.12         0.62        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       13.84        13.22        16.14         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-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       23.93         0.69         0.16        18.54        12.43         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69        12.76        17.49         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       12.26         0.49        20.55         0.72         0.26        12.95 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       16.31         1.55         1.48         6.18        19.50         0.36 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19         2.96         0.95        13.74         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 
       14.04         3.32         0.36        19.17        14.79         0.69 
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         0.72         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         2.14        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        0.20         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         0.62        10.68        12.56         1.15         0.66 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 
        3.02        22.26        13.41        13.51         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
       14.17         0.53        12.82        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-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-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-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.13         0.10         0.13         0.13 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.13         0.13         0.07         0.10         0.10         0.10 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
       12.03        21.99         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         1.02         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
      105.07        28.96        65.10         4.01        55.04        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-D7-6526 TCGA-D7-6528 TCGA-D7-6815 
       18.54        18.61        17.85        17.19        15.22        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-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       17.19         6.97        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-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-A74A TCGA-D7-A74B 
       11.44         9.76         2.96         4.34         7.40         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        0.62         7.79        16.24         6.58        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 
       21.27         8.12         0.39        19.53        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         1.55         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
       18.08        26.47         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-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GJ TCGA-HU-A4GN 
       12.30        11.84        24.20        22.75        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        10.19         0.26         2.10 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       19.36        17.69        12.30         9.67         8.88         8.81 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RN TCGA-IN-A6RO 
       27.42        21.21         3.45        18.38        13.08         1.41 
TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 
        6.44         6.87         5.56         1.81         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BT 
       60.56        28.90         3.72        19.73         4.31         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 
        4.67        16.67       122.30        37.91        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        16.87         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 
        0.92        37.74         5.46        31.10        21.73        22.36 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ 
       23.77        19.07        33.63        46.26        16.31         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU 
       17.85         9.27        23.41        15.65        19.30        23.57 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       64.57        14.33        59.18        11.70         8.68        49.25 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
        1.71         7.36         8.58         9.73        44.25         8.61 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J 
       55.43         6.58         5.72        40.08        29.98        21.11 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        4.21         0.79 

  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                           0.07                            0.07 
  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 
                           8.93                           11.92 
[1] "0.1 - 115.7 (8.9)"  "0.1 - 122.3 (11.9)"
[1] "hr=" "1.6"
D69V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 33(13Q12.11) MUTATED         0        1        7        3         6
  DEL PEAK 33(13Q12.11) WILD-TYPE       2       12       32       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        42         3         63         48
                                 vv
clus                              STAGE IIIC STAGE IV
  DEL PEAK 33(13Q12.11) MUTATED            4        6
  DEL PEAK 33(13Q12.11) WILD-TYPE         33       31
D69V3, multiclass
            clus
vv           DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  STAGE I                                0                               2
  STAGE IA                               1                              12
  STAGE IB                               7                              32
  STAGE II                               3                              28
  STAGE IIA                              6                              30
  STAGE IIB                              7                              42
  STAGE III                              0                               3
  STAGE IIIA                            14                              63
  STAGE IIIB                             7                              48
  STAGE IIIC                             4                              33
  STAGE IV                               6                              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 33(13Q12.11) MUTATED     2  16  27  11
  DEL PEAK 33(13Q12.11) WILD-TYPE  19  71 146  93
D69V4, multiclass
    clus
vv   DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  T1                             2                              19
  T2                            16                              71
  T3                            27                             146
  T4                            11                              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 33(13Q12.11) MUTATED    16  15  10  15
  DEL PEAK 33(13Q12.11) WILD-TYPE 106  92  65  64
D69V5, multiclass
    clus
vv   DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  N0                            16                             106
  N1                            15                              92
  N2                            10                              65
  N3                            15                              64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1  MX
  DEL PEAK 33(13Q12.11) MUTATED    51   3   3
  DEL PEAK 33(13Q12.11) WILD-TYPE 302  21  15
D69V6, multiclass
    clus
vv   DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  M0                            51                             302
  M1                             3                              21
  MX                             3                              15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V7, binary
                                 cls
clus                                0   1
  DEL PEAK 33(13Q12.11) MUTATED    13  44
  DEL PEAK 33(13Q12.11) WILD-TYPE 138 200
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q12.11) MUTATED     13   44
  DEL PEAK 33(13Q12.11) WILD-TYPE  138  200
        clus
vv       DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  FEMALE                            13                             138
  MALE                              44                             200
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 33(13Q12.11) MUTATED                                      11
  DEL PEAK 33(13Q12.11) WILD-TYPE                                    54
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 33(13Q12.11) MUTATED                                                       20
  DEL PEAK 33(13Q12.11) WILD-TYPE                                                    137
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 33(13Q12.11) MUTATED                                                                   7
  DEL PEAK 33(13Q12.11) WILD-TYPE                                                                62
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 33(13Q12.11) MUTATED                                                 11
  DEL PEAK 33(13Q12.11) WILD-TYPE                                               53
                                 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                                        7
D69V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 33(13Q12.11) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        11
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       20
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             11
  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                                                          54
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        137
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              62
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               53
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       7
  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"
D69V9, binary
                                 cls
clus                                0   1
  DEL PEAK 33(13Q12.11) MUTATED     3  54
  DEL PEAK 33(13Q12.11) WILD-TYPE   3 335
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q12.11) MUTATED      3   54
  DEL PEAK 33(13Q12.11) WILD-TYPE    3  335
     clus
vv    DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  NO                              3                               3
  YES                            54                             335
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 33(13Q12.11) MUTATED    44   4   3   4
  DEL PEAK 33(13Q12.11) WILD-TYPE 274  12  15  21
D69V10, multiclass
    clus
vv   DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  R0                            44                             274
  R1                             4                              12
  R2                             3                              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"
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                         5
                                 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      35
  DEL PEAK 33(13Q12.11) WILD-TYPE   208
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                                                                35
                                           clus
vv                                          DEL PEAK 33(13Q12.11) WILD-TYPE
  ASIAN                                                                  76
  BLACK OR AFRICAN AMERICAN                                               5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 208
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(70) Variable = DEL PEAK 34(14Q23.3) MUTATION ANALYSIS
D70V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 34(14Q23.3) MUTATED    72  40
  DEL PEAK 34(14Q23.3) WILD-TYPE 170  82
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                           112                            252 
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                            40                             82 
$`DEL PEAK 34(14Q23.3) MUTATED`
TCGA-BR-4183 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 
        6.61         9.57        10.13         7.00         0.82         0.62 
TCGA-BR-6803 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7959 
       31.20        35.24        15.42        28.01        18.54        18.71 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8361 TCGA-BR-8373 
       17.49         1.32        12.95         0.26        19.50        14.79 
TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8589 TCGA-BR-8678 
        0.26         5.39         0.72         9.21        15.81        11.54 
TCGA-BR-8686 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 
       15.68         0.66        22.26         0.92         0.72         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5801 TCGA-CD-5803 
       19.36         0.46        20.65         1.15        13.18         0.07 
TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A4MH 
        0.07         0.07         0.13         0.13         0.13         0.10 
TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       20.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5725 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       18.97        30.97        15.02        20.55        18.84        18.54 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-8576 TCGA-D7-A4YU 
        5.95        17.19         4.14        15.98         6.97        16.44 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-A72C 
       11.31        11.44         2.96         7.79        16.24         8.12 
TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8249 
        3.02        17.06         0.56        26.47        12.59        14.17 
TCGA-HU-A4G3 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H5 
        5.59         3.25        11.77         8.98         2.10        12.30 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       27.42        21.21         5.19        13.08         6.44         6.74 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-RD-A7C1 TCGA-RD-A8MV 
        1.81         2.53         5.56        28.90        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV 
       37.91       115.69         8.94         0.92         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PJ 
       13.02        31.10        23.77         7.73        46.26         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91Q 
       17.85        23.57        64.57        14.33        59.18        20.81 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-AA6B TCGA-ZQ-A9CR 
       44.25         8.61        29.98         0.79 

$`DEL PEAK 34(14Q23.3) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         6.61        34.68        15.95        13.12 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       13.68        39.12        32.78        13.84        13.22        16.14 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 
        1.25         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-7851 
        9.21        24.76        23.93         0.69         0.16        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
        0.95         0.69        12.76         0.82         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 
        0.49        20.55         0.72         0.26        16.31         1.55 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        1.48         7.40         6.18         0.36         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
        2.96         0.95        13.74         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8486 
        0.36        19.17         0.69        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         2.14        13.45         0.20         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         0.59         0.62        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       12.56         1.15         3.02        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4PE 
        0.79        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         6.35         0.13         0.13 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
        0.13         0.07         0.10         0.10         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-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 
       21.99         9.01         7.07        12.00        22.98         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        1.02         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        55.04 
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-D7-6522 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-D7-6822 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         0.23 
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-A6EZ TCGA-D7-A6F2 TCGA-D7-A748 
       14.76        13.71        11.24         9.76        15.65         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        7.40         7.13         0.62         6.58        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
       21.27         0.39        19.53        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 
       13.58         1.55         0.23        18.08         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.27        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       12.30        11.84        24.20        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        19.36        17.69         9.67         8.88         8.81 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RO 
        3.45        18.81         3.39        18.38         5.36         1.41 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        6.87         5.56        60.56         3.72        19.73         4.31 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
       11.05         8.61         4.67        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8E3 
       57.44        35.61        16.87         5.79        37.74        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PO 
       22.36        19.07        33.63        16.31         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       23.41        15.65        19.30        28.70        11.70         8.68 
TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A924 
       49.25         1.71         7.36         8.58         9.73        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6J TCGA-ZA-A8F6 
        4.54         6.58         5.72        40.08        21.11         4.21 

  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                          0.07                           0.07 
  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 
                        11.655                         11.635 
[1] "0.1 - 122.3 (11.7)" "0.1 - 116.4 (11.6)"
[1] "hr=" "1.1"
D70V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 34(14Q23.3) MUTATED         0        2       11       11        13
  DEL PEAK 34(14Q23.3) WILD-TYPE       2       11       28       20        23
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 34(14Q23.3) MUTATED          13         0         30         20
  DEL PEAK 34(14Q23.3) WILD-TYPE        36         3         47         35
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 34(14Q23.3) MUTATED            9        7
  DEL PEAK 34(14Q23.3) WILD-TYPE         28       30
D70V3, multiclass
            clus
vv           DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              2                             11
  STAGE IB                             11                             28
  STAGE II                             11                             20
  STAGE IIA                            13                             23
  STAGE IIB                            13                             36
  STAGE III                             0                              3
  STAGE IIIA                           30                             47
  STAGE IIIB                           20                             35
  STAGE IIIC                            9                             28
  STAGE IV                              7                             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 34(14Q23.3) MUTATED     4  26  58  28
  DEL PEAK 34(14Q23.3) WILD-TYPE  17  61 115  76
D70V4, multiclass
    clus
vv   DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  T1                            4                             17
  T2                           26                             61
  T3                           58                            115
  T4                           28                             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 34(14Q23.3) MUTATED   34 34 31 17
  DEL PEAK 34(14Q23.3) WILD-TYPE 88 73 44 62
D70V5, multiclass
    clus
vv   DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  N0                           34                             88
  N1                           34                             73
  N2                           31                             44
  N3                           17                             62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  DEL PEAK 34(14Q23.3) MUTATED   107   4   9
  DEL PEAK 34(14Q23.3) WILD-TYPE 246  20   9
D70V6, multiclass
    clus
vv   DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  M0                          107                            246
  M1                            4                             20
  MX                            9                              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V7, binary
                                cls
clus                               0   1
  DEL PEAK 34(14Q23.3) MUTATED    43  77
  DEL PEAK 34(14Q23.3) WILD-TYPE 108 167
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q23.3) MUTATED     43   77
  DEL PEAK 34(14Q23.3) WILD-TYPE  108  167
        clus
vv       DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  FEMALE                           43                            108
  MALE                             77                            167
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 34(14Q23.3) MUTATED                                      14
  DEL PEAK 34(14Q23.3) WILD-TYPE                                    51
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 34(14Q23.3) MUTATED                                                       47
  DEL PEAK 34(14Q23.3) WILD-TYPE                                                    110
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 34(14Q23.3) MUTATED                                                                  26
  DEL PEAK 34(14Q23.3) WILD-TYPE                                                                43
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 34(14Q23.3) MUTATED                                                 24
  DEL PEAK 34(14Q23.3) WILD-TYPE                                               40
                                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                                          4
  DEL PEAK 34(14Q23.3) WILD-TYPE                                        5
D70V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 34(14Q23.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       14
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      47
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           26
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            24
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     4
                                                                   clus
vv                                                                  DEL PEAK 34(14Q23.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         51
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       110
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             43
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              40
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      5
  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"
D70V9, binary
                                cls
clus                               0   1
  DEL PEAK 34(14Q23.3) MUTATED     1 119
  DEL PEAK 34(14Q23.3) WILD-TYPE   5 270
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q23.3) MUTATED      1  119
  DEL PEAK 34(14Q23.3) WILD-TYPE    5  270
     clus
vv    DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  NO                             1                              5
  YES                          119                            270
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 34(14Q23.3) MUTATED   104   1   3   7
  DEL PEAK 34(14Q23.3) WILD-TYPE 214  15  15  18
D70V10, multiclass
    clus
vv   DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  R0                          104                            214
  R1                            1                             15
  R2                            3                             15
  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                         1
  DEL PEAK 34(14Q23.3) WILD-TYPE    62                         5
                                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      78
  DEL PEAK 34(14Q23.3) WILD-TYPE   165
D70V12, multiclass
                                           clus
vv                                          DEL PEAK 34(14Q23.3) MUTATED
  ASIAN                                                               26
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               78
                                           clus
vv                                          DEL PEAK 34(14Q23.3) WILD-TYPE
  ASIAN                                                                 62
  BLACK OR AFRICAN AMERICAN                                              5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(71) Variable = DEL PEAK 35(14Q32.32) MUTATION ANALYSIS
D71V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 35(14Q32.32) MUTATED    75  36
  DEL PEAK 35(14Q32.32) WILD-TYPE 167  86
  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                            111                             253 
  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                             36                              86 
$`DEL PEAK 35(14Q32.32) MUTATED`
TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 
        6.61        18.35         9.57        10.13         7.00         0.82 
TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-6803 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
        0.62         1.25        31.20        35.24        15.42        28.01 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 
       18.71        17.49         1.32         0.49        12.95         0.26 
TCGA-BR-8361 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       19.50        14.79         0.26         5.39         0.72         9.21 
TCGA-BR-8589 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CS 
       15.81        11.54        15.68        10.68         0.66         0.92 
TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD 
       12.89         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-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 
        0.13         0.13         0.13         0.10        20.02         7.99 
TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4477 TCGA-CG-5733 
       54.08        29.98        47.05        19.07        30.97        21.07 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 
       20.55        18.84        18.54         5.95         4.14        15.98 
TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YY TCGA-D7-A6EX TCGA-D7-A6EZ 
        6.97        14.27        16.44        13.78        11.31         9.76 
TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-A72C TCGA-FP-7916 
        2.96         7.40         7.79        16.24         8.12         3.02 
TCGA-FP-8099 TCGA-FP-8631 TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GH 
       17.06         0.56        26.47        12.59        14.17        11.77 
TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
        8.98         2.10        12.30        27.42        21.21        18.81 
TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A93H 
        5.19         6.44         6.74         1.81         2.53        28.90 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DU 
       16.67       122.30        37.91         8.94        35.61         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PU TCGA-VQ-A8PX 
       13.02        31.10         7.73        46.26        23.57        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91Q TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A925 
       59.18        28.70        20.81         9.73        44.25         4.54 
TCGA-VQ-A928 TCGA-VQ-AA6B TCGA-ZQ-A9CR 
        5.72        29.98         0.79 

$`DEL PEAK 35(14Q32.32) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
        5.62        11.70         6.97         4.64         7.43        30.90 
TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 
        6.18         6.61        34.68        15.95        13.12        13.68 
TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       39.12        32.78        13.84        13.22        16.14         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         0.69         0.16        18.54        12.43         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 
        0.69        12.76         0.82         0.69        12.26        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.72         0.26        16.31         1.55         1.48         7.40 
TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18         0.36         0.26        22.19         2.96         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       13.74         4.31        14.04         3.32         0.36        19.17 
TCGA-BR-8380 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        0.69        15.85         3.72        20.22         1.12        12.79 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        2.14        13.45         0.20         7.53         0.49        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 
       16.44         0.59         0.62        12.56         1.15         3.02 
TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       22.26        13.41        13.51         0.79        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       12.82        13.51        20.42        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8525 TCGA-CD-8526 
        2.83         3.25        13.15         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-A487 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        6.35         0.13         0.13         0.07         0.10         0.10 
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-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       14.01        12.03        21.99         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         1.02         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-5732 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10         4.01        55.04         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 
       12.66        11.93        19.13        18.61        17.85        17.19 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.22        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         0.23        21.14        20.91 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
        5.92        15.16        14.76        13.71        11.24        11.44 
TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 
       15.65         4.34         7.13         0.62         6.58        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 
       72.23        21.27         0.39        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         1.55         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-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-A4GQ TCGA-HU-A4GT 
       22.75        25.81        21.37        29.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.25        10.19         0.26        12.95        19.36        17.69 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI 
        9.67         8.88         8.81         3.45         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NT TCGA-KB-A6F5 
        5.36        13.08         1.41         6.87         5.56         5.56 
TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT 
       60.56         3.72        19.73         4.31        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
        4.67        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E3 
       16.87         5.79         0.92        37.74        13.25        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PJ 
       22.36        23.77        19.07        33.63        16.31         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        19.30 
TCGA-VQ-A8PY TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91W 
       14.33        11.70         8.68        49.25         1.71         7.36 
TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-AA68 TCGA-VQ-AA6J 
        8.58         8.61        55.43         6.58        40.08        21.11 
TCGA-ZA-A8F6 
        4.21 

  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                           0.07                            0.07 
  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 
                          11.54                           11.70 
[1] "0.1 - 122.3 (11.5)" "0.1 - 116.4 (11.7)"
[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        8       12        12
  DEL PEAK 35(14Q32.32) WILD-TYPE       2       10       31       19        24
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 35(14Q32.32) MUTATED          15         0         32         17
  DEL PEAK 35(14Q32.32) WILD-TYPE        34         3         45         38
                                 vv
clus                              STAGE IIIC STAGE IV
  DEL PEAK 35(14Q32.32) MUTATED           10        6
  DEL PEAK 35(14Q32.32) WILD-TYPE         27       31
D71V3, multiclass
            clus
vv           DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  STAGE I                                0                               2
  STAGE IA                               3                              10
  STAGE IB                               8                              31
  STAGE II                              12                              19
  STAGE IIA                             12                              24
  STAGE IIB                             15                              34
  STAGE III                              0                               3
  STAGE IIIA                            32                              45
  STAGE IIIB                            17                              38
  STAGE IIIC                            10                              27
  STAGE IV                               6                              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 35(14Q32.32) MUTATED     4  27  58  26
  DEL PEAK 35(14Q32.32) WILD-TYPE  17  60 115  78
D71V4, multiclass
    clus
vv   DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  T1                             4                              17
  T2                            27                              60
  T3                            58                             115
  T4                            26                              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 35(14Q32.32) MUTATED   32 35 28 21
  DEL PEAK 35(14Q32.32) WILD-TYPE 90 72 47 58
D71V5, multiclass
    clus
vv   DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  N0                            32                              90
  N1                            35                              72
  N2                            28                              47
  N3                            21                              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"
                                 vv
clus                               M0  M1  MX
  DEL PEAK 35(14Q32.32) MUTATED   108   2   9
  DEL PEAK 35(14Q32.32) WILD-TYPE 245  22   9
D71V6, multiclass
    clus
vv   DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  M0                           108                             245
  M1                             2                              22
  MX                             9                               9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V7, binary
                                 cls
clus                                0   1
  DEL PEAK 35(14Q32.32) MUTATED    44  75
  DEL PEAK 35(14Q32.32) WILD-TYPE 107 169
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(14Q32.32) MUTATED     44   75
  DEL PEAK 35(14Q32.32) WILD-TYPE  107  169
        clus
vv       DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  FEMALE                            44                             107
  MALE                              75                             169
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 35(14Q32.32) MUTATED                                      14
  DEL PEAK 35(14Q32.32) WILD-TYPE                                    51
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 35(14Q32.32) MUTATED                                                       49
  DEL PEAK 35(14Q32.32) WILD-TYPE                                                    108
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 35(14Q32.32) MUTATED                                                                  22
  DEL PEAK 35(14Q32.32) WILD-TYPE                                                                47
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 35(14Q32.32) MUTATED                                                 20
  DEL PEAK 35(14Q32.32) WILD-TYPE                                               44
                                 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                                          4
  DEL PEAK 35(14Q32.32) WILD-TYPE                                        5
D71V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 35(14Q32.32) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        14
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       49
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            22
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      4
                                                                   clus
vv                                                                  DEL PEAK 35(14Q32.32) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          51
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        108
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              47
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               44
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       15
  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"
D71V9, binary
                                 cls
clus                                0   1
  DEL PEAK 35(14Q32.32) MUTATED     2 117
  DEL PEAK 35(14Q32.32) WILD-TYPE   4 272
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(14Q32.32) MUTATED      2  117
  DEL PEAK 35(14Q32.32) WILD-TYPE    4  272
     clus
vv    DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  NO                              2                               4
  YES                           117                             272
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 35(14Q32.32) MUTATED   101   2   3   7
  DEL PEAK 35(14Q32.32) WILD-TYPE 217  14  15  18
D71V10, multiclass
    clus
vv   DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  R0                           101                             217
  R1                             2                              14
  R2                             3                              15
  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                         1
  DEL PEAK 35(14Q32.32) WILD-TYPE    61                         5
                                 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      79
  DEL PEAK 35(14Q32.32) WILD-TYPE   164
D71V12, multiclass
                                           clus
vv                                          DEL PEAK 35(14Q32.32) MUTATED
  ASIAN                                                                27
  BLACK OR AFRICAN AMERICAN                                             1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                79
                                           clus
vv                                          DEL PEAK 35(14Q32.32) WILD-TYPE
  ASIAN                                                                  61
  BLACK OR AFRICAN AMERICAN                                               5
  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"

Clustering(72) Variable = DEL PEAK 36(15Q11.2) MUTATION ANALYSIS
D72V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 36(15Q11.2) MUTATED    68  30
  DEL PEAK 36(15Q11.2) WILD-TYPE 174  92
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                            98                            266 
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                            30                             92 
$`DEL PEAK 36(15Q11.2) MUTATED`
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7901 
       13.68         7.00         0.62        24.76        35.24         0.95 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8686 
       12.95         0.26        14.79         5.39         9.21        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 
        0.13         0.13         0.10        20.02         7.99        54.08 
TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4466 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 
        4.01        47.05        18.97         1.02        12.03        15.02 
TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6525 
       55.04        12.66        19.13        20.55        18.84         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8575 
       17.19         4.14        15.22        15.98        12.79         0.23 
TCGA-D7-8576 TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-8122 
        6.97        11.31         2.96        15.65         7.40         7.79 
TCGA-F1-6875 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8245 
       72.23        13.58         1.55         0.23        26.47        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
       14.17        12.10         3.25        25.81        11.77         8.98 
TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RI 
        6.25         2.10        17.69         9.67        27.42        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 
        5.36         5.19         1.41         5.56         1.81         2.53 
TCGA-KB-A6F7 TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 
       60.56         4.31        11.05        16.67        37.91       115.69 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8PK 
       35.61         5.79         0.92        37.74         5.46        17.85 
TCGA-VQ-A8PZ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       59.18        20.81         1.71         8.58         9.73        44.25 
TCGA-VQ-AA68 TCGA-VQ-AA6B 
       40.08        29.98 

$`DEL PEAK 36(15Q11.2) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         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-6563 TCGA-BR-6564 TCGA-BR-6566 
       15.95        13.12        10.13        39.12         0.82        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       13.84        13.22        16.14         1.25         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 
       30.90        31.20        32.94        12.82         9.21        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01         0.69         0.16        18.54        12.43 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        0.69        12.76        18.71        17.49         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        12.26         0.49        20.55         0.72         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         1.55         1.48         7.40         6.18        19.50 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        0.36         0.26        22.19         2.96         0.95        13.74 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 
        4.31        14.04         3.32         0.36        19.17         0.69 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 
        0.26        15.85         3.72         0.72        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         2.14        13.45         0.20         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 
        0.49        11.54        15.81        16.44         0.59         0.62 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       12.56         1.15         0.66         3.02         0.92        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       13.51        12.89         0.79        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-5802 
       11.57         5.13         2.83         3.25        13.15         0.30 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8528 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.07         0.07         0.10         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI 
        0.10         6.35         0.13         0.13         0.07         0.10 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
        0.10         3.02        27.02        15.95         1.02         8.05 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 
       14.01        29.98        19.07        12.03        21.99         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         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-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-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       18.54        18.61        17.85        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-8579 
       24.72        16.80        19.50        17.19        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74B 
       13.71        11.24        11.44         9.76         4.34         7.13 
TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        0.62        16.24         6.58        14.47        21.27         8.12 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        0.39        19.53         3.02        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8631 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        5.03         0.56        18.08         1.51         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-A4GD TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
       11.84        24.20        22.75        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
        6.51        10.19         0.26        12.95        19.36        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-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-KB-A6F5 TCGA-KB-A93H 
       13.08         6.44         6.74         6.87         5.56        28.90 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 
        3.72        19.73         8.61         4.67       122.30        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-VQ-A8DV 
      116.38        71.38        57.44         8.94        16.87        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       13.02        31.10        21.73        22.36        23.77         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PM 
       19.07        33.63        46.26        16.31         2.70         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        19.30        23.57        64.57 
TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91W 
       14.33        28.70        11.70         8.68        49.25         7.36 
TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6J 
        8.61        55.43         4.54         6.58         5.72        21.11 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        4.21         0.79 

  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                          0.07                           0.07 
  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 
                        11.540                         11.635 
[1] "0.1 - 115.7 (11.5)" "0.1 - 122.3 (11.6)"
[1] "hr=" "1.2"
D72V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 36(15Q11.2) MUTATED         0        4       12        7        11
  DEL PEAK 36(15Q11.2) WILD-TYPE       2        9       27       24        25
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 36(15Q11.2) MUTATED          10         0         31         13
  DEL PEAK 36(15Q11.2) WILD-TYPE        39         3         46         42
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 36(15Q11.2) MUTATED            7        9
  DEL PEAK 36(15Q11.2) WILD-TYPE         30       28
D72V3, multiclass
            clus
vv           DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              4                              9
  STAGE IB                             12                             27
  STAGE II                              7                             24
  STAGE IIA                            11                             25
  STAGE IIB                            10                             39
  STAGE III                             0                              3
  STAGE IIIA                           31                             46
  STAGE IIIB                           13                             42
  STAGE IIIC                            7                             30
  STAGE IV                              9                             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 36(15Q11.2) MUTATED     6  26  56  17
  DEL PEAK 36(15Q11.2) WILD-TYPE  15  61 117  87
D72V4, multiclass
    clus
vv   DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  T1                            6                             15
  T2                           26                             61
  T3                           56                            117
  T4                           17                             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 36(15Q11.2) MUTATED   33 27 25 19
  DEL PEAK 36(15Q11.2) WILD-TYPE 89 80 50 60
D72V5, multiclass
    clus
vv   DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  N0                           33                             89
  N1                           27                             80
  N2                           25                             50
  N3                           19                             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"
                                vv
clus                              M0  M1  MX
  DEL PEAK 36(15Q11.2) MUTATED    97   5   6
  DEL PEAK 36(15Q11.2) WILD-TYPE 256  19  12
D72V6, multiclass
    clus
vv   DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  M0                           97                            256
  M1                            5                             19
  MX                            6                             12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V7, binary
                                cls
clus                               0   1
  DEL PEAK 36(15Q11.2) MUTATED    40  68
  DEL PEAK 36(15Q11.2) WILD-TYPE 111 176
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(15Q11.2) MUTATED     40   68
  DEL PEAK 36(15Q11.2) WILD-TYPE  111  176
        clus
vv       DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  FEMALE                           40                            111
  MALE                             68                            176
[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                                    51
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 36(15Q11.2) MUTATED                                                       37
  DEL PEAK 36(15Q11.2) WILD-TYPE                                                    120
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 36(15Q11.2) MUTATED                                                                  21
  DEL PEAK 36(15Q11.2) WILD-TYPE                                                                48
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 36(15Q11.2) MUTATED                                                 25
  DEL PEAK 36(15Q11.2) WILD-TYPE                                               39
                                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                                          4
  DEL PEAK 36(15Q11.2) WILD-TYPE                                        5
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)                           21
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            25
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     4
                                                                   clus
vv                                                                  DEL PEAK 36(15Q11.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         51
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       120
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             48
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              39
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      5
  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"
D72V9, binary
                                cls
clus                               0   1
  DEL PEAK 36(15Q11.2) MUTATED     4 104
  DEL PEAK 36(15Q11.2) WILD-TYPE   2 285
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(15Q11.2) MUTATED      4  104
  DEL PEAK 36(15Q11.2) WILD-TYPE    2  285
     clus
vv    DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  NO                             4                              2
  YES                          104                            285
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 36(15Q11.2) MUTATED    91   6   3   4
  DEL PEAK 36(15Q11.2) WILD-TYPE 227  10  15  21
D72V10, multiclass
    clus
vv   DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  R0                           91                            227
  R1                            6                             10
  R2                            3                             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"
D72V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 36(15Q11.2) MUTATED      28                         1
  DEL PEAK 36(15Q11.2) WILD-TYPE    60                         5
                                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      63
  DEL PEAK 36(15Q11.2) WILD-TYPE   180
D72V12, multiclass
                                           clus
vv                                          DEL PEAK 36(15Q11.2) MUTATED
  ASIAN                                                               28
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               63
                                           clus
vv                                          DEL PEAK 36(15Q11.2) WILD-TYPE
  ASIAN                                                                 60
  BLACK OR AFRICAN AMERICAN                                              5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(73) Variable = DEL PEAK 37(15Q15.1) MUTATION ANALYSIS
D73V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 37(15Q15.1) MUTATED    71  31
  DEL PEAK 37(15Q15.1) WILD-TYPE 171  91
  DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE 
                           102                            262 
  DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE 
                            31                             91 
$`DEL PEAK 37(15Q15.1) MUTATED`
TCGA-BR-4267 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7704 TCGA-BR-7901 TCGA-BR-8077 
        6.18         0.62         1.25        35.24         0.95         0.69 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8686 TCGA-BR-8690 
       12.95         0.26        14.79         5.39        15.68        10.68 
TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-5801 TCGA-CD-8525 
       22.26         0.72        20.65        13.64        13.18         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A48A 
        0.07         0.07         0.13         0.16         0.13         0.13 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
        0.13         0.10        20.02         7.99        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5724 
       14.01        47.05        18.97        30.97         1.02        12.03 
TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6525 
       55.04        12.66        19.13        20.55        18.84         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8575 
       17.19         4.14        15.22        12.79        12.33         0.23 
TCGA-D7-8576 TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-8122 
        6.97        11.31         2.96        15.65         7.40         7.79 
TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7998 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A8CX 
       16.24        72.23        22.29        13.58         1.55         0.23 
TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4GP 
       26.47        12.59        14.17        12.10        22.75         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        17.69        12.30         9.67 
TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO 
       27.42        18.81        18.38         5.36         5.19         1.41 
TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-MX-A663 TCGA-RD-A7BS 
        6.44         5.56         1.81         2.53         4.31        11.05 
TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT 
       16.67        37.91       115.69        35.61         5.79        37.74 
TCGA-VQ-A8DU TCGA-VQ-A8PK TCGA-VQ-A8PU TCGA-VQ-A8PZ TCGA-VQ-A91Q TCGA-VQ-A91U 
        5.46        17.85        23.57        59.18        20.81         1.71 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-AA68 TCGA-VQ-AA6B 
        8.58         9.73        44.25         8.61        40.08        29.98 

$`DEL PEAK 37(15Q15.1) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         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-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.12        10.13        13.68         7.00        39.12         0.82 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        13.84        13.22        16.14         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-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01         0.69         0.16        18.54 
TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       12.43         0.69        12.76        18.71        17.49         0.82 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        1.32        12.26         0.49        20.55         0.72         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         1.55         1.48         7.40         6.18        19.50 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        0.36         0.26        22.19         2.96         0.95        13.74 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 
        4.31        14.04         3.32         0.36        19.17         0.69 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        0.26        15.85         3.72         0.72         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         2.14        13.45         0.20 
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         0.59 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS 
        0.62        12.56         1.15         0.66         3.02         0.92 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51        12.89         0.79        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-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8528 TCGA-CD-8531 TCGA-CD-8532 
        0.30         0.07         0.07         0.10         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG 
        0.13         0.10         6.35         0.13         0.13         0.07 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10         0.10         3.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 
        8.05        29.98        19.07        12.03        21.99         9.01 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 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-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-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 
       65.10         4.01        21.07         7.99        12.36        11.93 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 
       18.54        18.61        17.85        15.98        10.55        11.31 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-8579 
       24.72        16.80        19.50        17.19        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74B 
       13.71        11.24        11.44         9.76         4.34         7.13 
TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62         6.58        14.47        21.27         8.12         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 
       19.53         3.02        17.06        59.54         5.03         0.56 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 
       18.08         1.51         5.92        14.27        11.41        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-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
        3.25        25.81        11.77        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB 
        6.51        10.19         0.26        19.36         8.88         8.81 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS 
       21.21         3.45         3.39        13.08         6.74         6.87 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BT 
        5.56        60.56        28.90         3.72        19.73         8.61 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
        4.67       122.30        40.64       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        8.94        16.87         0.92        13.25        13.02        31.10 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        22.36        23.77         7.73        19.07        33.63 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       46.26        16.31         2.70         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91D 
       15.65        19.30        64.57        14.33        28.70        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91W TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
        8.68        49.25         7.36        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        5.72        21.11         4.21         0.79 

  DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE 
                          0.07                           0.07 
  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 
                        12.065                         11.555 
[1] "0.1 - 115.7 (12.1)" "0.1 - 122.3 (11.6)"
[1] "hr=" "1.2"
D73V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 37(15Q15.1) MUTATED         0        2       14        7         8
  DEL PEAK 37(15Q15.1) WILD-TYPE       2       11       25       24        28
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 37(15Q15.1) MUTATED          10         0         32         16
  DEL PEAK 37(15Q15.1) WILD-TYPE        39         3         45         39
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 37(15Q15.1) MUTATED            8       10
  DEL PEAK 37(15Q15.1) WILD-TYPE         29       27
D73V3, multiclass
            clus
vv           DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              2                             11
  STAGE IB                             14                             25
  STAGE II                              7                             24
  STAGE IIA                             8                             28
  STAGE IIB                            10                             39
  STAGE III                             0                              3
  STAGE IIIA                           32                             45
  STAGE IIIB                           16                             39
  STAGE IIIC                            8                             29
  STAGE IV                             10                             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 37(15Q15.1) MUTATED     4  30  55  20
  DEL PEAK 37(15Q15.1) WILD-TYPE  17  57 118  84
D73V4, multiclass
    clus
vv   DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE
  T1                            4                             17
  T2                           30                             57
  T3                           55                            118
  T4                           20                             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 37(15Q15.1) MUTATED   31 30 24 22
  DEL PEAK 37(15Q15.1) WILD-TYPE 91 77 51 57
D73V5, multiclass
    clus
vv   DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE
  N0                           31                             91
  N1                           30                             77
  N2                           24                             51
  N3                           22                             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"
                                vv
clus                              M0  M1  MX
  DEL PEAK 37(15Q15.1) MUTATED    98   5   9
  DEL PEAK 37(15Q15.1) WILD-TYPE 255  19   9
D73V6, multiclass
    clus
vv   DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE
  M0                           98                            255
  M1                            5                             19
  MX                            9                              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V7, binary
                                cls
clus                               0   1
  DEL PEAK 37(15Q15.1) MUTATED    40  72
  DEL PEAK 37(15Q15.1) WILD-TYPE 111 172
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(15Q15.1) MUTATED     40   72
  DEL PEAK 37(15Q15.1) WILD-TYPE  111  172
        clus
vv       DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE
  FEMALE                           40                            111
  MALE                             72                            172
[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                                    51
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 37(15Q15.1) MUTATED                                                       38
  DEL PEAK 37(15Q15.1) WILD-TYPE                                                    119
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 37(15Q15.1) MUTATED                                                                  23
  DEL PEAK 37(15Q15.1) WILD-TYPE                                                                46
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 37(15Q15.1) MUTATED                                                 26
  DEL PEAK 37(15Q15.1) WILD-TYPE                                               38
                                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                                        5
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)                           23
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            26
  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                                                         51
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       119
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             46
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      5
  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"
D73V9, binary
                                cls
clus                               0   1
  DEL PEAK 37(15Q15.1) MUTATED     4 108
  DEL PEAK 37(15Q15.1) WILD-TYPE   2 281
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(15Q15.1) MUTATED      4  108
  DEL PEAK 37(15Q15.1) WILD-TYPE    2  281
     clus
vv    DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE
  NO                             4                              2
  YES                          108                            281
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 37(15Q15.1) MUTATED    92   7   3   6
  DEL PEAK 37(15Q15.1) WILD-TYPE 226   9  15  19
D73V10, multiclass
    clus
vv   DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE
  R0                           92                            226
  R1                            7                              9
  R2                            3                             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"
D73V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 37(15Q15.1) MUTATED      27                         1
  DEL PEAK 37(15Q15.1) WILD-TYPE    61                         5
                                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      67
  DEL PEAK 37(15Q15.1) WILD-TYPE   176
D73V12, multiclass
                                           clus
vv                                          DEL PEAK 37(15Q15.1) MUTATED
  ASIAN                                                               27
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               67
                                           clus
vv                                          DEL PEAK 37(15Q15.1) WILD-TYPE
  ASIAN                                                                 61
  BLACK OR AFRICAN AMERICAN                                              5
  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"

Clustering(74) Variable = DEL PEAK 38(16P13.3) MUTATION ANALYSIS
D74V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 38(16P13.3) MUTATED    54  23
  DEL PEAK 38(16P13.3) WILD-TYPE 188  99
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                            77                            287 
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                            23                             99 
$`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         0.95 
TCGA-BR-7959 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8365 TCGA-BR-8373 
       18.71        12.95         0.26        16.31         2.96        14.79 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 
        0.49        11.54         0.66        22.26         0.92         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         6.35         0.13         0.13         0.13         0.10 
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         7.79        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        17.69        12.30         9.67        27.42 
TCGA-IN-8663 TCGA-IN-A6RR TCGA-IN-A6RS TCGA-KB-A6F5 TCGA-KB-A93H TCGA-RD-A7BS 
        3.39         6.74         6.87         5.56        28.90        11.05 
TCGA-RD-A7C1 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       16.67        35.61         5.79        37.74         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8PC TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PU 
       13.02        46.26         2.70        17.85         1.87        23.57 
TCGA-VQ-A8PX TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-AA68 TCGA-VQ-AA6J 
       64.57        44.25         8.61        40.08        21.11 

$`DEL PEAK 38(16P13.3) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
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-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.12        10.13        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        0.62        32.78        13.84        13.22        16.14         1.25 
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-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       24.76        23.93         0.69         0.16        18.54        12.43 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69        12.76        17.49         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8295 
       12.26         0.49        20.55         0.72         0.26         1.55 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
        1.48         7.40         6.18        19.50         0.36         0.26 
TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       22.19         0.95        13.74         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        0.36        19.17         0.69         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         0.72         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-8680 
       15.81         2.14        13.45         0.20         7.53        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         0.59        15.68         0.62        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        1.15         3.02        13.41        13.51        12.89         0.79 
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-5802 TCGA-CD-8527 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 
        0.10         0.13         0.10         0.10         0.13         0.10 
TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        0.13         0.07         0.10         0.10        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 
        4.01        14.01        29.98        21.99         9.01        18.97 
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         1.02 
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        55.04        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-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85         5.95        17.19         4.14 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 
       15.98        12.79        10.55        11.31        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19         0.23         6.97        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-A6F2 TCGA-D7-A748 
       13.71        11.24        11.44         9.76        15.65         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 
        7.13         0.62        16.24         6.58        14.47        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
        8.12         0.39        19.53         3.02        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB 
       59.54         5.03         0.56         1.55         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 
       26.47         1.51        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-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-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 
       10.19         0.26         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-A6RJ 
        8.81        21.21         3.45        18.81        18.38         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU 
        5.19        13.08         1.41         6.44         5.56         1.81 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BT 
        2.53        60.56         3.72        19.73         4.31         8.61 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        4.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-VQ-A8DL TCGA-VQ-A8E2 
       71.38        57.44         8.94        16.87         0.92        31.10 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        22.36        23.77         7.73        19.07        33.63 
TCGA-VQ-A8PD TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PY 
       16.31         9.27        23.41        15.65        19.30        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q 
       59.18        28.70        11.70         8.68        49.25        20.81 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A924 TCGA-VQ-A925 
        1.71         7.36         8.58         9.73        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6B TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        6.58         5.72        29.98         4.21         0.79 

  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                          0.07                           0.07 
  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 
                         11.54                          11.70 
[1] "0.1 - 72.2 (11.5)"  "0.1 - 122.3 (11.7)"
[1] "hr=" "1.1"
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       2        8       32       22        28
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 38(16P13.3) MUTATED          11         0         25          5
  DEL PEAK 38(16P13.3) WILD-TYPE        38         3         52         50
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 38(16P13.3) MUTATED            4        7
  DEL PEAK 38(16P13.3) WILD-TYPE         33       30
D74V3, multiclass
            clus
vv           DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              5                              8
  STAGE IB                              7                             32
  STAGE II                              9                             22
  STAGE IIA                             8                             28
  STAGE IIB                            11                             38
  STAGE III                             0                              3
  STAGE IIIA                           25                             52
  STAGE IIIB                            5                             50
  STAGE IIIC                            4                             33
  STAGE IV                              7                             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 38(16P13.3) MUTATED     4  16  45  17
  DEL PEAK 38(16P13.3) WILD-TYPE  17  71 128  87
D74V4, multiclass
    clus
vv   DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  T1                            4                             17
  T2                           16                             71
  T3                           45                            128
  T4                           17                             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 38(16P13.3) MUTATED   26 30 14 12
  DEL PEAK 38(16P13.3) WILD-TYPE 96 77 61 67
D74V5, multiclass
    clus
vv   DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  N0                           26                             96
  N1                           30                             77
  N2                           14                             61
  N3                           12                             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"
                                vv
clus                              M0  M1  MX
  DEL PEAK 38(16P13.3) MUTATED    79   4   2
  DEL PEAK 38(16P13.3) WILD-TYPE 274  20  16
D74V6, multiclass
    clus
vv   DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  M0                           79                            274
  M1                            4                             20
  MX                            2                             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V7, binary
                                cls
clus                               0   1
  DEL PEAK 38(16P13.3) MUTATED    28  57
  DEL PEAK 38(16P13.3) WILD-TYPE 123 187
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16P13.3) MUTATED     28   57
  DEL PEAK 38(16P13.3) WILD-TYPE  123  187
        clus
vv       DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  FEMALE                           28                            123
  MALE                             57                            187
[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                                    57
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 38(16P13.3) MUTATED                                                       31
  DEL PEAK 38(16P13.3) WILD-TYPE                                                    126
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 38(16P13.3) MUTATED                                                                  13
  DEL PEAK 38(16P13.3) WILD-TYPE                                                                56
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 38(16P13.3) MUTATED                                                 21
  DEL PEAK 38(16P13.3) WILD-TYPE                                               43
                                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                                        6
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)                           13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            21
  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                                                         57
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             56
  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                                                       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"
D74V9, binary
                                cls
clus                               0   1
  DEL PEAK 38(16P13.3) MUTATED     2  83
  DEL PEAK 38(16P13.3) WILD-TYPE   4 306
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16P13.3) MUTATED      2   83
  DEL PEAK 38(16P13.3) WILD-TYPE    4  306
     clus
vv    DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  NO                             2                              4
  YES                           83                            306
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 38(16P13.3) MUTATED    65   4   3   6
  DEL PEAK 38(16P13.3) WILD-TYPE 253  12  15  19
D74V10, multiclass
    clus
vv   DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  R0                           65                            253
  R1                            4                             12
  R2                            3                             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"
D74V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 38(16P13.3) MUTATED      26                         3
  DEL PEAK 38(16P13.3) WILD-TYPE    62                         3
                                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      45
  DEL PEAK 38(16P13.3) WILD-TYPE   198
D74V12, multiclass
                                           clus
vv                                          DEL PEAK 38(16P13.3) MUTATED
  ASIAN                                                               26
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               45
                                           clus
vv                                          DEL PEAK 38(16P13.3) WILD-TYPE
  ASIAN                                                                 62
  BLACK OR AFRICAN AMERICAN                                              3
  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"

Clustering(75) Variable = DEL PEAK 39(16Q23.1) MUTATION ANALYSIS
D75V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 39(16Q23.1) MUTATED    96  52
  DEL PEAK 39(16Q23.1) WILD-TYPE 146  70
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                           148                            216 
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                            52                             70 
$`DEL PEAK 39(16Q23.1) MUTATED`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4279 
        5.62        11.70         6.61         6.97        18.35         9.57 
TCGA-BR-4280 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6706 TCGA-BR-7703 
        6.61        10.13         7.00         0.82        13.22        24.76 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7959 
       35.24        15.42         0.69        18.54         0.95        18.71 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        1.32         0.69         0.49         0.26        12.95         0.26 
TCGA-BR-8291 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8372 
       16.31        19.50         0.36         0.26         2.96        19.17 
TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8687 
       14.79         0.72         0.49        11.54        16.44         0.62 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4PE 
        1.15         0.66        22.26         0.72        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        1.15        13.64        13.15         0.30         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C 
        0.07         0.16         0.13         6.35         0.13         0.13 
TCGA-CD-A4MH TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4444 
        0.10        15.95         7.99         8.05        54.08        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5723 
       19.07        12.03         7.07        22.98        30.97       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5727 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       12.03        15.02        79.07        12.36        12.66        11.93 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-8573 
        5.95        17.19        15.22        12.79        10.55        19.50 
TCGA-D7-8575 TCGA-D7-A4YT TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6EV TCGA-D7-A6EX 
        0.23        14.27        15.16        13.78        11.24        11.31 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7916 TCGA-FP-7998 
        2.96        15.65        16.24        72.23         3.02        22.29 
TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 
        1.55        18.08         1.51         5.92        12.59        12.10 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GP 
        0.76         5.59        12.30        22.75        11.77         8.98 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H5 
        6.25        10.19         0.26         2.10        17.69        12.30 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RN 
        9.67        27.42         3.45        18.81        18.38        13.08 
TCGA-IN-A6RP TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A663 
        6.44         1.81         5.56        60.56        28.90         4.31 
TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL 
       11.05        16.67         8.94        35.61         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PK 
       37.74         5.46        13.02         7.73        46.26        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        28.70         8.68 
TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       49.25         1.71         8.58         9.73        44.25         8.61 
TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-ZQ-A9CR 
        4.54         5.72        40.08         0.79 

$`DEL PEAK 39(16Q23.1) WILD-TYPE`
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-6453 
        4.64         7.43        30.90         6.18        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.12        13.68        39.12         0.62        32.78        13.84 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       16.14         1.25         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 
       32.94        12.82         9.21        23.93        28.01         0.16 
TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 
       12.43         0.69        12.76        17.49         0.82        12.26 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       20.55         0.72         1.55         1.48         7.40         6.18 
TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       22.19         0.95        13.74         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
        0.36         0.69         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         2.14 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 
       13.45         0.20         7.53        15.81         0.59        15.68 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       10.68        12.56         3.02         0.92        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         0.79        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         0.13         0.13 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.07         0.10         0.10        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4460 TCGA-CG-4465 
        1.02         4.01        14.01        29.98        21.99         9.01 
TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       18.97        12.00         6.97         1.02         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
        6.02         0.99        28.96        65.10         4.01        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       21.07         7.99        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-6822 
       18.61        17.85         4.14        15.98        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       24.72        16.80        17.19         6.97        21.14        20.91 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ 
       16.44         5.92        14.76        13.71        11.44         9.76 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 
        4.34         7.40         7.13         0.62         7.79         6.58 
TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 
       14.47        21.27         8.12         0.39        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         6.87 
TCGA-IN-A7NT TCGA-IP-7968 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BT TCGA-RD-A7BW 
        5.56         2.53         3.72        19.73         8.61         4.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 
       57.44        16.87        13.25        31.10        21.73        22.36 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PO 
       23.77        19.07        33.63        16.31         2.70         9.27 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91Q 
       15.65        19.30        23.57        59.18        11.70        20.81 
TCGA-VQ-A91W TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 
        7.36        55.43         6.58        29.98        21.11         4.21 

  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                          0.07                           0.07 
  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 
                        11.145                         12.130 
[1] "0.1 - 105.1 (11.1)" "0.1 - 122.3 (12.1)"
[1] "hr=" "1.1"
D75V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 39(16Q23.1) MUTATED         0        6       16       17        13
  DEL PEAK 39(16Q23.1) WILD-TYPE       2        7       23       14        23
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 39(16Q23.1) MUTATED          17         2         41         14
  DEL PEAK 39(16Q23.1) WILD-TYPE        32         1         36         41
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 39(16Q23.1) MUTATED           20       11
  DEL PEAK 39(16Q23.1) WILD-TYPE         17       26
D75V3, multiclass
            clus
vv           DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              6                              7
  STAGE IB                             16                             23
  STAGE II                             17                             14
  STAGE IIA                            13                             23
  STAGE IIB                            17                             32
  STAGE III                             2                              1
  STAGE IIIA                           41                             36
  STAGE IIIB                           14                             41
  STAGE IIIC                           20                             17
  STAGE IV                             11                             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 39(16Q23.1) MUTATED     9  39  73  38
  DEL PEAK 39(16Q23.1) WILD-TYPE  12  48 100  66
D75V4, multiclass
    clus
vv   DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  T1                            9                             12
  T2                           39                             48
  T3                           73                            100
  T4                           38                             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"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 39(16Q23.1) MUTATED   46 48 28 36
  DEL PEAK 39(16Q23.1) WILD-TYPE 76 59 47 43
D75V5, multiclass
    clus
vv   DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  N0                           46                             76
  N1                           48                             59
  N2                           28                             47
  N3                           36                             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"
                                vv
clus                              M0  M1  MX
  DEL PEAK 39(16Q23.1) MUTATED   151   4   6
  DEL PEAK 39(16Q23.1) WILD-TYPE 202  20  12
D75V6, multiclass
    clus
vv   DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  M0                          151                            202
  M1                            4                             20
  MX                            6                             12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V7, binary
                                cls
clus                               0   1
  DEL PEAK 39(16Q23.1) MUTATED    56 105
  DEL PEAK 39(16Q23.1) WILD-TYPE  95 139
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(16Q23.1) MUTATED     56  105
  DEL PEAK 39(16Q23.1) WILD-TYPE   95  139
        clus
vv       DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  FEMALE                           56                             95
  MALE                            105                            139
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 39(16Q23.1) MUTATED                                      22
  DEL PEAK 39(16Q23.1) WILD-TYPE                                    43
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 39(16Q23.1) MUTATED                                                       59
  DEL PEAK 39(16Q23.1) WILD-TYPE                                                     98
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 39(16Q23.1) MUTATED                                                                  25
  DEL PEAK 39(16Q23.1) WILD-TYPE                                                                44
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 39(16Q23.1) MUTATED                                                 33
  DEL PEAK 39(16Q23.1) WILD-TYPE                                               31
                                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                                          4
  DEL PEAK 39(16Q23.1) WILD-TYPE                                        5
D75V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 39(16Q23.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       22
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      59
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           25
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            33
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     4
                                                                   clus
vv                                                                  DEL PEAK 39(16Q23.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         43
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        98
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             44
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              31
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      2
  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"
D75V9, binary
                                cls
clus                               0   1
  DEL PEAK 39(16Q23.1) MUTATED     5 156
  DEL PEAK 39(16Q23.1) WILD-TYPE   1 233
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(16Q23.1) MUTATED      5  156
  DEL PEAK 39(16Q23.1) WILD-TYPE    1  233
     clus
vv    DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  NO                             5                              1
  YES                          156                            233
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 39(16Q23.1) MUTATED   131   8   4  10
  DEL PEAK 39(16Q23.1) WILD-TYPE 187   8  14  15
D75V10, multiclass
    clus
vv   DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  R0                          131                            187
  R1                            8                              8
  R2                            4                             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"
D75V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 39(16Q23.1) MUTATED      37                         2
  DEL PEAK 39(16Q23.1) WILD-TYPE    51                         4
                                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      96
  DEL PEAK 39(16Q23.1) WILD-TYPE   147
D75V12, multiclass
                                           clus
vv                                          DEL PEAK 39(16Q23.1) MUTATED
  ASIAN                                                               37
  BLACK OR AFRICAN AMERICAN                                            2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               96
                                           clus
vv                                          DEL PEAK 39(16Q23.1) WILD-TYPE
  ASIAN                                                                 51
  BLACK OR AFRICAN AMERICAN                                              4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                147
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(76) Variable = DEL PEAK 40(17P13.3) MUTATION ANALYSIS
D76V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 40(17P13.3) MUTATED    95  47
  DEL PEAK 40(17P13.3) WILD-TYPE 147  75
  DEL PEAK 40(17P13.3) MUTATED DEL PEAK 40(17P13.3) WILD-TYPE 
                           142                            222 
  DEL PEAK 40(17P13.3) MUTATED DEL PEAK 40(17P13.3) WILD-TYPE 
                            47                             75 
$`DEL PEAK 40(17P13.3) MUTATED`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       11.70         6.61         6.18        10.13        13.68         7.00 
TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7723 
        0.62         1.25         9.21        35.24        15.42        18.54 
TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 
       18.71         1.32         0.69         0.49        12.95         0.26 
TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8369 TCGA-BR-8373 
       16.31         1.48         7.40         0.36        14.04        14.79 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 
        5.39         0.72        11.54        16.44         0.59        10.68 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J8 
        1.15         0.66        22.26         0.92         0.72        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 
       20.65        20.42         1.15        13.64         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-CG-4300 
        0.13         6.35         0.13         0.13         0.13        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4444 
        3.02        27.02         7.99         4.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5727 
       19.07         7.07        22.98        30.97         1.02        79.07 
TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
        4.01        55.04        11.93        20.55        18.84        18.54 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6820 
        5.95        17.19         4.14        15.22        12.79        11.31 
TCGA-D7-6822 TCGA-D7-8576 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A 
       12.33         6.97        16.44        11.31        15.65         7.40 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8211 
        7.79        72.23         8.12         3.02        17.06        13.58 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8245 TCGA-HU-8249 
        1.55         0.23        26.47         1.51        12.59        14.17 
TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY 
       12.10        22.75        11.77         8.98         6.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
        2.10        12.95        12.30        27.42        21.21        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A7NU TCGA-IP-7968 
        3.39        18.38         5.19         1.41         1.81         2.53 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N6 
        5.56        28.90         8.61        16.67       115.69         8.94 
TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PC 
        0.92         5.46        13.25        31.10         7.73        46.26 
TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
        2.70         1.87        23.57        64.57        14.33        59.18 
TCGA-VQ-A91Q TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A928 
       20.81         8.58         9.73        44.25         8.61         5.72 
TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       40.08        29.98        21.11         0.79 

$`DEL PEAK 40(17P13.3) WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        5.62         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-6563 
        9.57         6.61        34.68        15.95        13.12        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        0.82        32.78        13.84        13.22        16.14         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         0.69         0.16        12.43         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 
        0.69        12.76        17.49         0.82        12.26        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        0.72         0.26         1.55         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         2.96         0.95        13.74         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        0.36        19.17         0.69         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         2.14 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8686 
       13.45         0.20         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 
        0.62        12.56         3.02        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.79        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 
        0.13         0.07         0.10         0.10         0.10        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-4465 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 
        9.01        18.97        12.00         6.97         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-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-D7-6815 TCGA-D7-6818 TCGA-D7-8570 TCGA-D7-8572 
       18.61        17.85        15.98        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         0.23        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-A748 TCGA-D7-A74B TCGA-EQ-5647 
       11.44         9.76         2.96         4.34         7.13         0.62 
TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
       16.24         6.58        14.47        21.27         0.39        19.53 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HF-A5NB TCGA-HU-8243 
       22.29        59.54         5.03         0.56        18.08         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-A4GJ 
       12.30        11.84        24.20         3.25        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H4 
       29.98         0.10         6.51        10.19        19.36        17.69 
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-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-KB-A6F7 TCGA-MX-A5UG 
        6.44         6.74         6.87         5.56        60.56         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
       19.73         4.31        11.05         4.67       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-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        5.79        37.74        13.02        21.73        22.36        23.77 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PP 
       19.07        33.63        16.31        17.85         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       15.65        19.30        28.70        11.70         8.68        49.25 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-ZA-A8F6 
        1.71         7.36        55.43         4.54         6.58         4.21 

  DEL PEAK 40(17P13.3) MUTATED DEL PEAK 40(17P13.3) WILD-TYPE 
                          0.07                           0.07 
  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 
                         9.930                         12.145 
[1] "0.1 - 115.7 (9.9)"  "0.1 - 122.3 (12.1)"
[1] "hr=" "1"  
D76V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 40(17P13.3) MUTATED         0        5       17       13        14
  DEL PEAK 40(17P13.3) WILD-TYPE       2        8       22       18        22
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 40(17P13.3) MUTATED          18         0         33         21
  DEL PEAK 40(17P13.3) WILD-TYPE        31         3         44         34
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 40(17P13.3) MUTATED           12       15
  DEL PEAK 40(17P13.3) WILD-TYPE         25       22
D76V3, multiclass
            clus
vv           DEL PEAK 40(17P13.3) MUTATED DEL PEAK 40(17P13.3) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              5                              8
  STAGE IB                             17                             22
  STAGE II                             13                             18
  STAGE IIA                            14                             22
  STAGE IIB                            18                             31
  STAGE III                             0                              3
  STAGE IIIA                           33                             44
  STAGE IIIB                           21                             34
  STAGE IIIC                           12                             25
  STAGE IV                             15                             22
[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     5  39  71  34
  DEL PEAK 40(17P13.3) WILD-TYPE  16  48 102  70
D76V4, multiclass
    clus
vv   DEL PEAK 40(17P13.3) MUTATED DEL PEAK 40(17P13.3) WILD-TYPE
  T1                            5                             16
  T2                           39                             48
  T3                           71                            102
  T4                           34                             70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 40(17P13.3) MUTATED   49 40 30 30
  DEL PEAK 40(17P13.3) WILD-TYPE 73 67 45 49
D76V5, multiclass
    clus
vv   DEL PEAK 40(17P13.3) MUTATED DEL PEAK 40(17P13.3) WILD-TYPE
  N0                           49                             73
  N1                           40                             67
  N2                           30                             45
  N3                           30                             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"
                                vv
clus                              M0  M1  MX
  DEL PEAK 40(17P13.3) MUTATED   135   7   9
  DEL PEAK 40(17P13.3) WILD-TYPE 218  17   9
D76V6, multiclass
    clus
vv   DEL PEAK 40(17P13.3) MUTATED DEL PEAK 40(17P13.3) WILD-TYPE
  M0                          135                            218
  M1                            7                             17
  MX                            9                              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V7, binary
                                cls
clus                               0   1
  DEL PEAK 40(17P13.3) MUTATED    52  99
  DEL PEAK 40(17P13.3) WILD-TYPE  99 145
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17P13.3) MUTATED     52   99
  DEL PEAK 40(17P13.3) WILD-TYPE   99  145
        clus
vv       DEL PEAK 40(17P13.3) MUTATED DEL PEAK 40(17P13.3) WILD-TYPE
  FEMALE                           52                             99
  MALE                             99                            145
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 40(17P13.3) MUTATED                                      16
  DEL PEAK 40(17P13.3) WILD-TYPE                                    49
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 40(17P13.3) MUTATED                                                       52
  DEL PEAK 40(17P13.3) WILD-TYPE                                                    105
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 40(17P13.3) MUTATED                                                                  29
  DEL PEAK 40(17P13.3) WILD-TYPE                                                                40
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 40(17P13.3) MUTATED                                                 33
  DEL PEAK 40(17P13.3) WILD-TYPE                                               31
                                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                                          6
  DEL PEAK 40(17P13.3) WILD-TYPE                                        3
D76V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 40(17P13.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       16
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      52
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           29
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            33
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     6
                                                                   clus
vv                                                                  DEL PEAK 40(17P13.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       105
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              31
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       3
[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     5 146
  DEL PEAK 40(17P13.3) WILD-TYPE   1 243
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17P13.3) MUTATED      5  146
  DEL PEAK 40(17P13.3) WILD-TYPE    1  243
     clus
vv    DEL PEAK 40(17P13.3) MUTATED DEL PEAK 40(17P13.3) WILD-TYPE
  NO                             5                              1
  YES                          146                            243
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 40(17P13.3) MUTATED   125   8   6   5
  DEL PEAK 40(17P13.3) WILD-TYPE 193   8  12  20
D76V10, multiclass
    clus
vv   DEL PEAK 40(17P13.3) MUTATED DEL PEAK 40(17P13.3) WILD-TYPE
  R0                          125                            193
  R1                            8                              8
  R2                            6                             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"
D76V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 40(17P13.3) MUTATED      35                         2
  DEL PEAK 40(17P13.3) WILD-TYPE    53                         4
                                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      89
  DEL PEAK 40(17P13.3) WILD-TYPE   154
D76V12, multiclass
                                           clus
vv                                          DEL PEAK 40(17P13.3) MUTATED
  ASIAN                                                               35
  BLACK OR AFRICAN AMERICAN                                            2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               89
                                           clus
vv                                          DEL PEAK 40(17P13.3) WILD-TYPE
  ASIAN                                                                 53
  BLACK OR AFRICAN AMERICAN                                              4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                154
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(77) Variable = DEL PEAK 41(17P12) MUTATION ANALYSIS
D77V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 41(17P12) MUTATED    98  51
  DEL PEAK 41(17P12) WILD-TYPE 144  71
  DEL PEAK 41(17P12) MUTATED DEL PEAK 41(17P12) WILD-TYPE 
                         149                          215 
  DEL PEAK 41(17P12) MUTATED DEL PEAK 41(17P12) WILD-TYPE 
                          51                           71 
$`DEL PEAK 41(17P12) MUTATED`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 
       11.70         6.61         6.18        10.13         7.00         0.62 
TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7723 TCGA-BR-7959 
        1.25         9.21        35.24        15.42        18.54        18.71 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        1.32         0.69         0.49        12.95         0.26        16.31 
TCGA-BR-8296 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8483 
        1.48        19.50         0.36        14.04        14.79         5.39 
TCGA-BR-8484 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44U 
        0.72        11.54        16.44         0.59        10.68         1.15 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.66        22.26         0.92         0.72        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8524 TCGA-CD-8525 
       20.42         1.15         3.25        13.15         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 
        0.07         0.10         0.13         0.13         0.13         6.35 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 
        0.13         0.13         0.13         0.10        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 
       27.02         7.99         8.05        54.08         4.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 
       47.05        19.07         7.07        30.97         1.02         1.02 
TCGA-CG-5725 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5579 TCGA-D7-6519 
       15.02        79.07         4.01        55.04        11.93        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.84        18.54         5.95        17.19         4.14        15.22 
TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8576 TCGA-D7-A4YU TCGA-D7-A6EX 
       15.98        11.31        12.33         6.97        16.44        11.31 
TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A72C 
       15.65         7.40         7.79        16.24        72.23         8.12 
TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HJ-7597 
        3.02        17.06        13.58         0.56         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-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4HD 
        8.98         6.25         2.10        12.95        12.30        27.42 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO 
       21.21        18.81         3.39        18.38         5.19         1.41 
TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H 
        6.44         6.87         1.81         2.53         5.56        28.90 
TCGA-MX-A663 TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-VQ-A8DL 
        4.31         8.61        16.67       115.69         8.94         0.92 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PC 
        5.46        13.25        13.02        31.10         7.73        46.26 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
        2.70        17.85         1.87        23.57        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91Q TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       59.18        20.81         8.58         9.73        44.25         8.61 
TCGA-VQ-A925 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZQ-A9CR 
        4.54        40.08        29.98        21.11         0.79 

$`DEL PEAK 41(17P12) WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        5.62         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        13.12        13.68 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12         0.82        32.78        13.84        13.22        16.14 
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         0.69         0.16        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 
        0.95         0.69        12.76        17.49         0.82        12.26 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       20.55         0.72         0.26         1.55         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19         2.96         0.95        13.74         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 
        3.32         0.36        19.17         0.69         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        3.72         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        2.14        13.45         0.20         7.53         0.49        15.81 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
       15.68         0.62        12.56         3.02        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         0.79        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       19.36         0.46        13.64        11.57         5.13         2.83 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8531 
       13.18         0.30         0.07         0.07         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.10         0.10         0.13         0.07         0.10         0.10 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 
       15.95         1.02        14.01        12.03        21.99         9.01 
TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 
       18.97        12.00        22.98         6.97         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 
        0.99       105.07        12.03        28.96        65.10        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 
        7.99        12.36        12.66        19.13        18.61        17.85 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       12.79        10.55        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 
        0.23        21.14        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-A6F0 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 
        2.96         4.34         7.13         0.62         6.58        14.47 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
       21.27         0.39        19.53        22.29        59.54         5.03 
TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 
        1.55        18.08         5.92        14.27        11.41        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-A4GQ TCGA-HU-A4GT 
        3.25        25.81        21.37        29.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
       10.19         0.26        19.36        17.69         9.67         8.88 
TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A7NT 
        8.81         3.45         5.36        13.08         6.74         5.56 
TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV 
       60.56         3.72        19.73        11.05         4.67       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-A7EB TCGA-VQ-A8DT TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       16.87         5.79        37.74        21.73        22.36        23.77 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       19.07        33.63        16.31         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91U 
       19.30        28.70        11.70         8.68        49.25         1.71 
TCGA-VQ-A91W TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-ZA-A8F6 
        7.36        55.43         6.58         5.72         4.21 

  DEL PEAK 41(17P12) MUTATED DEL PEAK 41(17P12) WILD-TYPE 
                        0.07                         0.07 
  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 
                        9.73                        12.26 
[1] "0.1 - 115.7 (9.7)"  "0.1 - 122.3 (12.3)"
[1] "hr=" "1.1"
D77V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 41(17P12) MUTATED         0        6       17       15        14
  DEL PEAK 41(17P12) WILD-TYPE       2        7       22       16        22
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 41(17P12) MUTATED          18         0         32         23
  DEL PEAK 41(17P12) WILD-TYPE        31         3         45         32
                              vv
clus                           STAGE IIIC STAGE IV
  DEL PEAK 41(17P12) MUTATED           13       16
  DEL PEAK 41(17P12) WILD-TYPE         24       21
D77V3, multiclass
            clus
vv           DEL PEAK 41(17P12) MUTATED DEL PEAK 41(17P12) WILD-TYPE
  STAGE I                             0                            2
  STAGE IA                            6                            7
  STAGE IB                           17                           22
  STAGE II                           15                           16
  STAGE IIA                          14                           22
  STAGE IIB                          18                           31
  STAGE III                           0                            3
  STAGE IIIA                         32                           45
  STAGE IIIB                         23                           32
  STAGE IIIC                         13                           24
  STAGE IV                           16                           21
[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     7  41  71  36
  DEL PEAK 41(17P12) WILD-TYPE  14  46 102  68
D77V4, multiclass
    clus
vv   DEL PEAK 41(17P12) MUTATED DEL PEAK 41(17P12) WILD-TYPE
  T1                          7                           14
  T2                         41                           46
  T3                         71                          102
  T4                         36                           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"
                              vv
clus                           N0 N1 N2 N3
  DEL PEAK 41(17P12) MUTATED   50 41 34 30
  DEL PEAK 41(17P12) WILD-TYPE 72 66 41 49
D77V5, multiclass
    clus
vv   DEL PEAK 41(17P12) MUTATED DEL PEAK 41(17P12) WILD-TYPE
  N0                         50                           72
  N1                         41                           66
  N2                         34                           41
  N3                         30                           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"
                              vv
clus                            M0  M1  MX
  DEL PEAK 41(17P12) MUTATED   138   8  11
  DEL PEAK 41(17P12) WILD-TYPE 215  16   7
D77V6, multiclass
    clus
vv   DEL PEAK 41(17P12) MUTATED DEL PEAK 41(17P12) WILD-TYPE
  M0                        138                          215
  M1                          8                           16
  MX                         11                            7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V7, binary
                              cls
clus                             0   1
  DEL PEAK 41(17P12) MUTATED    53 104
  DEL PEAK 41(17P12) WILD-TYPE  98 140
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 41(17P12) MUTATED     53  104
  DEL PEAK 41(17P12) WILD-TYPE   98  140
        clus
vv       DEL PEAK 41(17P12) MUTATED DEL PEAK 41(17P12) WILD-TYPE
  FEMALE                         53                           98
  MALE                          104                          140
[1] 2 2
[1] FALSE
                              vv
clus                           STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 41(17P12) MUTATED                                      14
  DEL PEAK 41(17P12) WILD-TYPE                                    51
                              vv
clus                           STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 41(17P12) MUTATED                                                       56
  DEL PEAK 41(17P12) WILD-TYPE                                                    101
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 41(17P12) MUTATED                                                                  34
  DEL PEAK 41(17P12) WILD-TYPE                                                                35
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 41(17P12) MUTATED                                                 34
  DEL PEAK 41(17P12) WILD-TYPE                                               30
                              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                                          6
  DEL PEAK 41(17P12) WILD-TYPE                                        3
D77V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 41(17P12) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     14
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    56
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         34
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                          34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                  4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   6
                                                                   clus
vv                                                                  DEL PEAK 41(17P12) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       51
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     101
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            30
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     3
[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     4 153
  DEL PEAK 41(17P12) WILD-TYPE   2 236
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 41(17P12) MUTATED      4  153
  DEL PEAK 41(17P12) WILD-TYPE    2  236
     clus
vv    DEL PEAK 41(17P12) MUTATED DEL PEAK 41(17P12) WILD-TYPE
  NO                           4                            2
  YES                        153                          236
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 41(17P12) MUTATED   129   7   8   5
  DEL PEAK 41(17P12) WILD-TYPE 189   9  10  20
D77V10, multiclass
    clus
vv   DEL PEAK 41(17P12) MUTATED DEL PEAK 41(17P12) WILD-TYPE
  R0                        129                          189
  R1                          7                            9
  R2                          8                           10
  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                         3
  DEL PEAK 41(17P12) WILD-TYPE    53                         3
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 41(17P12) MUTATED                                           1    91
  DEL PEAK 41(17P12) WILD-TYPE                                         0   152
D77V12, multiclass
                                           clus
vv                                          DEL PEAK 41(17P12) MUTATED
  ASIAN                                                             35
  BLACK OR AFRICAN AMERICAN                                          3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                             91
                                           clus
vv                                          DEL PEAK 41(17P12) WILD-TYPE
  ASIAN                                                               53
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              152
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(78) Variable = DEL PEAK 42(17Q24.3) MUTATION ANALYSIS
D78V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 42(17Q24.3) MUTATED    40  23
  DEL PEAK 42(17Q24.3) WILD-TYPE 202  99
  DEL PEAK 42(17Q24.3) MUTATED DEL PEAK 42(17Q24.3) WILD-TYPE 
                            63                            301 
  DEL PEAK 42(17Q24.3) MUTATED DEL PEAK 42(17Q24.3) WILD-TYPE 
                            23                             99 
$`DEL PEAK 42(17Q24.3) MUTATED`
TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7959 TCGA-BR-8077 
        7.00         0.62        35.24        15.42        18.71         0.69 
TCGA-BR-8291 TCGA-BR-8361 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8485 TCGA-BR-8683 
       16.31        19.50        14.79         3.72         9.21         0.59 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF 
        1.15         0.66         0.72        13.51        20.65         1.15 
TCGA-BR-A4QI TCGA-CD-8524 TCGA-CD-8528 TCGA-CD-8533 TCGA-CD-A489 TCGA-CD-A48C 
       13.64         0.07         0.10         0.13         0.13         0.13 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 
        0.10        20.02        54.08         4.01        14.01        47.05 
TCGA-CG-4469 TCGA-CG-5730 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-8576 
        7.07         4.01        11.93        17.19        15.22         6.97 
TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A74A TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-HU-8243 
       16.44        11.31         7.40        16.24         0.23         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GP TCGA-HU-A4H2 TCGA-IN-8462 TCGA-IN-8663 
       12.59        14.17         8.98        12.95        18.81         3.39 
TCGA-KB-A93H TCGA-MX-A663 TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N6 
       28.90         4.31         8.61        16.67       115.69         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8PC TCGA-VQ-A8PX TCGA-VQ-A91X TCGA-VQ-A91Y 
        5.79         5.46        46.26        64.57         8.58         9.73 
TCGA-VQ-A925 TCGA-VQ-A928 TCGA-ZQ-A9CR 
        4.54         5.72         0.79 

$`DEL PEAK 42(17Q24.3) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         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        13.12        10.13        13.68        39.12         0.82 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        13.84        13.22        16.14         1.25         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         0.69         0.16        18.54 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 
       12.43         0.95         0.69        12.76        17.49         0.82 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        1.32        12.26         0.49        20.55         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       12.95         0.26         1.55         1.48         7.40         6.18 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        0.36         0.26        22.19         2.96         0.95        13.74 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 
        4.31        14.04         3.32         0.36        19.17         0.69 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 
        0.26        15.85         5.39         0.72        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         2.14        13.45         0.20         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        15.81        16.44        15.68         0.62 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       10.68        12.56         3.02        22.26         0.92        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       13.51        12.89         0.79        14.17         0.53        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM 
        0.66        19.36         0.46        20.42        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-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-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A 
        0.10         0.13         0.10         6.35         0.13         0.13 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.07         0.10         0.10         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
        1.02         7.99         8.05        29.98        19.07        12.03 
TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
       21.99         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         1.02         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-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 
       55.04        21.07         7.99        12.36        12.66        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         5.95 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
        4.14        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-D7-8578 
       24.72        16.80        19.50        17.19         0.23        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-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       13.71        11.24        11.44         9.76         2.96        15.65 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 
        4.34         7.13         0.62         7.79         6.58        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27         8.12         0.39        19.53         3.02 
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-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8602 
        1.55        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-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        19.36        17.69        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RI 
        8.88         8.81        27.42        21.21         3.45        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-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        6.87         5.56         1.81         2.53         5.56        60.56 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
        3.72        19.73        11.05         4.67       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-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        0.92        37.74        13.25        13.02        31.10        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       22.36        23.77         7.73        19.07        33.63        16.31 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.70        17.85         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       19.30        23.57        14.33        59.18        28.70        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Z 
        8.68        49.25        20.81         1.71         7.36        44.25 
TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J 
        8.61        55.43         6.58        40.08        29.98        21.11 
TCGA-ZA-A8F6 
        4.21 

  DEL PEAK 42(17Q24.3) MUTATED DEL PEAK 42(17Q24.3) WILD-TYPE 
                          0.07                           0.07 
  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 
                          8.94                          12.00 
[1] "0.1 - 115.7 (8.9)"  "0.1 - 122.3 (12.0)"
[1] "hr=" "1.2"
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       2       12       37       28        29
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 42(17Q24.3) MUTATED           8         0         17         13
  DEL PEAK 42(17Q24.3) WILD-TYPE        41         3         60         42
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 42(17Q24.3) MUTATED            7        7
  DEL PEAK 42(17Q24.3) WILD-TYPE         30       30
D78V3, multiclass
            clus
vv           DEL PEAK 42(17Q24.3) MUTATED DEL PEAK 42(17Q24.3) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              1                             12
  STAGE IB                              2                             37
  STAGE II                              3                             28
  STAGE IIA                             7                             29
  STAGE IIB                             8                             41
  STAGE III                             0                              3
  STAGE IIIA                           17                             60
  STAGE IIIB                           13                             42
  STAGE IIIC                            7                             30
  STAGE IV                              7                             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 42(17Q24.3) MUTATED     1  10  34  21
  DEL PEAK 42(17Q24.3) WILD-TYPE  20  77 139  83
D78V4, multiclass
    clus
vv   DEL PEAK 42(17Q24.3) MUTATED DEL PEAK 42(17Q24.3) WILD-TYPE
  T1                            1                             20
  T2                           10                             77
  T3                           34                            139
  T4                           21                             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 42(17Q24.3) MUTATED    16  15  21  14
  DEL PEAK 42(17Q24.3) WILD-TYPE 106  92  54  65
D78V5, multiclass
    clus
vv   DEL PEAK 42(17Q24.3) MUTATED DEL PEAK 42(17Q24.3) WILD-TYPE
  N0                           16                            106
  N1                           15                             92
  N2                           21                             54
  N3                           14                             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                              M0  M1  MX
  DEL PEAK 42(17Q24.3) MUTATED    64   3   3
  DEL PEAK 42(17Q24.3) WILD-TYPE 289  21  15
D78V6, multiclass
    clus
vv   DEL PEAK 42(17Q24.3) MUTATED DEL PEAK 42(17Q24.3) WILD-TYPE
  M0                           64                            289
  M1                            3                             21
  MX                            3                             15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V7, binary
                                cls
clus                               0   1
  DEL PEAK 42(17Q24.3) MUTATED    28  42
  DEL PEAK 42(17Q24.3) WILD-TYPE 123 202
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(17Q24.3) MUTATED     28   42
  DEL PEAK 42(17Q24.3) WILD-TYPE  123  202
        clus
vv       DEL PEAK 42(17Q24.3) MUTATED DEL PEAK 42(17Q24.3) WILD-TYPE
  FEMALE                           28                            123
  MALE                             42                            202
[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                                    58
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 42(17Q24.3) MUTATED                                                       27
  DEL PEAK 42(17Q24.3) WILD-TYPE                                                    130
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 42(17Q24.3) MUTATED                                                                  13
  DEL PEAK 42(17Q24.3) WILD-TYPE                                                                56
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 42(17Q24.3) MUTATED                                                 16
  DEL PEAK 42(17Q24.3) WILD-TYPE                                               48
                                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                                          2
  DEL PEAK 42(17Q24.3) WILD-TYPE                                        7
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)                           13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
                                                                   clus
vv                                                                  DEL PEAK 42(17Q24.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         58
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             56
  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                                                       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"
D78V9, binary
                                cls
clus                               0   1
  DEL PEAK 42(17Q24.3) MUTATED     0  70
  DEL PEAK 42(17Q24.3) WILD-TYPE   6 319
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(17Q24.3) MUTATED      0   70
  DEL PEAK 42(17Q24.3) WILD-TYPE    6  319
     clus
vv    DEL PEAK 42(17Q24.3) MUTATED DEL PEAK 42(17Q24.3) WILD-TYPE
  NO                             0                              6
  YES                           70                            319
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 42(17Q24.3) MUTATED    52   3   6   6
  DEL PEAK 42(17Q24.3) WILD-TYPE 266  13  12  19
D78V10, multiclass
    clus
vv   DEL PEAK 42(17Q24.3) MUTATED DEL PEAK 42(17Q24.3) WILD-TYPE
  R0                           52                            266
  R1                            3                             13
  R2                            6                             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"
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                         6
                                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      45
  DEL PEAK 42(17Q24.3) WILD-TYPE   198
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                                                               45
                                           clus
vv                                          DEL PEAK 42(17Q24.3) WILD-TYPE
  ASIAN                                                                 73
  BLACK OR AFRICAN AMERICAN                                              6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                198
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(79) Variable = DEL PEAK 43(18Q12.2) MUTATION ANALYSIS
D79V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 43(18Q12.2) MUTATED   100  43
  DEL PEAK 43(18Q12.2) WILD-TYPE 142  79
  DEL PEAK 43(18Q12.2) MUTATED DEL PEAK 43(18Q12.2) WILD-TYPE 
                           143                            221 
  DEL PEAK 43(18Q12.2) MUTATED DEL PEAK 43(18Q12.2) WILD-TYPE 
                            43                             79 
$`DEL PEAK 43(18Q12.2) MUTATED`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6457 
       11.70         6.61         6.18         9.57        10.13        13.68 
TCGA-BR-6564 TCGA-BR-6709 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7722 TCGA-BR-7723 
        0.82         1.25        35.24        15.42         0.16        18.54 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8364 
        0.95         0.69         1.32        12.95        16.31        22.19 
TCGA-BR-8366 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8677 
        0.95        14.04         3.32        20.22        15.81         0.49 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 
        0.59        15.68         0.62        10.68         1.15         0.66 
TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-CD-5799 
       22.26        12.89         0.66        13.51        13.64         3.25 
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-8532 TCGA-CD-8533 TCGA-CD-A486 
        0.07         0.10         0.13         0.10         0.13         6.35 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4436 
        0.13         0.13         0.10        20.02         3.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4466 
        8.05        54.08         4.01        47.05        19.07        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5724 
        7.07        12.00        22.98        30.97         1.02        12.03 
TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 
        4.01        55.04        12.36        19.13        20.55        18.54 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6822 TCGA-D7-8573 
        5.95        17.19         4.14        15.98        12.33        19.50 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
        0.23         6.97        21.14        14.27        16.44        15.16 
TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 
       11.24         9.76         2.96        15.65         7.40         0.62 
TCGA-EQ-8122 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
        7.79         8.12        19.53         3.02        22.29        17.06 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8604 
       13.58         0.56         1.55         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-A4H6 TCGA-IN-7808 
        6.25         2.10        12.95        17.69         9.67         3.45 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU 
       18.38         5.19         1.41         6.74         5.56         1.81 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-RD-A7C1 TCGA-RD-A8MW 
        2.53         5.56        60.56        28.90        16.67        37.91 
TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
      115.69        35.61         5.79         0.92        37.74         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PK TCGA-VQ-A8PU TCGA-VQ-A91X 
       13.25        31.10         7.73        17.85        23.57         8.58 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-AA6B TCGA-ZQ-A9CR 
       44.25         8.61         4.54        29.98         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 
        5.62         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        13.12         7.00        39.12 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        0.62        32.78        13.84        13.22        16.14         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         0.69        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         0.82         0.69        12.26         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 
       20.55         0.72         0.26         0.26         1.55         1.48 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8365 
        7.40         6.18        19.50         0.36         0.26         2.96 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 
       13.74         4.31         0.36        19.17        14.79         0.69 
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         0.72         9.21 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79         2.14        13.45         0.20         7.53 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4CS 
       11.54        15.81        16.44        12.56         3.02         0.92 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51         0.79         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       12.82        19.36         0.46        20.65        20.42         1.15 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-8530 TCGA-CD-8531 
       11.57         5.13         2.83        13.15         0.16         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI 
        0.13         0.10         0.13         0.13         0.07         0.10 
TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 
        0.10        27.02        15.95         1.02        14.01        29.98 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 
       12.03        21.99         9.01         6.97         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-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-A748 TCGA-D7-A74B 
       14.76        13.71        11.31        11.44         4.34         7.13 
TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
       16.24         6.58        14.47        72.23        21.27         0.39 
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-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
       13.08         6.44         6.87         3.72        19.73         4.31 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 
       11.05         8.61         4.67       122.30        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-VQ-A8DZ TCGA-VQ-A8E3 
       71.38        57.44         8.94        16.87        13.02        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       22.36        23.77        19.07        33.63        46.26        16.31 
TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
        2.70         1.87         9.27        23.41        15.65        19.30 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        59.18        28.70        11.70         8.68 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A924 
       49.25        20.81         1.71         7.36         9.73        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6J TCGA-ZA-A8F6 
        6.58         5.72        40.08        21.11         4.21 

  DEL PEAK 43(18Q12.2) MUTATED DEL PEAK 43(18Q12.2) WILD-TYPE 
                          0.07                           0.07 
  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 
                          9.67                          12.30 
[1] "0.1 - 115.7 (9.7)"  "0.1 - 122.3 (12.3)"
[1] "hr=" "1"  
D79V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 43(18Q12.2) MUTATED         0        4       13       15        16
  DEL PEAK 43(18Q12.2) WILD-TYPE       2        9       26       16        20
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 43(18Q12.2) MUTATED          19         1         34         25
  DEL PEAK 43(18Q12.2) WILD-TYPE        30         2         43         30
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 43(18Q12.2) MUTATED            9       14
  DEL PEAK 43(18Q12.2) WILD-TYPE         28       23
D79V3, multiclass
            clus
vv           DEL PEAK 43(18Q12.2) MUTATED DEL PEAK 43(18Q12.2) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              4                              9
  STAGE IB                             13                             26
  STAGE II                             15                             16
  STAGE IIA                            16                             20
  STAGE IIB                            19                             30
  STAGE III                             1                              2
  STAGE IIIA                           34                             43
  STAGE IIIB                           25                             30
  STAGE IIIC                            9                             28
  STAGE IV                             14                             23
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 43(18Q12.2) MUTATED    6 35 87 24
  DEL PEAK 43(18Q12.2) WILD-TYPE 15 52 86 80
D79V4, multiclass
    clus
vv   DEL PEAK 43(18Q12.2) MUTATED DEL PEAK 43(18Q12.2) WILD-TYPE
  T1                            6                             15
  T2                           35                             52
  T3                           87                             86
  T4                           24                             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 43(18Q12.2) MUTATED   43 45 32 31
  DEL PEAK 43(18Q12.2) WILD-TYPE 79 62 43 48
D79V5, multiclass
    clus
vv   DEL PEAK 43(18Q12.2) MUTATED DEL PEAK 43(18Q12.2) WILD-TYPE
  N0                           43                             79
  N1                           45                             62
  N2                           32                             43
  N3                           31                             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"
                                vv
clus                              M0  M1  MX
  DEL PEAK 43(18Q12.2) MUTATED   137   9   9
  DEL PEAK 43(18Q12.2) WILD-TYPE 216  15   9
D79V6, multiclass
    clus
vv   DEL PEAK 43(18Q12.2) MUTATED DEL PEAK 43(18Q12.2) WILD-TYPE
  M0                          137                            216
  M1                            9                             15
  MX                            9                              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V7, binary
                                cls
clus                               0   1
  DEL PEAK 43(18Q12.2) MUTATED    56  99
  DEL PEAK 43(18Q12.2) WILD-TYPE  95 145
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(18Q12.2) MUTATED     56   99
  DEL PEAK 43(18Q12.2) WILD-TYPE   95  145
        clus
vv       DEL PEAK 43(18Q12.2) MUTATED DEL PEAK 43(18Q12.2) WILD-TYPE
  FEMALE                           56                             95
  MALE                             99                            145
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 43(18Q12.2) MUTATED                                      24
  DEL PEAK 43(18Q12.2) WILD-TYPE                                    41
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 43(18Q12.2) MUTATED                                                       58
  DEL PEAK 43(18Q12.2) WILD-TYPE                                                     99
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 43(18Q12.2) MUTATED                                                                  30
  DEL PEAK 43(18Q12.2) WILD-TYPE                                                                39
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 43(18Q12.2) MUTATED                                                 32
  DEL PEAK 43(18Q12.2) WILD-TYPE                                               32
                                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                                          1
  DEL PEAK 43(18Q12.2) WILD-TYPE                                        8
D79V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 43(18Q12.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       24
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      58
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           30
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     1
                                                                   clus
vv                                                                  DEL PEAK 43(18Q12.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         41
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        99
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              32
  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"
D79V9, binary
                                cls
clus                               0   1
  DEL PEAK 43(18Q12.2) MUTATED     2 153
  DEL PEAK 43(18Q12.2) WILD-TYPE   4 236
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(18Q12.2) MUTATED      2  153
  DEL PEAK 43(18Q12.2) WILD-TYPE    4  236
     clus
vv    DEL PEAK 43(18Q12.2) MUTATED DEL PEAK 43(18Q12.2) WILD-TYPE
  NO                             2                              4
  YES                          153                            236
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 43(18Q12.2) MUTATED   121   9   6   9
  DEL PEAK 43(18Q12.2) WILD-TYPE 197   7  12  16
D79V10, multiclass
    clus
vv   DEL PEAK 43(18Q12.2) MUTATED DEL PEAK 43(18Q12.2) WILD-TYPE
  R0                          121                            197
  R1                            9                              7
  R2                            6                             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"
D79V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 43(18Q12.2) MUTATED      42                         0
  DEL PEAK 43(18Q12.2) WILD-TYPE    46                         6
                                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      89
  DEL PEAK 43(18Q12.2) WILD-TYPE   154
D79V12, multiclass
                                           clus
vv                                          DEL PEAK 43(18Q12.2) MUTATED
  ASIAN                                                               42
  BLACK OR AFRICAN AMERICAN                                            0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               89
                                           clus
vv                                          DEL PEAK 43(18Q12.2) WILD-TYPE
  ASIAN                                                                 46
  BLACK OR AFRICAN AMERICAN                                              6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                154
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(80) Variable = DEL PEAK 44(18Q21.2) MUTATION ANALYSIS
D80V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 44(18Q21.2) MUTATED   115  49
  DEL PEAK 44(18Q21.2) WILD-TYPE 127  73
  DEL PEAK 44(18Q21.2) MUTATED DEL PEAK 44(18Q21.2) WILD-TYPE 
                           164                            200 
  DEL PEAK 44(18Q21.2) MUTATED DEL PEAK 44(18Q21.2) WILD-TYPE 
                            49                             73 
$`DEL PEAK 44(18Q21.2) MUTATED`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6457 
       11.70         6.61         6.18         9.57        10.13        13.68 
TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6709 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
        7.00         0.82         1.25        35.24        15.42        28.01 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8060 TCGA-BR-8286 
        0.16        18.54         0.95         0.69         1.32        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8369 
        0.26        16.31         7.40        22.19         0.95        14.04 
TCGA-BR-8370 TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8677 
        3.32         5.39        20.22         1.12        15.81         0.49 
TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U 
       15.81         0.59        15.68         0.62        10.68         1.15 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J6 TCGA-BR-A4J8 
        0.66        22.26         0.92        12.89         0.66        13.51 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       20.42        13.64         3.25        13.15        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         6.35         0.13         0.13 
TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        0.10         3.02        27.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
        4.01        47.05        18.97         7.07        12.00        22.98 
TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5730 TCGA-CG-5732 
       30.97         1.02         1.02        12.03         4.01        55.04 
TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6525 
       12.36        11.93        19.13        20.55        18.54         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 
       17.19         4.14        15.98        12.33        24.72        19.50 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
        0.23         6.97        21.14        14.27        16.44        15.16 
TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 
       11.24         9.76         2.96        15.65         7.40         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        7.79        16.24         8.12        19.53         3.02        22.29 
TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HU-8243 
       17.06        13.58         0.56         1.55         0.23         5.92 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GD 
       14.17        12.10        10.62        24.30        12.30        22.75 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
       11.77         8.98         6.25         2.10        12.95        17.69 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL 
       12.30         9.67         3.45        18.81        18.38         5.19 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 
        1.41         6.44         6.74         5.56         1.81         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 
        5.56        60.56        28.90        16.67        37.91       115.69 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E2 
       35.61         5.79         0.92        37.74        13.25        31.10 
TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PD TCGA-VQ-A8PK TCGA-VQ-A8PU TCGA-VQ-A91K 
       21.73         7.73        16.31        17.85        23.57        49.25 
TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 
        1.71         8.58         9.73        44.25         8.61         4.54 
TCGA-VQ-AA6B TCGA-ZQ-A9CR 
       29.98         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 
        5.62         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        13.12        39.12         0.62 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        13.84        13.22        16.14         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         0.69        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 
        0.82         0.69        12.26         0.49        20.55         0.72 
TCGA-BR-8285 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        0.26         1.55         1.48         6.18        19.50         0.36 
TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8371 TCGA-BR-8372 
        0.26         2.96        13.74         4.31         0.36        19.17 
TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 
       14.79         0.69         0.26        15.85         3.72         0.72 
TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        9.21        12.79         2.14        13.45         0.20         7.53 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
       11.54        16.44        12.56         3.02        13.41        13.51 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 
        0.79         0.72        14.17         0.53        12.82        19.36 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.65         1.15        11.57         5.13         2.83 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 
        0.16         0.10         0.13         0.10         0.13         0.13 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4305 TCGA-CG-4306 
        0.07         0.10         0.10        20.02        15.95         1.02 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 
       14.01        29.98        19.07        12.03        21.99         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-A748 TCGA-D7-A74B 
       14.76        13.71        11.31        11.44         4.34         7.13 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-8209 
        6.58        14.47        72.23        21.27         0.39        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-MX-A5UG TCGA-MX-A5UJ 
        3.39         5.36        13.08         6.87         3.72        19.73 
TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 
        4.31        11.05         8.61         4.67       122.30        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-VQ-A8DU 
      116.38        71.38        57.44         8.94        16.87         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       13.02        22.36        23.77        19.07        33.63        46.26 
TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
        2.70         1.87         9.27        23.41        15.65        19.30 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        59.18        28.70        11.70         8.68 
TCGA-VQ-A91Q TCGA-VQ-A91W TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 
       20.81         7.36        55.43         6.58         5.72        40.08 
TCGA-VQ-AA6J TCGA-ZA-A8F6 
       21.11         4.21 

  DEL PEAK 44(18Q21.2) MUTATED DEL PEAK 44(18Q21.2) WILD-TYPE 
                          0.07                           0.07 
  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 
                         9.745                         12.495 
[1] "0.1 - 115.7 (9.7)"  "0.1 - 122.3 (12.5)"
[1] "hr=" "1"  
D80V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 44(18Q21.2) MUTATED         0        4       16       16        18
  DEL PEAK 44(18Q21.2) WILD-TYPE       2        9       23       15        18
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 44(18Q21.2) MUTATED          22         1         37         26
  DEL PEAK 44(18Q21.2) WILD-TYPE        27         2         40         29
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 44(18Q21.2) MUTATED           15       16
  DEL PEAK 44(18Q21.2) WILD-TYPE         22       21
D80V3, multiclass
            clus
vv           DEL PEAK 44(18Q21.2) MUTATED DEL PEAK 44(18Q21.2) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              4                              9
  STAGE IB                             16                             23
  STAGE II                             16                             15
  STAGE IIA                            18                             18
  STAGE IIB                            22                             27
  STAGE III                             1                              2
  STAGE IIIA                           37                             40
  STAGE IIIB                           26                             29
  STAGE IIIC                           15                             22
  STAGE IV                             16                             21
[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 40 95 32
  DEL PEAK 44(18Q21.2) WILD-TYPE 14 47 78 72
D80V4, multiclass
    clus
vv   DEL PEAK 44(18Q21.2) MUTATED DEL PEAK 44(18Q21.2) WILD-TYPE
  T1                            7                             14
  T2                           40                             47
  T3                           95                             78
  T4                           32                             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"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 44(18Q21.2) MUTATED   49 51 33 39
  DEL PEAK 44(18Q21.2) WILD-TYPE 73 56 42 40
D80V5, multiclass
    clus
vv   DEL PEAK 44(18Q21.2) MUTATED DEL PEAK 44(18Q21.2) WILD-TYPE
  N0                           49                             73
  N1                           51                             56
  N2                           33                             42
  N3                           39                             40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  DEL PEAK 44(18Q21.2) MUTATED   155  11  11
  DEL PEAK 44(18Q21.2) WILD-TYPE 198  13   7
D80V6, multiclass
    clus
vv   DEL PEAK 44(18Q21.2) MUTATED DEL PEAK 44(18Q21.2) WILD-TYPE
  M0                          155                            198
  M1                           11                             13
  MX                           11                              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V7, binary
                                cls
clus                               0   1
  DEL PEAK 44(18Q21.2) MUTATED    63 114
  DEL PEAK 44(18Q21.2) WILD-TYPE  88 130
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(18Q21.2) MUTATED     63  114
  DEL PEAK 44(18Q21.2) WILD-TYPE   88  130
        clus
vv       DEL PEAK 44(18Q21.2) MUTATED DEL PEAK 44(18Q21.2) WILD-TYPE
  FEMALE                           63                             88
  MALE                            114                            130
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 44(18Q21.2) MUTATED                                      25
  DEL PEAK 44(18Q21.2) WILD-TYPE                                    40
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 44(18Q21.2) MUTATED                                                       68
  DEL PEAK 44(18Q21.2) WILD-TYPE                                                     89
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 44(18Q21.2) MUTATED                                                                  36
  DEL PEAK 44(18Q21.2) WILD-TYPE                                                                33
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 44(18Q21.2) MUTATED                                                 34
  DEL PEAK 44(18Q21.2) WILD-TYPE                                               30
                                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                                          2
  DEL PEAK 44(18Q21.2) WILD-TYPE                                        7
D80V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 44(18Q21.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       25
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      68
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
                                                                   clus
vv                                                                  DEL PEAK 44(18Q21.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         40
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        89
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             33
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              30
  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"
D80V9, binary
                                cls
clus                               0   1
  DEL PEAK 44(18Q21.2) MUTATED     2 175
  DEL PEAK 44(18Q21.2) WILD-TYPE   4 214
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(18Q21.2) MUTATED      2  175
  DEL PEAK 44(18Q21.2) WILD-TYPE    4  214
     clus
vv    DEL PEAK 44(18Q21.2) MUTATED DEL PEAK 44(18Q21.2) WILD-TYPE
  NO                             2                              4
  YES                          175                            214
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 44(18Q21.2) MUTATED   140  10   7  10
  DEL PEAK 44(18Q21.2) WILD-TYPE 178   6  11  15
D80V10, multiclass
    clus
vv   DEL PEAK 44(18Q21.2) MUTATED DEL PEAK 44(18Q21.2) WILD-TYPE
  R0                          140                            178
  R1                           10                              6
  R2                            7                             11
  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                         0
  DEL PEAK 44(18Q21.2) WILD-TYPE    42                         6
                                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     107
  DEL PEAK 44(18Q21.2) WILD-TYPE   136
D80V12, multiclass
                                           clus
vv                                          DEL PEAK 44(18Q21.2) MUTATED
  ASIAN                                                               46
  BLACK OR AFRICAN AMERICAN                                            0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              107
                                           clus
vv                                          DEL PEAK 44(18Q21.2) WILD-TYPE
  ASIAN                                                                 42
  BLACK OR AFRICAN AMERICAN                                              6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                136
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(81) Variable = DEL PEAK 45(19P13.3) MUTATION ANALYSIS
D81V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 45(19P13.3) MUTATED    82  44
  DEL PEAK 45(19P13.3) WILD-TYPE 160  78
  DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE 
                           126                            238 
  DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE 
                            44                             78 
$`DEL PEAK 45(19P13.3) MUTATED`
TCGA-BR-4183 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7716 
        6.61         7.00         0.62         9.21        35.24        28.01 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8289 
       18.54         0.95         1.32         0.69        12.95         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8485 TCGA-BR-8486 
       16.31         1.55        14.04        14.79         9.21        20.22 
TCGA-BR-8678 TCGA-BR-8690 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 
       11.54        10.68        22.26         0.92        12.89         0.72 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8524 
       20.65         1.15         3.25        13.15         0.30         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8533 
        0.07         0.07         0.07         0.13         0.16         0.13 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         6.35         0.13         0.13         0.13         0.13 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 
        0.10        20.02         7.99        54.08         4.01        29.98 
TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5724 
       19.07        21.99        18.97        22.98         1.02        12.03 
TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6520 TCGA-D7-6525 
       15.02         4.01        55.04        12.66        18.84         5.95 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8573 
        4.14        15.98        12.79        10.55        11.31        19.50 
TCGA-D7-8578 TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C 
       21.14         2.96        15.65         7.79        72.23         8.12 
TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-A4GH 
        3.02        17.06         0.56         5.92        12.59        11.77 
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        17.69        12.30 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
        9.67        27.42        21.21        18.81         3.39        18.38 
TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU 
        5.19         1.41         6.74         6.87         5.56         1.81 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-RD-A7BT TCGA-RD-A7BW 
        2.53         5.56        60.56        28.90         8.61         4.67 
TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       37.91         8.94         5.79         0.92        37.74         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       13.25        13.02        31.10         7.73         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
        1.87        23.57         1.71         8.58         9.73        44.25 
TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6J TCGA-ZQ-A9CR 
        8.61         4.54         5.72        40.08        21.11         0.79 

$`DEL PEAK 45(19P13.3) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
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-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       13.12        10.13        13.68        39.12         0.82        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       13.84        13.22        16.14         1.25         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-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 
       15.42         0.69         0.16        12.43         0.69        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49         0.82        12.26         0.49        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        0.72         0.26         1.48         7.40         6.18        19.50 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        0.36         0.26        22.19         2.96         0.95        13.74 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 
        4.31         3.32         0.36        19.17         0.69         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         0.72         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         2.14        13.45         0.20         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         0.59        15.68         0.62        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
        1.15         0.66         3.02        13.41        13.51         0.79 
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 
        0.07         0.10         0.10         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4465 
        1.02         8.05        14.01        47.05        12.03         9.01 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 
        7.07        12.00        30.97         6.97         1.02         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-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-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6822 
       18.54        18.61        17.85        17.19        15.22        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 
       24.72        16.80        17.19         0.23         6.97        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-A748 
       13.71        11.24        11.31        11.44         9.76         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 
        7.40         7.13         0.62        16.24         6.58        14.47 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
       21.27         0.39        19.53        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         1.55         0.23        18.08        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       14.27        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-A4GQ TCGA-HU-A4GT 
       22.75        25.81        21.37        29.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 
       10.19         0.26        19.36         8.88         8.81         3.45 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        5.36        13.08         6.44         3.72        19.73         4.31 
TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       11.05        16.67       122.30        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A8E3 TCGA-VQ-A8P2 
       71.38        57.44        35.61        16.87        21.73        22.36 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PO 
       23.77        19.07        33.63        46.26        16.31         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       23.41        15.65        19.30        64.57        14.33        59.18 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91W 
       28.70        11.70         8.68        49.25        20.81         7.36 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-AA6B TCGA-ZA-A8F6 
       55.43         6.58        29.98         4.21 

  DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE 
                          0.07                           0.07 
  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 
                         8.610                         12.395 
[1] "0.1 - 72.2 (8.6)"   "0.1 - 122.3 (12.4)"
[1] "hr=" "1.3"
D81V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 45(19P13.3) MUTATED         0        6       13       13        12
  DEL PEAK 45(19P13.3) WILD-TYPE       2        7       26       18        24
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 45(19P13.3) MUTATED          21         0         28         14
  DEL PEAK 45(19P13.3) WILD-TYPE        28         3         49         41
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 45(19P13.3) MUTATED           10       15
  DEL PEAK 45(19P13.3) WILD-TYPE         27       22
D81V3, multiclass
            clus
vv           DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              6                              7
  STAGE IB                             13                             26
  STAGE II                             13                             18
  STAGE IIA                            12                             24
  STAGE IIB                            21                             28
  STAGE III                             0                              3
  STAGE IIIA                           28                             49
  STAGE IIIB                           14                             41
  STAGE IIIC                           10                             27
  STAGE IV                             15                             22
[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  33  65  28
  DEL PEAK 45(19P13.3) WILD-TYPE  14  54 108  76
D81V4, multiclass
    clus
vv   DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE
  T1                            7                             14
  T2                           33                             54
  T3                           65                            108
  T4                           28                             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 45(19P13.3) MUTATED   42 40 24 27
  DEL PEAK 45(19P13.3) WILD-TYPE 80 67 51 52
D81V5, multiclass
    clus
vv   DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE
  N0                           42                             80
  N1                           40                             67
  N2                           24                             51
  N3                           27                             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"
                                vv
clus                              M0  M1  MX
  DEL PEAK 45(19P13.3) MUTATED   121   8   8
  DEL PEAK 45(19P13.3) WILD-TYPE 232  16  10
D81V6, multiclass
    clus
vv   DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE
  M0                          121                            232
  M1                            8                             16
  MX                            8                             10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V7, binary
                                cls
clus                               0   1
  DEL PEAK 45(19P13.3) MUTATED    45  92
  DEL PEAK 45(19P13.3) WILD-TYPE 106 152
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(19P13.3) MUTATED     45   92
  DEL PEAK 45(19P13.3) WILD-TYPE  106  152
        clus
vv       DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE
  FEMALE                           45                            106
  MALE                             92                            152
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 45(19P13.3) MUTATED                                      14
  DEL PEAK 45(19P13.3) WILD-TYPE                                    51
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 45(19P13.3) MUTATED                                                       52
  DEL PEAK 45(19P13.3) WILD-TYPE                                                    105
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 45(19P13.3) MUTATED                                                                  33
  DEL PEAK 45(19P13.3) WILD-TYPE                                                                36
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 45(19P13.3) MUTATED                                                 25
  DEL PEAK 45(19P13.3) WILD-TYPE                                               39
                                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                                          2
  DEL PEAK 45(19P13.3) WILD-TYPE                                        7
D81V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 45(19P13.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       14
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      52
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           33
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            25
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
                                                                   clus
vv                                                                  DEL PEAK 45(19P13.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         51
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       105
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              39
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      3
  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"
D81V9, binary
                                cls
clus                               0   1
  DEL PEAK 45(19P13.3) MUTATED     5 132
  DEL PEAK 45(19P13.3) WILD-TYPE   1 257
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(19P13.3) MUTATED      5  132
  DEL PEAK 45(19P13.3) WILD-TYPE    1  257
     clus
vv    DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE
  NO                             5                              1
  YES                          132                            257
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 45(19P13.3) MUTATED   110   2   9   6
  DEL PEAK 45(19P13.3) WILD-TYPE 208  14   9  19
D81V10, multiclass
    clus
vv   DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE
  R0                          110                            208
  R1                            2                             14
  R2                            9                              9
  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                         3
  DEL PEAK 45(19P13.3) WILD-TYPE    51                         3
                                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      73
  DEL PEAK 45(19P13.3) WILD-TYPE   170
D81V12, multiclass
                                           clus
vv                                          DEL PEAK 45(19P13.3) MUTATED
  ASIAN                                                               37
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               73
                                           clus
vv                                          DEL PEAK 45(19P13.3) WILD-TYPE
  ASIAN                                                                 51
  BLACK OR AFRICAN AMERICAN                                              3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                170
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(82) Variable = DEL PEAK 46(19Q13.11) MUTATION ANALYSIS
D82V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 46(19Q13.11) MUTATED    42  19
  DEL PEAK 46(19Q13.11) WILD-TYPE 200 103
  DEL PEAK 46(19Q13.11) MUTATED DEL PEAK 46(19Q13.11) WILD-TYPE 
                             61                             303 
  DEL PEAK 46(19Q13.11) MUTATED DEL PEAK 46(19Q13.11) WILD-TYPE 
                             19                             103 
$`DEL PEAK 46(19Q13.11) MUTATED`
TCGA-BR-4183 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7723 TCGA-BR-7901 
        6.61         9.21        35.24        15.42        18.54         0.95 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8369 TCGA-BR-8678 TCGA-BR-A4CS 
        1.32         0.69         0.26        14.04        11.54         0.92 
TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8533 
        1.15         3.25        13.15         0.07         0.13         0.13 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CG-4300 TCGA-CG-4440 TCGA-CG-4466 TCGA-CG-5724 
        6.35         0.13        20.02         4.01        18.97        12.03 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8573 
       17.19         4.14        15.22        12.79        11.31        19.50 
TCGA-D7-A4YY TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-FP-8099 
       13.78        11.31         2.96        15.65         0.62        17.06 
TCGA-FP-8631 TCGA-HU-8243 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H2 
        0.56         5.92        11.77         8.98         6.25        12.95 
TCGA-HU-A4H4 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU 
       17.69        27.42        18.38         6.87         5.56         1.81 
TCGA-KB-A93H TCGA-RD-A8MW TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8P3 TCGA-VQ-A8PK 
       28.90        37.91         5.46        13.02        23.77        17.85 
TCGA-VQ-A8PU TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-AA6J 
       23.57         8.58        44.25         8.61         4.54        21.11 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK 46(19Q13.11) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
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-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.12        10.13        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        0.62        32.78        13.84        13.22        16.14         1.25 
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         0.69         0.16        12.43 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 
        0.69        12.76        18.71        17.49         0.82        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 
        0.49        20.55         0.72         0.26        12.95        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        1.55         1.48         7.40         6.18        19.50         0.36 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19         2.96         0.95        13.74         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 
        3.32         0.36        19.17        14.79         0.69         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         0.72         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         2.14        13.45         0.20 
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         0.59        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        0.62        10.68        12.56         1.15         0.66         3.02 
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         0.79         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-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 
        2.83        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.07         0.10         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        0.10         0.13         0.13         0.13         0.07         0.10 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10         0.10         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        7.99         8.05        54.08        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 
       19.07        12.03        21.99         9.01         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         1.02         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        55.04        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-D7-6815 TCGA-D7-6818 TCGA-D7-6822 
       18.61        17.85         5.95        15.98        10.55        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       24.72        16.80        17.19         0.23         6.97        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 
       20.91        14.27        16.44         5.92        15.16        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74A 
       13.71        11.24        11.44         9.76         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        7.13         7.79        16.24         6.58        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27         8.12         0.39        19.53         3.02        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB 
       59.54         5.03        13.58         1.55         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       26.47         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-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       11.84        24.20         3.25        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
       29.98         0.10         6.51        10.19         0.26         2.10 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       19.36        12.30         9.67         8.88         8.81        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45        18.81         3.39         5.36         5.19        13.08 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        1.41         6.44         6.74         2.53         5.56        60.56 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        3.72        19.73         4.31        11.05         8.61         4.67 
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-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        16.87         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P5 
       37.74        13.25        31.10        21.73        22.36         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PM 
       19.07        33.63        46.26        16.31         2.70         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        19.30        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q 
       59.18        28.70        11.70         8.68        49.25        20.81 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
        1.71         7.36         9.73        55.43         6.58         5.72 
TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-ZA-A8F6 
       40.08        29.98         4.21 

  DEL PEAK 46(19Q13.11) MUTATED DEL PEAK 46(19Q13.11) WILD-TYPE 
                           0.07                            0.07 
  DEL PEAK 46(19Q13.11) MUTATED DEL PEAK 46(19Q13.11) WILD-TYPE 
                          44.25                          122.30 
  DEL PEAK 46(19Q13.11) MUTATED DEL PEAK 46(19Q13.11) WILD-TYPE 
                          11.31                           11.84 
[1] "0.1 - 44.2 (11.3)"  "0.1 - 122.3 (11.8)"
[1] "hr=" "1.1"
D82V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 46(19Q13.11) MUTATED         0        2        6        7         6
  DEL PEAK 46(19Q13.11) WILD-TYPE       2       11       33       24        30
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 46(19Q13.11) MUTATED           6         0         11         12
  DEL PEAK 46(19Q13.11) WILD-TYPE        43         3         66         43
                                 vv
clus                              STAGE IIIC STAGE IV
  DEL PEAK 46(19Q13.11) MUTATED            5        7
  DEL PEAK 46(19Q13.11) WILD-TYPE         32       30
D82V3, multiclass
            clus
vv           DEL PEAK 46(19Q13.11) MUTATED DEL PEAK 46(19Q13.11) WILD-TYPE
  STAGE I                                0                               2
  STAGE IA                               2                              11
  STAGE IB                               6                              33
  STAGE II                               7                              24
  STAGE IIA                              6                              30
  STAGE IIB                              6                              43
  STAGE III                              0                               3
  STAGE IIIA                            11                              66
  STAGE IIIB                            12                              43
  STAGE IIIC                             5                              32
  STAGE IV                               7                              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 46(19Q13.11) MUTATED     3  13  32  14
  DEL PEAK 46(19Q13.11) WILD-TYPE  18  74 141  90
D82V4, multiclass
    clus
vv   DEL PEAK 46(19Q13.11) MUTATED DEL PEAK 46(19Q13.11) WILD-TYPE
  T1                             3                              18
  T2                            13                              74
  T3                            32                             141
  T4                            14                              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 46(19Q13.11) MUTATED    18  15  13  16
  DEL PEAK 46(19Q13.11) WILD-TYPE 104  92  62  63
D82V5, multiclass
    clus
vv   DEL PEAK 46(19Q13.11) MUTATED DEL PEAK 46(19Q13.11) WILD-TYPE
  N0                            18                             104
  N1                            15                              92
  N2                            13                              62
  N3                            16                              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                               M0  M1  MX
  DEL PEAK 46(19Q13.11) MUTATED    55   6   3
  DEL PEAK 46(19Q13.11) WILD-TYPE 298  18  15
D82V6, multiclass
    clus
vv   DEL PEAK 46(19Q13.11) MUTATED DEL PEAK 46(19Q13.11) WILD-TYPE
  M0                            55                             298
  M1                             6                              18
  MX                             3                              15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V7, binary
                                 cls
clus                                0   1
  DEL PEAK 46(19Q13.11) MUTATED    23  41
  DEL PEAK 46(19Q13.11) WILD-TYPE 128 203
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 46(19Q13.11) MUTATED     23   41
  DEL PEAK 46(19Q13.11) WILD-TYPE  128  203
        clus
vv       DEL PEAK 46(19Q13.11) MUTATED DEL PEAK 46(19Q13.11) WILD-TYPE
  FEMALE                            23                             128
  MALE                              41                             203
[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                                    60
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 46(19Q13.11) MUTATED                                                       23
  DEL PEAK 46(19Q13.11) WILD-TYPE                                                    134
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 46(19Q13.11) MUTATED                                                                  13
  DEL PEAK 46(19Q13.11) WILD-TYPE                                                                56
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 46(19Q13.11) MUTATED                                                 19
  DEL PEAK 46(19Q13.11) WILD-TYPE                                               45
                                 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                                        8
D82V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 46(19Q13.11) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       23
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            13
  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                                                      1
                                                                   clus
vv                                                                  DEL PEAK 46(19Q13.11) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          60
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              56
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               45
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       20
  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"
D82V9, binary
                                 cls
clus                                0   1
  DEL PEAK 46(19Q13.11) MUTATED     1  63
  DEL PEAK 46(19Q13.11) WILD-TYPE   5 326
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 46(19Q13.11) MUTATED      1   63
  DEL PEAK 46(19Q13.11) WILD-TYPE    5  326
     clus
vv    DEL PEAK 46(19Q13.11) MUTATED DEL PEAK 46(19Q13.11) WILD-TYPE
  NO                              1                               5
  YES                            63                             326
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 46(19Q13.11) MUTATED    53   0   5   3
  DEL PEAK 46(19Q13.11) WILD-TYPE 265  16  13  22
D82V10, multiclass
    clus
vv   DEL PEAK 46(19Q13.11) MUTATED DEL PEAK 46(19Q13.11) WILD-TYPE
  R0                            53                             265
  R1                             0                              16
  R2                             5                              13
  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                         2
  DEL PEAK 46(19Q13.11) WILD-TYPE    73                         4
                                 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      41
  DEL PEAK 46(19Q13.11) WILD-TYPE   202
D82V12, multiclass
                                           clus
vv                                          DEL PEAK 46(19Q13.11) MUTATED
  ASIAN                                                                15
  BLACK OR AFRICAN AMERICAN                                             2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                41
                                           clus
vv                                          DEL PEAK 46(19Q13.11) WILD-TYPE
  ASIAN                                                                  73
  BLACK OR AFRICAN AMERICAN                                               4
  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"

Clustering(83) Variable = DEL PEAK 47(20P12.1) MUTATION ANALYSIS
D83V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 47(20P12.1) MUTATED    15  17
  DEL PEAK 47(20P12.1) WILD-TYPE 227 105
  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                            32                            332 
  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                            17                            105 
$`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        10.13         0.82        18.54         0.26        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         0.13         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         4.14         0.23         6.97 
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-IP-7968 TCGA-RD-A8MW TCGA-VQ-A8DU TCGA-VQ-A8P3 TCGA-VQ-A8PC TCGA-VQ-A8PK 
        2.53        37.91         5.46        23.77        46.26        17.85 
TCGA-VQ-A925 TCGA-VQ-AA68 
        4.54        40.08 

$`DEL PEAK 47(20P12.1) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         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-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 
       13.12        13.68         7.00        39.12         0.62        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       13.84        13.22        16.14         1.25         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-7722 
       35.24        23.93        15.42        28.01         0.69         0.16 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         0.95         0.69        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
        0.82         1.32         0.69        12.26         0.49        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.72         0.26        12.95        16.31         1.55         1.48 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        19.50         0.36         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
        2.96         0.95        13.74         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 
        0.36        19.17        14.79         0.69         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         0.72         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         2.14        13.45         0.20         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         0.59        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        0.62        10.68        12.56         1.15         0.66         3.02 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 
       22.26         0.92        13.41        13.51         0.79         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-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-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         6.35         0.13 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.13         0.13         0.07         0.10         0.10         0.10 
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-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-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       22.98        30.97         1.02         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-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       11.93        19.13        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
        5.95        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8578 
       12.33        24.72        16.80        19.50        17.19        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        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-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 
        2.96        15.65         4.34         7.40         7.13         7.79 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        6.58        14.47        72.23        21.27         8.12         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53         3.02        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         1.55         0.23        18.08        26.47 
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-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-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        22.75        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        17.69        12.30         9.67 
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-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
        3.39        18.38         5.19        13.08         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
        6.87         5.56         1.81         5.56        60.56        28.90 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        3.72        19.73         4.31        11.05         8.61         4.67 
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-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        16.87         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 
       37.74        13.25        13.02        31.10        21.73        22.36 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PM 
        7.73        19.07        33.63        16.31         2.70         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        19.30        23.57        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        59.18        28.70        11.70         8.68        49.25 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       20.81         1.71         7.36         8.58         9.73        44.25 
TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6B TCGA-VQ-AA6J 
        8.61        55.43         6.58         5.72        29.98        21.11 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        4.21         0.79 

  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                          0.07                           0.07 
  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 
                          8.55                          11.70 
[1] "0.1 - 46.3 (8.6)"   "0.1 - 122.3 (11.7)"
[1] "hr=" "1.9"
D83V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 47(20P12.1) MUTATED         0        1        4        2         2
  DEL PEAK 47(20P12.1) WILD-TYPE       2       12       35       29        34
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 47(20P12.1) MUTATED           4         0          8          8
  DEL PEAK 47(20P12.1) WILD-TYPE        45         3         69         47
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 47(20P12.1) MUTATED            1        4
  DEL PEAK 47(20P12.1) WILD-TYPE         36       33
D83V3, multiclass
            clus
vv           DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              1                             12
  STAGE IB                              4                             35
  STAGE II                              2                             29
  STAGE IIA                             2                             34
  STAGE IIB                             4                             45
  STAGE III                             0                              3
  STAGE IIIA                            8                             69
  STAGE IIIB                            8                             47
  STAGE IIIC                            1                             36
  STAGE IV                              4                             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 47(20P12.1) MUTATED     2   7  17   8
  DEL PEAK 47(20P12.1) WILD-TYPE  19  80 156  96
D83V4, multiclass
    clus
vv   DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE
  T1                            2                             19
  T2                            7                             80
  T3                           17                            156
  T4                            8                             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 47(20P12.1) MUTATED     9  10   8   7
  DEL PEAK 47(20P12.1) WILD-TYPE 113  97  67  72
D83V5, multiclass
    clus
vv   DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE
  N0                            9                            113
  N1                           10                             97
  N2                            8                             67
  N3                            7                             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"
                                vv
clus                              M0  M1  MX
  DEL PEAK 47(20P12.1) MUTATED    28   3   3
  DEL PEAK 47(20P12.1) WILD-TYPE 325  21  15
D83V6, multiclass
    clus
vv   DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE
  M0                           28                            325
  M1                            3                             21
  MX                            3                             15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V7, binary
                                cls
clus                               0   1
  DEL PEAK 47(20P12.1) MUTATED    14  20
  DEL PEAK 47(20P12.1) WILD-TYPE 137 224
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(20P12.1) MUTATED     14   20
  DEL PEAK 47(20P12.1) WILD-TYPE  137  224
        clus
vv       DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE
  FEMALE                           14                            137
  MALE                             20                            224
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 47(20P12.1) MUTATED                                       2
  DEL PEAK 47(20P12.1) WILD-TYPE                                    63
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 47(20P12.1) MUTATED                                                       16
  DEL PEAK 47(20P12.1) WILD-TYPE                                                    141
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 47(20P12.1) MUTATED                                                                   3
  DEL PEAK 47(20P12.1) WILD-TYPE                                                                66
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 47(20P12.1) MUTATED                                                  9
  DEL PEAK 47(20P12.1) WILD-TYPE                                               55
                                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                                        8
D83V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 47(20P12.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      16
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             9
  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                                                         63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       141
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             66
  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                                                       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"
D83V9, binary
                                cls
clus                               0   1
  DEL PEAK 47(20P12.1) MUTATED     2  32
  DEL PEAK 47(20P12.1) WILD-TYPE   4 357
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(20P12.1) MUTATED      2   32
  DEL PEAK 47(20P12.1) WILD-TYPE    4  357
     clus
vv    DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE
  NO                             2                              4
  YES                           32                            357
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 47(20P12.1) MUTATED    28   1   3   1
  DEL PEAK 47(20P12.1) WILD-TYPE 290  15  15  24
D83V10, multiclass
    clus
vv   DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE
  R0                           28                            290
  R1                            1                             15
  R2                            3                             15
  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                         0
  DEL PEAK 47(20P12.1) WILD-TYPE    82                         6
                                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      23
  DEL PEAK 47(20P12.1) WILD-TYPE   220
D83V12, multiclass
                                           clus
vv                                          DEL PEAK 47(20P12.1) MUTATED
  ASIAN                                                                6
  BLACK OR AFRICAN AMERICAN                                            0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               23
                                           clus
vv                                          DEL PEAK 47(20P12.1) WILD-TYPE
  ASIAN                                                                 82
  BLACK OR AFRICAN AMERICAN                                              6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(84) Variable = DEL PEAK 48(21Q11.2) MUTATION ANALYSIS
D84V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 48(21Q11.2) MUTATED    97  50
  DEL PEAK 48(21Q11.2) WILD-TYPE 145  72
  DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE 
                           147                            217 
  DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE 
                            50                             72 
$`DEL PEAK 48(21Q11.2) MUTATED`
TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 
       11.70         6.97        13.68         7.00         0.82         0.62 
TCGA-BR-6803 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7959 
       31.20        35.24        15.42        28.01        18.54        18.71 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8291 TCGA-BR-8296 
        1.32        12.26         0.49         0.72        16.31         1.48 
TCGA-BR-8361 TCGA-BR-8365 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8483 
       19.50         2.96         4.31        14.04        14.79         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8686 
        0.72         9.21        20.22        11.54         0.59        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY 
        0.62        10.68         0.66        22.26         0.92        12.89 
TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.72        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8535 
       13.64         0.07         0.07         0.07         0.16         0.13 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 
        0.13         0.13         0.13         0.13         0.10        20.02 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4475 
       54.08         4.01        47.05        12.03        18.97        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5728 
       30.97         6.97         1.02         1.02        12.03        65.10 
TCGA-CG-5730 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6525 TCGA-D7-6526 
        4.01        11.93        19.13        20.55         5.95        17.19 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8578 TCGA-D7-A4YU 
       15.98        12.79        11.31        12.33        21.14        16.44 
TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C 
       11.31        15.65         0.62         7.79        72.23         8.12 
TCGA-FP-7829 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8249 
       19.53         1.55         0.23        26.47         1.51        14.17 
TCGA-HU-8604 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GP TCGA-HU-A4GY TCGA-HU-A4H3 
       12.10        11.84         3.25         8.98         0.26        19.36 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 
       12.30         9.67        27.42        21.21        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A7NT 
       18.38         5.36         5.19         1.41         6.74         5.56 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A663 
        1.81         2.53         5.56        60.56        28.90         4.31 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      122.30        37.91       115.69        57.44         8.94        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E3 
        5.79         0.92        37.74        13.25        13.02        21.73 
TCGA-VQ-A8P5 TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PP TCGA-VQ-A8PU 
        7.73         2.70        17.85         1.87        23.41        23.57 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U 
       64.57        14.33        28.70        49.25        20.81         1.71 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 
        8.58         9.73        44.25         8.61        55.43         4.54 
TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-ZQ-A9CR 
       40.08        29.98         0.79 

$`DEL PEAK 48(21Q11.2) WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        5.62         6.61         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        13.12 
TCGA-BR-6456 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       10.13        39.12        32.78        13.84        13.22        16.14 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 
        1.25         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-7851 
        9.21        24.76        23.93         0.69         0.16        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        0.95         0.69        12.76        17.49         0.82         0.69 
TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8297 
       20.55         0.26        12.95         0.26         1.55         7.40 
TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.36         0.26        22.19         0.95        13.74 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 
        3.32         0.36        19.17         0.69         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        3.72         1.12        12.79        15.81         2.14        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-A44T 
        0.20         7.53         0.49        15.81        16.44        12.56 
TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 
        1.15         3.02        13.41        13.51         0.79        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4QL TCGA-BR-A4QM 
        0.53        12.82         0.66        19.36        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-8525 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-8536 TCGA-CD-A486 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 
        0.10         6.35         0.07         0.10         0.10         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 
       27.02        15.95         1.02         7.99         8.05        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 
       29.98        19.07        21.99         9.01         7.07        12.00 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       79.07        55.04        21.07         7.99        12.36        12.66 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6528 
       18.84        18.54        18.61        17.85         4.14        15.22 
TCGA-D7-6818 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       10.55        24.72        16.80        19.50        17.19         0.23 
TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
        6.97        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-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 
        4.34         7.40         7.13        16.24         6.58        14.47 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       21.27         0.39         3.02        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-A5NB TCGA-HU-8243 TCGA-HU-8244 
        5.03        13.58         0.56        18.08         5.92        14.27 
TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       12.59        11.41        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       12.30        24.20        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-A4H0 
       29.98         0.10         6.51         6.25        10.19         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-A6RN 
       12.95        17.69         8.88         8.81         3.45        13.08 
TCGA-IN-A6RP TCGA-IN-A6RS TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BT 
        6.44         6.87         3.72        19.73        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB 
        4.67        16.67        40.64       116.38        71.38        16.87 
TCGA-VQ-A8DU TCGA-VQ-A8E2 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
        5.46        31.10        22.36        23.77        19.07        33.63 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PZ 
       46.26        16.31         9.27        15.65        19.30        59.18 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91W TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6J 
       11.70         8.68         7.36         6.58         5.72        21.11 
TCGA-ZA-A8F6 
        4.21 

  DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE 
                          0.07                           0.07 
  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 
                         11.84                          11.44 
[1] "0.1 - 122.3 (11.8)" "0.1 - 116.4 (11.4)"
[1] "hr=" "1"  
D84V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 48(21Q11.2) MUTATED         0        4       18        9        16
  DEL PEAK 48(21Q11.2) WILD-TYPE       2        9       21       22        20
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 48(21Q11.2) MUTATED          20         0         39         21
  DEL PEAK 48(21Q11.2) WILD-TYPE        29         3         38         34
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 48(21Q11.2) MUTATED           14       13
  DEL PEAK 48(21Q11.2) WILD-TYPE         23       24
D84V3, multiclass
            clus
vv           DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              4                              9
  STAGE IB                             18                             21
  STAGE II                              9                             22
  STAGE IIA                            16                             20
  STAGE IIB                            20                             29
  STAGE III                             0                              3
  STAGE IIIA                           39                             38
  STAGE IIIB                           21                             34
  STAGE IIIC                           14                             23
  STAGE IV                             13                             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 48(21Q11.2) MUTATED    6 36 76 37
  DEL PEAK 48(21Q11.2) WILD-TYPE 15 51 97 67
D84V4, multiclass
    clus
vv   DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE
  T1                            6                             15
  T2                           36                             51
  T3                           76                             97
  T4                           37                             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"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 48(21Q11.2) MUTATED   45 47 35 28
  DEL PEAK 48(21Q11.2) WILD-TYPE 77 60 40 51
D84V5, multiclass
    clus
vv   DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE
  N0                           45                             77
  N1                           47                             60
  N2                           35                             40
  N3                           28                             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  DEL PEAK 48(21Q11.2) MUTATED   143   7   8
  DEL PEAK 48(21Q11.2) WILD-TYPE 210  17  10
D84V6, multiclass
    clus
vv   DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE
  M0                          143                            210
  M1                            7                             17
  MX                            8                             10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V7, binary
                                cls
clus                               0   1
  DEL PEAK 48(21Q11.2) MUTATED    65  93
  DEL PEAK 48(21Q11.2) WILD-TYPE  86 151
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(21Q11.2) MUTATED     65   93
  DEL PEAK 48(21Q11.2) WILD-TYPE   86  151
        clus
vv       DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE
  FEMALE                           65                             86
  MALE                             93                            151
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 48(21Q11.2) MUTATED                                      21
  DEL PEAK 48(21Q11.2) WILD-TYPE                                    44
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 48(21Q11.2) MUTATED                                                       59
  DEL PEAK 48(21Q11.2) WILD-TYPE                                                     98
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 48(21Q11.2) MUTATED                                                                  33
  DEL PEAK 48(21Q11.2) WILD-TYPE                                                                36
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 48(21Q11.2) MUTATED                                                 29
  DEL PEAK 48(21Q11.2) WILD-TYPE                                               35
                                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                                          5
  DEL PEAK 48(21Q11.2) WILD-TYPE                                        4
D84V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 48(21Q11.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       21
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      59
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           33
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            29
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     5
                                                                   clus
vv                                                                  DEL PEAK 48(21Q11.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         44
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        98
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      7
  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"
D84V9, binary
                                cls
clus                               0   1
  DEL PEAK 48(21Q11.2) MUTATED     4 154
  DEL PEAK 48(21Q11.2) WILD-TYPE   2 235
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(21Q11.2) MUTATED      4  154
  DEL PEAK 48(21Q11.2) WILD-TYPE    2  235
     clus
vv    DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE
  NO                             4                              2
  YES                          154                            235
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 48(21Q11.2) MUTATED   129   8   8   6
  DEL PEAK 48(21Q11.2) WILD-TYPE 189   8  10  19
D84V10, multiclass
    clus
vv   DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE
  R0                          129                            189
  R1                            8                              8
  R2                            8                             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"
D84V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 48(21Q11.2) MUTATED      32                         2
  DEL PEAK 48(21Q11.2) WILD-TYPE    56                         4
                                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      97
  DEL PEAK 48(21Q11.2) WILD-TYPE   146
D84V12, multiclass
                                           clus
vv                                          DEL PEAK 48(21Q11.2) MUTATED
  ASIAN                                                               32
  BLACK OR AFRICAN AMERICAN                                            2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               97
                                           clus
vv                                          DEL PEAK 48(21Q11.2) WILD-TYPE
  ASIAN                                                                 56
  BLACK OR AFRICAN AMERICAN                                              4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                146
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(85) Variable = DEL PEAK 49(21Q22.3) MUTATION ANALYSIS
D85V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 49(21Q22.3) MUTATED   102  49
  DEL PEAK 49(21Q22.3) WILD-TYPE 140  73
  DEL PEAK 49(21Q22.3) MUTATED DEL PEAK 49(21Q22.3) WILD-TYPE 
                           151                            213 
  DEL PEAK 49(21Q22.3) MUTATED DEL PEAK 49(21Q22.3) WILD-TYPE 
                            49                             73 
$`DEL PEAK 49(21Q22.3) MUTATED`
TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 
       11.70         6.97        18.35        13.68         7.00         0.82 
TCGA-BR-6565 TCGA-BR-6803 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7959 
        0.62        31.20        35.24        15.42        28.01        18.71 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8291 TCGA-BR-8296 
        0.82         1.32         0.49         0.72        16.31         1.48 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8483 
        7.40        19.50         4.31        14.04        14.79         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 
        0.72         9.21        11.54         0.59        15.68        10.68 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J8 
        0.66        22.26         0.92        12.89         0.72        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-8524 TCGA-CD-8526 
        0.46        20.65         1.15        13.64         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A48A 
        0.07         0.10         0.16         0.13         0.13         0.13 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
        0.13         0.10        20.02         8.05        54.08         4.01 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       47.05        19.07        12.03        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 
       30.97         6.97         1.02        12.03        15.02        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6525 
        4.01        55.04        11.93        19.13        20.55         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8578 
       17.19         4.14        15.98        12.79        11.31        21.14 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 
       14.27        16.44        11.31        15.65         7.40         0.62 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-A4BF TCGA-FP-A8CX 
       72.23         8.12        19.53        17.06         1.55         0.23 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G8 TCGA-HU-A4GC 
       26.47         1.51        14.17        12.10        11.84         3.25 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        8.98         6.25         0.26        12.95        19.36        17.69 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       12.30         9.67        21.21        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU 
        5.36         5.19         1.41         6.74         5.56         1.81 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A663 TCGA-RD-A7C1 
        2.53         5.56        60.56        28.90         4.31        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      122.30        37.91       115.69        57.44         8.94        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8P5 TCGA-VQ-A8PC 
        5.79         0.92        37.74        13.25         7.73        46.26 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PP TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       17.85         1.87        23.41        23.57        64.57        14.33 
TCGA-VQ-A91A TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y 
       28.70        49.25        20.81         1.71         8.58         9.73 
TCGA-VQ-A91Z TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J 
       44.25        55.43         4.54        40.08        29.98        21.11 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK 49(21Q22.3) WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 
        5.62         6.61         4.64         7.43        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        13.12        10.13 
TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       39.12        32.78        13.84        13.22        16.14         1.25 
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-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       24.76        23.93         0.69         0.16        18.54        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 
        0.95         0.69        12.76        17.49         0.69        12.26 
TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8360 
       20.55         0.26        12.95         0.26         1.55         6.18 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        0.36         0.26        22.19         2.96         0.95        13.74 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 
        3.32         0.36        19.17         0.69         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        3.72        20.22         1.12        12.79        15.81         2.14 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       13.45         0.20         7.53         0.49        15.81        16.44 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
        0.62        12.56         1.15         3.02        13.41        13.51 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.79        14.17         0.53        12.82         0.66        19.36 
TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       20.42        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8529 TCGA-CD-8531 
       13.18         0.30         0.07         0.07         0.13         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MG 
        0.10         0.13         0.10         6.35         0.13         0.07 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10         0.10         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4472 
        7.99        14.01        29.98        21.99         9.01        12.00 
TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 
        1.02         0.99         6.02         0.99       105.07        28.96 
TCGA-CG-5727 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6520 
       79.07        21.07         7.99        12.36        12.66        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 
       18.54        18.61        17.85        15.22        10.55        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         0.23         6.97 
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-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A748 TCGA-D7-A74B 
       11.24        11.44         9.76         2.96         4.34         7.13 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 
        7.79        16.24         6.58        14.47        21.27         0.39 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
        3.02        22.29        59.54         5.03        13.58         0.56 
TCGA-HF-A5NB TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 
       18.08         5.92        14.27        12.59        11.41        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD 
        0.76        24.30         5.59        12.30        24.20        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-A4H0 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 
       10.19         2.10         8.88         8.81        27.42         3.45 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS 
       13.08         6.44         6.87         3.72        19.73        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB 
        8.61         4.67        40.64       116.38        71.38        16.87 
TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        5.46        13.02        31.10        21.73        22.36        23.77 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PQ 
       19.07        33.63        16.31         2.70         9.27        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91W TCGA-VQ-A922 
       19.30        59.18        11.70         8.68         7.36         8.61 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-ZA-A8F6 
        6.58         5.72         4.21 

  DEL PEAK 49(21Q22.3) MUTATED DEL PEAK 49(21Q22.3) WILD-TYPE 
                          0.07                           0.07 
  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 
                         11.93                          11.41 
[1] "0.1 - 122.3 (11.9)" "0.1 - 116.4 (11.4)"
[1] "hr=" "1.2"
D85V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 49(21Q22.3) MUTATED         0        3       18       11        16
  DEL PEAK 49(21Q22.3) WILD-TYPE       2       10       21       20        20
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 49(21Q22.3) MUTATED          19         1         41         22
  DEL PEAK 49(21Q22.3) WILD-TYPE        30         2         36         33
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 49(21Q22.3) MUTATED           14       12
  DEL PEAK 49(21Q22.3) WILD-TYPE         23       25
D85V3, multiclass
            clus
vv           DEL PEAK 49(21Q22.3) MUTATED DEL PEAK 49(21Q22.3) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              3                             10
  STAGE IB                             18                             21
  STAGE II                             11                             20
  STAGE IIA                            16                             20
  STAGE IIB                            19                             30
  STAGE III                             1                              2
  STAGE IIIA                           41                             36
  STAGE IIIB                           22                             33
  STAGE IIIC                           14                             23
  STAGE IV                             12                             25
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 49(21Q22.3) MUTATED    5 41 76 36
  DEL PEAK 49(21Q22.3) WILD-TYPE 16 46 97 68
D85V4, multiclass
    clus
vv   DEL PEAK 49(21Q22.3) MUTATED DEL PEAK 49(21Q22.3) WILD-TYPE
  T1                            5                             16
  T2                           41                             46
  T3                           76                             97
  T4                           36                             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"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 49(21Q22.3) MUTATED   44 49 35 31
  DEL PEAK 49(21Q22.3) WILD-TYPE 78 58 40 48
D85V5, multiclass
    clus
vv   DEL PEAK 49(21Q22.3) MUTATED DEL PEAK 49(21Q22.3) WILD-TYPE
  N0                           44                             78
  N1                           49                             58
  N2                           35                             40
  N3                           31                             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"
                                vv
clus                              M0  M1  MX
  DEL PEAK 49(21Q22.3) MUTATED   150   5   8
  DEL PEAK 49(21Q22.3) WILD-TYPE 203  19  10
D85V6, multiclass
    clus
vv   DEL PEAK 49(21Q22.3) MUTATED DEL PEAK 49(21Q22.3) WILD-TYPE
  M0                          150                            203
  M1                            5                             19
  MX                            8                             10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V7, binary
                                cls
clus                               0   1
  DEL PEAK 49(21Q22.3) MUTATED    63 100
  DEL PEAK 49(21Q22.3) WILD-TYPE  88 144
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 49(21Q22.3) MUTATED     63  100
  DEL PEAK 49(21Q22.3) WILD-TYPE   88  144
        clus
vv       DEL PEAK 49(21Q22.3) MUTATED DEL PEAK 49(21Q22.3) WILD-TYPE
  FEMALE                           63                             88
  MALE                            100                            144
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 49(21Q22.3) MUTATED                                      23
  DEL PEAK 49(21Q22.3) WILD-TYPE                                    42
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 49(21Q22.3) MUTATED                                                       58
  DEL PEAK 49(21Q22.3) WILD-TYPE                                                     99
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 49(21Q22.3) MUTATED                                                                  35
  DEL PEAK 49(21Q22.3) WILD-TYPE                                                                34
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 49(21Q22.3) MUTATED                                                 29
  DEL PEAK 49(21Q22.3) WILD-TYPE                                               35
                                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                                          5
  DEL PEAK 49(21Q22.3) WILD-TYPE                                        4
D85V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 49(21Q22.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       23
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      58
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            29
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     5
                                                                   clus
vv                                                                  DEL PEAK 49(21Q22.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         42
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        99
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             34
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      6
  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"
D85V9, binary
                                cls
clus                               0   1
  DEL PEAK 49(21Q22.3) MUTATED     4 159
  DEL PEAK 49(21Q22.3) WILD-TYPE   2 230
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 49(21Q22.3) MUTATED      4  159
  DEL PEAK 49(21Q22.3) WILD-TYPE    2  230
     clus
vv    DEL PEAK 49(21Q22.3) MUTATED DEL PEAK 49(21Q22.3) WILD-TYPE
  NO                             4                              2
  YES                          159                            230
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 49(21Q22.3) MUTATED   136   8   6   8
  DEL PEAK 49(21Q22.3) WILD-TYPE 182   8  12  17
D85V10, multiclass
    clus
vv   DEL PEAK 49(21Q22.3) MUTATED DEL PEAK 49(21Q22.3) WILD-TYPE
  R0                          136                            182
  R1                            8                              8
  R2                            6                             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"
D85V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 49(21Q22.3) MUTATED      33                         2
  DEL PEAK 49(21Q22.3) WILD-TYPE    55                         4
                                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      99
  DEL PEAK 49(21Q22.3) WILD-TYPE   144
D85V12, multiclass
                                           clus
vv                                          DEL PEAK 49(21Q22.3) MUTATED
  ASIAN                                                               33
  BLACK OR AFRICAN AMERICAN                                            2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               99
                                           clus
vv                                          DEL PEAK 49(21Q22.3) WILD-TYPE
  ASIAN                                                                 55
  BLACK OR AFRICAN AMERICAN                                              4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  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"

Clustering(86) Variable = DEL PEAK 50(22Q13.31) MUTATION ANALYSIS
D86V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 50(22Q13.31) MUTATED    84  46
  DEL PEAK 50(22Q13.31) WILD-TYPE 158  76
  DEL PEAK 50(22Q13.31) MUTATED DEL PEAK 50(22Q13.31) WILD-TYPE 
                            130                             234 
  DEL PEAK 50(22Q13.31) MUTATED DEL PEAK 50(22Q13.31) WILD-TYPE 
                             46                              76 
$`DEL PEAK 50(22Q13.31) MUTATED`
TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 
        6.61        18.35         6.18        10.13         7.00         0.82 
TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-8058 TCGA-BR-8059 
        0.62         1.25         9.21        15.42        17.49         0.82 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
        1.32         0.69         0.49         1.55         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8369 TCGA-BR-8484 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       19.50        14.04         0.72         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J1 
        0.59         0.62        10.68        22.26        12.89         0.72 
TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 
       19.36        20.65         1.15        13.64         3.25        13.15 
TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A487 
        0.07         0.07         0.16         0.13         6.35         0.13 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4437 
        0.13         0.13         0.13         0.10         3.02         8.05 
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-4466 TCGA-CG-4477 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-5578 
       18.97        30.97        12.03        15.02        55.04        12.66 
TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       11.93        20.55         5.95        17.19         4.14        15.22 
TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8575 
       12.79        11.31        12.33        24.72        19.50         0.23 
TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 
       21.14        16.44        11.31        15.65         7.40         0.62 
TCGA-EQ-A4SO TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8243 
       16.24        19.53        17.06         0.56         1.55         5.92 
TCGA-HU-8249 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
       14.17        22.75         8.98         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       17.69         9.67        27.42         3.39        18.38         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IP-7968 
        5.19        13.08         6.44         6.74         1.81         2.53 
TCGA-KB-A6F5 TCGA-MX-A663 TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N9 
        5.56         4.31         8.61        16.67       115.69        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        37.74         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8P3 TCGA-VQ-A8PC TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PU 
       31.10        23.77        46.26        17.85         1.87        23.57 
TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y 
       14.33        28.70        20.81         1.71         8.58         9.73 
TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-AA6B TCGA-ZQ-A9CR 
        8.61         4.54        29.98         0.79 

$`DEL PEAK 50(22Q13.31) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
        5.62        11.70         6.97         4.64         7.43        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        13.12        13.68 
TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       39.12        32.78        13.84        13.22        16.14         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-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.24        23.93        28.01         0.69         0.16        18.54 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8078 
       12.43         0.95         0.69        12.76        18.71        12.26 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       20.55         0.72         0.26        12.95         0.26        16.31 
TCGA-BR-8296 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        1.48         0.36         0.26        22.19         2.96         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       13.74         4.31         3.32         0.36        19.17        14.79 
TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 
        0.69         0.26        15.85         3.72         5.39         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         2.14        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A44U 
        0.20         7.53        15.81        15.68        12.56         1.15 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
        0.66         3.02         0.92        13.41        13.51         0.79 
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-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 
       20.42        11.57         5.13         2.83        13.18         0.30 
TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 
        0.07         0.07         0.07         0.10         0.13         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.10         0.13         0.10         0.07         0.10         0.10 
TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4443 
       20.02        27.02        15.95         1.02         7.99        29.98 
TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 
       12.03         9.01         7.07        12.00        22.98         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        1.02         1.02         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-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       12.36        19.13        18.84        18.54        18.61        17.85 
TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8579 
       15.98        10.55        16.80        17.19         6.97        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-A748 TCGA-D7-A74B 
       11.24        11.44         9.76         2.96         4.34         7.13 
TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.79         6.58        14.47        72.23        21.27         8.12 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        0.39         3.02        22.29        59.54         5.03        13.58 
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-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-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-A4GU TCGA-HU-A4GX 
       21.37        29.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       19.36        12.30         8.88         8.81        21.21         3.45 
TCGA-IN-8462 TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NT TCGA-KB-A6F7 TCGA-KB-A93H 
       18.81         1.41         6.87         5.56        60.56        28.90 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
        3.72        19.73        11.05         4.67       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-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       21.73        22.36         7.73        19.07        33.63        16.31 
TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX 
        2.70         9.27        23.41        15.65        19.30        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91W TCGA-VQ-A91Z 
       59.18        11.70         8.68        49.25         7.36        44.25 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6J TCGA-ZA-A8F6 
       55.43         6.58         5.72        40.08        21.11         4.21 

  DEL PEAK 50(22Q13.31) MUTATED DEL PEAK 50(22Q13.31) WILD-TYPE 
                           0.07                            0.07 
  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 
                          9.700                          12.065 
[1] "0.1 - 115.7 (9.7)"  "0.1 - 122.3 (12.1)"
[1] "hr=" "1.3"
D86V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 50(22Q13.31) MUTATED         0        0       15       11        12
  DEL PEAK 50(22Q13.31) WILD-TYPE       2       13       24       20        24
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 50(22Q13.31) MUTATED          16         1         34         22
  DEL PEAK 50(22Q13.31) WILD-TYPE        33         2         43         33
                                 vv
clus                              STAGE IIIC STAGE IV
  DEL PEAK 50(22Q13.31) MUTATED           12       13
  DEL PEAK 50(22Q13.31) WILD-TYPE         25       24
D86V3, multiclass
            clus
vv           DEL PEAK 50(22Q13.31) MUTATED DEL PEAK 50(22Q13.31) WILD-TYPE
  STAGE I                                0                               2
  STAGE IA                               0                              13
  STAGE IB                              15                              24
  STAGE II                              11                              20
  STAGE IIA                             12                              24
  STAGE IIB                             16                              33
  STAGE III                              1                               2
  STAGE IIIA                            34                              43
  STAGE IIIB                            22                              33
  STAGE IIIC                            12                              25
  STAGE IV                              13                              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 50(22Q13.31) MUTATED     4  32  67  34
  DEL PEAK 50(22Q13.31) WILD-TYPE  17  55 106  70
D86V4, multiclass
    clus
vv   DEL PEAK 50(22Q13.31) MUTATED DEL PEAK 50(22Q13.31) WILD-TYPE
  T1                             4                              17
  T2                            32                              55
  T3                            67                             106
  T4                            34                              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2 N3
  DEL PEAK 50(22Q13.31) MUTATED   37 36 34 30
  DEL PEAK 50(22Q13.31) WILD-TYPE 85 71 41 49
D86V5, multiclass
    clus
vv   DEL PEAK 50(22Q13.31) MUTATED DEL PEAK 50(22Q13.31) WILD-TYPE
  N0                            37                              85
  N1                            36                              71
  N2                            34                              41
  N3                            30                              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"
                                 vv
clus                               M0  M1  MX
  DEL PEAK 50(22Q13.31) MUTATED   129   6   6
  DEL PEAK 50(22Q13.31) WILD-TYPE 224  18  12
D86V6, multiclass
    clus
vv   DEL PEAK 50(22Q13.31) MUTATED DEL PEAK 50(22Q13.31) WILD-TYPE
  M0                           129                             224
  M1                             6                              18
  MX                             6                              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V7, binary
                                 cls
clus                                0   1
  DEL PEAK 50(22Q13.31) MUTATED    50  91
  DEL PEAK 50(22Q13.31) WILD-TYPE 101 153
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 50(22Q13.31) MUTATED     50   91
  DEL PEAK 50(22Q13.31) WILD-TYPE  101  153
        clus
vv       DEL PEAK 50(22Q13.31) MUTATED DEL PEAK 50(22Q13.31) WILD-TYPE
  FEMALE                            50                             101
  MALE                              91                             153
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 50(22Q13.31) MUTATED                                      17
  DEL PEAK 50(22Q13.31) WILD-TYPE                                    48
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 50(22Q13.31) MUTATED                                                       54
  DEL PEAK 50(22Q13.31) WILD-TYPE                                                    103
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 50(22Q13.31) MUTATED                                                                  23
  DEL PEAK 50(22Q13.31) WILD-TYPE                                                                46
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 50(22Q13.31) MUTATED                                                 32
  DEL PEAK 50(22Q13.31) WILD-TYPE                                               32
                                 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                                          4
  DEL PEAK 50(22Q13.31) WILD-TYPE                                        5
D86V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 50(22Q13.31) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        17
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       54
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            23
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      4
                                                                   clus
vv                                                                  DEL PEAK 50(22Q13.31) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        103
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              46
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       12
  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"
D86V9, binary
                                 cls
clus                                0   1
  DEL PEAK 50(22Q13.31) MUTATED     4 137
  DEL PEAK 50(22Q13.31) WILD-TYPE   2 252
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 50(22Q13.31) MUTATED      4  137
  DEL PEAK 50(22Q13.31) WILD-TYPE    2  252
     clus
vv    DEL PEAK 50(22Q13.31) MUTATED DEL PEAK 50(22Q13.31) WILD-TYPE
  NO                              4                               2
  YES                           137                             252
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 50(22Q13.31) MUTATED   110   7   9   8
  DEL PEAK 50(22Q13.31) WILD-TYPE 208   9   9  17
D86V10, multiclass
    clus
vv   DEL PEAK 50(22Q13.31) MUTATED DEL PEAK 50(22Q13.31) WILD-TYPE
  R0                           110                             208
  R1                             7                               9
  R2                             9                               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"
D86V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 50(22Q13.31) MUTATED      31                         1
  DEL PEAK 50(22Q13.31) WILD-TYPE    57                         5
                                 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      87
  DEL PEAK 50(22Q13.31) WILD-TYPE   156
D86V12, multiclass
                                           clus
vv                                          DEL PEAK 50(22Q13.31) MUTATED
  ASIAN                                                                31
  BLACK OR AFRICAN AMERICAN                                             1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                87
                                           clus
vv                                          DEL PEAK 50(22Q13.31) WILD-TYPE
  ASIAN                                                                  57
  BLACK OR AFRICAN AMERICAN                                               5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               0
  WHITE                                                                 156
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(87) Variable = DEL PEAK 51(XP22.2) MUTATION ANALYSIS
D87V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 51(XP22.2) MUTATED    49  25
  DEL PEAK 51(XP22.2) WILD-TYPE 193  97
  DEL PEAK 51(XP22.2) MUTATED DEL PEAK 51(XP22.2) WILD-TYPE 
                           74                           290 
  DEL PEAK 51(XP22.2) MUTATED DEL PEAK 51(XP22.2) WILD-TYPE 
                           25                            97 
$`DEL PEAK 51(XP22.2) MUTATED`
TCGA-BR-4191 TCGA-BR-6458 TCGA-BR-7716 TCGA-BR-8059 TCGA-BR-8289 TCGA-BR-8297 
       18.35         7.00        28.01         0.82         0.26         7.40 
TCGA-BR-8362 TCGA-BR-8369 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8590 TCGA-BR-8680 
        0.36        14.04         9.21        20.22         2.14        15.81 
TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4J6 TCGA-BR-A4PD 
        0.59        10.68         1.15        22.26         0.66        20.65 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8531 
        1.15        13.64         3.25         0.30         0.07         0.10 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MH TCGA-CG-4438 
        0.13         0.13         0.13         0.13         0.10        54.08 
TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-5718 TCGA-CG-5725 
       14.01        47.05        19.07        21.99         1.02        15.02 
TCGA-CG-5734 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
        7.99        11.93        17.19         4.14        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
       12.79        12.33         0.23        11.31         9.76         2.96 
TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-FP-8211 TCGA-FP-A4BF TCGA-HU-A4G3 
       15.65         7.40         0.62        13.58         1.55         5.59 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GU TCGA-HU-A4H5 TCGA-IN-7806 TCGA-IN-7808 
       22.75        25.81         6.25        12.30        21.21         3.45 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RP TCGA-RD-A8N6 TCGA-VQ-A8P3 
        3.39        18.38         5.19         6.44         8.94        23.77 
TCGA-VQ-A8PC TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       46.26         1.87        23.57         9.73        44.25         8.61 
TCGA-VQ-A928 TCGA-VQ-AA68 
        5.72        40.08 

$`DEL PEAK 51(XP22.2) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         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-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.12        10.13        13.68        39.12         0.82         0.62 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        13.84        13.22        16.14         1.25         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         0.69         0.16 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       18.54        12.43         0.95         0.69        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49         1.32         0.69        12.26         0.49        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.72         0.26        12.95        16.31         1.55         1.48 
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         2.96         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       13.74         4.31         3.32         0.36        19.17        14.79 
TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
        0.69         0.26        15.85         3.72         5.39         0.72 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        15.81        13.45         0.20         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T 
        0.49        11.54        16.44        15.68         0.62        12.56 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        0.66         3.02         0.92        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 
        0.79         0.72        14.17         0.53        12.82        19.36 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       13.51         0.46        20.42        11.57         5.13         2.83 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.15        13.18         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A486 
        0.10         0.13         0.16         0.10         0.10         6.35 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
        0.13         0.13         0.07         0.10         0.10        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-4455 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
        4.01        29.98        12.03         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 
       12.00        22.98        30.97         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-D7-5577 TCGA-D7-5578 
       65.10         4.01        55.04        21.07        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-D7-6525 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
        5.95        10.55        11.31        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       17.19         6.97        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-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 
       11.44         4.34         7.13         7.79        16.24         6.58 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27         8.12         0.39        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 
        3.02        22.29        17.06        59.54         5.03         0.56 
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-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH 
       24.30        12.30        11.84        24.20         3.25        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.51        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        17.69         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RN 
        8.88         8.81        27.42        18.81         5.36        13.08 
TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 
        1.41         6.74         6.87         5.56         1.81         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        5.56        60.56        28.90         3.72        19.73         4.31 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         4.67        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-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       16.87         5.79         0.92        37.74         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       13.02        31.10        21.73        22.36         7.73        19.07 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PP 
       33.63        16.31         2.70        17.85         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        19.30        64.57        14.33        59.18        28.70 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W 
       11.70         8.68        49.25        20.81         1.71         7.36 
TCGA-VQ-A91X TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-AA6B TCGA-VQ-AA6J 
        8.58        55.43         4.54         6.58        29.98        21.11 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        4.21         0.79 

  DEL PEAK 51(XP22.2) MUTATED DEL PEAK 51(XP22.2) WILD-TYPE 
                         0.07                          0.07 
  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 
                        9.075                        12.015 
[1] "0.1 - 54.1 (9.1)"   "0.1 - 122.3 (12.0)"
[1] "hr=" "1.2"
D87V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 51(XP22.2) MUTATED         0        1        7        8         6
  DEL PEAK 51(XP22.2) WILD-TYPE       2       12       32       23        30
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 51(XP22.2) MUTATED          11         2         19          6
  DEL PEAK 51(XP22.2) WILD-TYPE        38         1         58         49
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 51(XP22.2) MUTATED            7        8
  DEL PEAK 51(XP22.2) WILD-TYPE         30       29
D87V3, multiclass
            clus
vv           DEL PEAK 51(XP22.2) MUTATED DEL PEAK 51(XP22.2) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             1                            12
  STAGE IB                             7                            32
  STAGE II                             8                            23
  STAGE IIA                            6                            30
  STAGE IIB                           11                            38
  STAGE III                            2                             1
  STAGE IIIA                          19                            58
  STAGE IIIB                           6                            49
  STAGE IIIC                           7                            30
  STAGE IV                             8                            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 51(XP22.2) MUTATED     3  19  34  20
  DEL PEAK 51(XP22.2) WILD-TYPE  18  68 139  84
D87V4, multiclass
    clus
vv   DEL PEAK 51(XP22.2) MUTATED DEL PEAK 51(XP22.2) WILD-TYPE
  T1                           3                            18
  T2                          19                            68
  T3                          34                           139
  T4                          20                            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 51(XP22.2) MUTATED    19  24  18  15
  DEL PEAK 51(XP22.2) WILD-TYPE 103  83  57  64
D87V5, multiclass
    clus
vv   DEL PEAK 51(XP22.2) MUTATED DEL PEAK 51(XP22.2) WILD-TYPE
  N0                          19                           103
  N1                          24                            83
  N2                          18                            57
  N3                          15                            64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK 51(XP22.2) MUTATED    71   5   1
  DEL PEAK 51(XP22.2) WILD-TYPE 282  19  17
D87V6, multiclass
    clus
vv   DEL PEAK 51(XP22.2) MUTATED DEL PEAK 51(XP22.2) WILD-TYPE
  M0                          71                           282
  M1                           5                            19
  MX                           1                            17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V7, binary
                               cls
clus                              0   1
  DEL PEAK 51(XP22.2) MUTATED    26  51
  DEL PEAK 51(XP22.2) WILD-TYPE 125 193
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XP22.2) MUTATED     26   51
  DEL PEAK 51(XP22.2) WILD-TYPE  125  193
        clus
vv       DEL PEAK 51(XP22.2) MUTATED DEL PEAK 51(XP22.2) WILD-TYPE
  FEMALE                          26                           125
  MALE                            51                           193
[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                                    56
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 51(XP22.2) MUTATED                                                       28
  DEL PEAK 51(XP22.2) WILD-TYPE                                                    129
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 51(XP22.2) MUTATED                                                                  12
  DEL PEAK 51(XP22.2) WILD-TYPE                                                                57
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 51(XP22.2) MUTATED                                                 20
  DEL PEAK 51(XP22.2) WILD-TYPE                                               44
                               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                                          3
  DEL PEAK 51(XP22.2) WILD-TYPE                                        6
D87V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 51(XP22.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     28
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          12
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    3
                                                                   clus
vv                                                                  DEL PEAK 51(XP22.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            57
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             44
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     5
  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"
D87V9, binary
                               cls
clus                              0   1
  DEL PEAK 51(XP22.2) MUTATED     1  76
  DEL PEAK 51(XP22.2) WILD-TYPE   5 313
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XP22.2) MUTATED      1   76
  DEL PEAK 51(XP22.2) WILD-TYPE    5  313
     clus
vv    DEL PEAK 51(XP22.2) MUTATED DEL PEAK 51(XP22.2) WILD-TYPE
  NO                            1                             5
  YES                          76                           313
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 51(XP22.2) MUTATED    63   3   3   2
  DEL PEAK 51(XP22.2) WILD-TYPE 255  13  15  23
D87V10, multiclass
    clus
vv   DEL PEAK 51(XP22.2) MUTATED DEL PEAK 51(XP22.2) WILD-TYPE
  R0                          63                           255
  R1                           3                            13
  R2                           3                            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"
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                         6
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 51(XP22.2) MUTATED                                           0    51
  DEL PEAK 51(XP22.2) WILD-TYPE                                         1   192
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                                                              51
                                           clus
vv                                          DEL PEAK 51(XP22.2) WILD-TYPE
  ASIAN                                                                71
  BLACK OR AFRICAN AMERICAN                                             6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               192
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(88) Variable = DEL PEAK 52(XP21.1) MUTATION ANALYSIS
D88V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 52(XP21.1) MUTATED    38  22
  DEL PEAK 52(XP21.1) WILD-TYPE 204 100
  DEL PEAK 52(XP21.1) MUTATED DEL PEAK 52(XP21.1) WILD-TYPE 
                           60                           304 
  DEL PEAK 52(XP21.1) MUTATED DEL PEAK 52(XP21.1) WILD-TYPE 
                           22                           100 
$`DEL PEAK 52(XP21.1) MUTATED`
TCGA-BR-4191 TCGA-BR-6458 TCGA-BR-8059 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8362 
       18.35         7.00         0.82        16.31         7.40         0.36 
TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8683 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ 
        2.96        14.04         0.59         1.15         0.66        22.26 
TCGA-BR-A4J6 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-8524 TCGA-CD-8533 
        0.66        20.65         1.15        13.64         0.07         0.13 
TCGA-CD-A489 TCGA-CD-A4MH TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4444 
        0.13         0.10         8.05        54.08        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4469 TCGA-CG-5725 TCGA-CG-5734 TCGA-D7-5579 
       19.07        21.99         7.07        15.02         7.99        11.93 
TCGA-D7-6518 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6822 
       19.13         5.95        15.22        15.98        12.79        12.33 
TCGA-D7-8575 TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 
        0.23        11.31         9.76        15.65         7.40         0.62 
TCGA-FP-8211 TCGA-FP-A4BF TCGA-HU-A4GD TCGA-HU-A4H5 TCGA-IN-7808 TCGA-IN-8663 
       13.58         1.55        22.75        12.30         3.45         3.39 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RP TCGA-KB-A93H TCGA-RD-A8N6 TCGA-VQ-A8PC 
       18.38         5.19         6.44        28.90         8.94        46.26 
TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-AA68 TCGA-VQ-AA6J 
       23.57        14.33        44.25         8.61        40.08        21.11 

$`DEL PEAK 52(XP21.1) WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         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-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.12        10.13        13.68        39.12         0.82         0.62 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        13.84        13.22        16.14         1.25         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         0.69 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
        0.16        18.54        12.43         0.95         0.69        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49         1.32         0.69        12.26         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 
       20.55         0.72         0.26        12.95         0.26         1.55 
TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 
        1.48         6.18        19.50         0.26        22.19         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       13.74         4.31         3.32         0.36        19.17        14.79 
TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
        0.69         0.26        15.85         3.72         5.39         0.72 
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         2.14 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         0.20         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A453 
       16.44        15.68         0.62        10.68        12.56         3.02 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.92        13.41        13.51        12.89         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
       14.17         0.53        12.82        19.36        13.51         0.46 
TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       20.42        11.57         5.13         2.83         3.25        13.15 
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-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        0.10         6.35         0.13         0.13         0.13         0.07 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10         0.10        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4465 
        1.02         7.99         4.01        14.01        12.03         9.01 
TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97        12.00        22.98        30.97         6.97         1.02 
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-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        55.04        21.07 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.36        12.66        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 
       17.85        17.19         4.14        10.55        11.31        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19         6.97        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-A6F0 TCGA-D7-A748 TCGA-D7-A74B 
       13.71        11.24        11.44         2.96         4.34         7.13 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.79        16.24         6.58        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
        8.12         0.39        19.53         3.02        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-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-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        17.69         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RJ 
        8.88         8.81        27.42        21.21        18.81         5.36 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU 
       13.08         1.41         6.74         6.87         5.56         1.81 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        2.53         5.56        60.56         3.72        19.73         4.31 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         4.67        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-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       16.87         5.79         0.92        37.74         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       13.02        31.10        21.73        22.36        23.77         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       19.07        33.63        16.31         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        19.30        64.57        59.18 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U 
       28.70        11.70         8.68        49.25        20.81         1.71 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
        7.36         8.58         9.73        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-AA6B TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        5.72        29.98         4.21         0.79 

  DEL PEAK 52(XP21.1) MUTATED DEL PEAK 52(XP21.1) WILD-TYPE 
                         0.07                          0.07 
  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 
                       11.620                        11.635 
[1] "0.1 - 54.1 (11.6)"  "0.1 - 122.3 (11.6)"
[1] "hr=" "1.2"
D88V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 52(XP21.1) MUTATED         0        1        6        5         5
  DEL PEAK 52(XP21.1) WILD-TYPE       2       12       33       26        31
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 52(XP21.1) MUTATED           8         2         18          6
  DEL PEAK 52(XP21.1) WILD-TYPE        41         1         59         49
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 52(XP21.1) MUTATED            4        5
  DEL PEAK 52(XP21.1) WILD-TYPE         33       32
D88V3, multiclass
            clus
vv           DEL PEAK 52(XP21.1) MUTATED DEL PEAK 52(XP21.1) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             1                            12
  STAGE IB                             6                            33
  STAGE II                             5                            26
  STAGE IIA                            5                            31
  STAGE IIB                            8                            41
  STAGE III                            2                             1
  STAGE IIIA                          18                            59
  STAGE IIIB                           6                            49
  STAGE IIIC                           4                            33
  STAGE IV                             5                            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 52(XP21.1) MUTATED     3  16  27  15
  DEL PEAK 52(XP21.1) WILD-TYPE  18  71 146  89
D88V4, multiclass
    clus
vv   DEL PEAK 52(XP21.1) MUTATED DEL PEAK 52(XP21.1) WILD-TYPE
  T1                           3                            18
  T2                          16                            71
  T3                          27                           146
  T4                          15                            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
  DEL PEAK 52(XP21.1) MUTATED    16  18  16  11
  DEL PEAK 52(XP21.1) WILD-TYPE 106  89  59  68
D88V5, multiclass
    clus
vv   DEL PEAK 52(XP21.1) MUTATED DEL PEAK 52(XP21.1) WILD-TYPE
  N0                          16                           106
  N1                          18                            89
  N2                          16                            59
  N3                          11                            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"
                               vv
clus                             M0  M1  MX
  DEL PEAK 52(XP21.1) MUTATED    58   3   1
  DEL PEAK 52(XP21.1) WILD-TYPE 295  21  17
D88V6, multiclass
    clus
vv   DEL PEAK 52(XP21.1) MUTATED DEL PEAK 52(XP21.1) WILD-TYPE
  M0                          58                           295
  M1                           3                            21
  MX                           1                            17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V7, binary
                               cls
clus                              0   1
  DEL PEAK 52(XP21.1) MUTATED    21  41
  DEL PEAK 52(XP21.1) WILD-TYPE 130 203
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 52(XP21.1) MUTATED     21   41
  DEL PEAK 52(XP21.1) WILD-TYPE  130  203
        clus
vv       DEL PEAK 52(XP21.1) MUTATED DEL PEAK 52(XP21.1) WILD-TYPE
  FEMALE                          21                           130
  MALE                            41                           203
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 52(XP21.1) MUTATED                                       8
  DEL PEAK 52(XP21.1) WILD-TYPE                                    57
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 52(XP21.1) MUTATED                                                       21
  DEL PEAK 52(XP21.1) WILD-TYPE                                                    136
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 52(XP21.1) MUTATED                                                                  11
  DEL PEAK 52(XP21.1) WILD-TYPE                                                                58
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 52(XP21.1) MUTATED                                                 17
  DEL PEAK 52(XP21.1) WILD-TYPE                                               47
                               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                                          2
  DEL PEAK 52(XP21.1) WILD-TYPE                                        7
D88V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 52(XP21.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     21
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    2
                                                                   clus
vv                                                                  DEL PEAK 52(XP21.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        57
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      136
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            58
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             47
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     7
  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"
D88V9, binary
                               cls
clus                              0   1
  DEL PEAK 52(XP21.1) MUTATED     1  61
  DEL PEAK 52(XP21.1) WILD-TYPE   5 328
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 52(XP21.1) MUTATED      1   61
  DEL PEAK 52(XP21.1) WILD-TYPE    5  328
     clus
vv    DEL PEAK 52(XP21.1) MUTATED DEL PEAK 52(XP21.1) WILD-TYPE
  NO                            1                             5
  YES                          61                           328
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 52(XP21.1) MUTATED    50   5   2   2
  DEL PEAK 52(XP21.1) WILD-TYPE 268  11  16  23
D88V10, multiclass
    clus
vv   DEL PEAK 52(XP21.1) MUTATED DEL PEAK 52(XP21.1) WILD-TYPE
  R0                          50                           268
  R1                           5                            11
  R2                           2                            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"
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                         5
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 52(XP21.1) MUTATED                                           0    41
  DEL PEAK 52(XP21.1) WILD-TYPE                                         1   202
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                                                              41
                                           clus
vv                                          DEL PEAK 52(XP21.1) WILD-TYPE
  ASIAN                                                                78
  BLACK OR AFRICAN AMERICAN                                             5
  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"

Clustering(89) Variable = DEL PEAK 53(XQ21.33) MUTATION ANALYSIS
D89V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 53(XQ21.33) MUTATED    33  12
  DEL PEAK 53(XQ21.33) WILD-TYPE 209 110
  DEL PEAK 53(XQ21.33) MUTATED DEL PEAK 53(XQ21.33) WILD-TYPE 
                            45                            319 
  DEL PEAK 53(XQ21.33) MUTATED DEL PEAK 53(XQ21.33) WILD-TYPE 
                            12                            110 
$`DEL PEAK 53(XQ21.33) MUTATED`
TCGA-B7-5818 TCGA-BR-7197 TCGA-BR-7716 TCGA-BR-8058 TCGA-BR-8291 TCGA-BR-8361 
       11.70         9.21        28.01        17.49        16.31        19.50 
TCGA-BR-8365 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ 
        2.96        11.54        15.81         1.15         0.66        22.26 
TCGA-BR-A4CS TCGA-BR-A4J8 TCGA-CD-5800 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-A489 
        0.92        13.51        13.15         0.07         0.13         0.13 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       20.02         3.02         7.99        29.98        47.05        19.07 
TCGA-CG-4469 TCGA-CG-5725 TCGA-D7-6519 TCGA-D7-6528 TCGA-D7-6822 TCGA-D7-8575 
        7.07        15.02        20.55        15.22        12.33         0.23 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A74A TCGA-EQ-8122 TCGA-FP-8211 TCGA-HU-A4H5 
       11.31         9.76         7.40         7.79        13.58        12.30 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-A6RI TCGA-IN-A6RR TCGA-VQ-A8DT TCGA-VQ-A8P5 
       27.42        21.21        18.38         6.74        37.74         7.73 
TCGA-VQ-A8PU TCGA-VQ-A91Q TCGA-VQ-A91X 
       23.57        20.81         8.58 

$`DEL PEAK 53(XQ21.33) WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62         6.61         6.97         4.64         7.43        18.35 
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-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.12        10.13        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        0.62        32.78        13.84        13.22        16.14         1.25 
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-7715 TCGA-BR-7717 TCGA-BR-7722 
       24.76        35.24        23.93        15.42         0.69         0.16 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       18.54        12.43         0.95         0.69        12.76        18.71 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
        0.82         1.32         0.69        12.26         0.49        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 
        0.72         0.26        12.95         0.26         1.55         1.48 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 
        7.40         6.18         0.36         0.26        22.19         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       13.74         4.31        14.04         3.32         0.36        19.17 
TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       14.79         0.69         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 
        0.72         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-8682 
        2.14        13.45         0.20         7.53         0.49        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A453 
        0.59        15.68         0.62        10.68        12.56         3.02 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         0.79         0.72        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-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-8525 
        3.25        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8526 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-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         0.10         6.35         0.13         0.13         0.13 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 
        0.07         0.10         0.10         0.10        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 
        1.02         8.05        54.08         4.01        14.01        12.03 
TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
       21.99         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         1.02         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 
       55.04        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         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19         4.14        15.98        12.79        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         6.97        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-A6F2 
       14.76        13.71        11.24        11.44         2.96        15.65 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 
        4.34         7.13         0.62        16.24         6.58        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27         8.12         0.39        19.53         3.02 
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         1.55 
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-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        17.69         9.67         8.88         8.81 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45        18.81         3.39         5.36         5.19        13.08 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 
        1.41         6.44         6.87         5.56         1.81         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        5.56        60.56        28.90         3.72        19.73         4.31 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         4.67        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-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV 
       35.61        16.87         5.79         0.92         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       13.02        31.10        21.73        22.36        23.77        19.07 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       33.63        46.26        16.31         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        19.30        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91U 
       59.18        28.70        11.70         8.68        49.25         1.71 
TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 
        7.36         9.73        44.25         8.61        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 
        6.58         5.72        40.08        29.98        21.11         4.21 
TCGA-ZQ-A9CR 
        0.79 

  DEL PEAK 53(XQ21.33) MUTATED DEL PEAK 53(XQ21.33) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 53(XQ21.33) MUTATED DEL PEAK 53(XQ21.33) WILD-TYPE 
                         47.05                         122.30 
  DEL PEAK 53(XQ21.33) MUTATED DEL PEAK 53(XQ21.33) WILD-TYPE 
                         12.33                          11.41 
[1] "0.1 - 47.0 (12.3)"  "0.1 - 122.3 (11.4)"
[1] "hr=" "1.3"
D89V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 53(XQ21.33) MUTATED         0        1        8        5         3
  DEL PEAK 53(XQ21.33) WILD-TYPE       2       12       31       26        33
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 53(XQ21.33) MUTATED           5         0         10          7
  DEL PEAK 53(XQ21.33) WILD-TYPE        44         3         67         48
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 53(XQ21.33) MUTATED            2        6
  DEL PEAK 53(XQ21.33) WILD-TYPE         35       31
D89V3, multiclass
            clus
vv           DEL PEAK 53(XQ21.33) MUTATED DEL PEAK 53(XQ21.33) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              1                             12
  STAGE IB                              8                             31
  STAGE II                              5                             26
  STAGE IIA                             3                             33
  STAGE IIB                             5                             44
  STAGE III                             0                              3
  STAGE IIIA                           10                             67
  STAGE IIIB                            7                             48
  STAGE IIIC                            2                             35
  STAGE IV                              6                             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 53(XQ21.33) MUTATED     2  13  24   9
  DEL PEAK 53(XQ21.33) WILD-TYPE  19  74 149  95
D89V4, multiclass
    clus
vv   DEL PEAK 53(XQ21.33) MUTATED DEL PEAK 53(XQ21.33) WILD-TYPE
  T1                            2                             19
  T2                           13                             74
  T3                           24                            149
  T4                            9                             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 53(XQ21.33) MUTATED    16  13  11   7
  DEL PEAK 53(XQ21.33) WILD-TYPE 106  94  64  72
D89V5, multiclass
    clus
vv   DEL PEAK 53(XQ21.33) MUTATED DEL PEAK 53(XQ21.33) WILD-TYPE
  N0                           16                            106
  N1                           13                             94
  N2                           11                             64
  N3                            7                             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"
                                vv
clus                              M0  M1  MX
  DEL PEAK 53(XQ21.33) MUTATED    43   3   2
  DEL PEAK 53(XQ21.33) WILD-TYPE 310  21  16
D89V6, multiclass
    clus
vv   DEL PEAK 53(XQ21.33) MUTATED DEL PEAK 53(XQ21.33) WILD-TYPE
  M0                           43                            310
  M1                            3                             21
  MX                            2                             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V7, binary
                                cls
clus                               0   1
  DEL PEAK 53(XQ21.33) MUTATED    15  33
  DEL PEAK 53(XQ21.33) WILD-TYPE 136 211
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 53(XQ21.33) MUTATED     15   33
  DEL PEAK 53(XQ21.33) WILD-TYPE  136  211
        clus
vv       DEL PEAK 53(XQ21.33) MUTATED DEL PEAK 53(XQ21.33) WILD-TYPE
  FEMALE                           15                            136
  MALE                             33                            211
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 53(XQ21.33) MUTATED                                       7
  DEL PEAK 53(XQ21.33) WILD-TYPE                                    58
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 53(XQ21.33) MUTATED                                                       17
  DEL PEAK 53(XQ21.33) WILD-TYPE                                                    140
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 53(XQ21.33) MUTATED                                                                   9
  DEL PEAK 53(XQ21.33) WILD-TYPE                                                                60
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 53(XQ21.33) MUTATED                                                 10
  DEL PEAK 53(XQ21.33) WILD-TYPE                                               54
                                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                                          0
  DEL PEAK 53(XQ21.33) WILD-TYPE                                        9
D89V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 53(XQ21.33) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      17
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            9
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     0
                                                                   clus
vv                                                                  DEL PEAK 53(XQ21.33) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         58
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       140
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             60
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              54
  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"
D89V9, binary
                                cls
clus                               0   1
  DEL PEAK 53(XQ21.33) MUTATED     1  47
  DEL PEAK 53(XQ21.33) WILD-TYPE   5 342
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 53(XQ21.33) MUTATED      1   47
  DEL PEAK 53(XQ21.33) WILD-TYPE    5  342
     clus
vv    DEL PEAK 53(XQ21.33) MUTATED DEL PEAK 53(XQ21.33) WILD-TYPE
  NO                             1                              5
  YES                           47                            342
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 53(XQ21.33) MUTATED    41   3   1   1
  DEL PEAK 53(XQ21.33) WILD-TYPE 277  13  17  24
D89V10, multiclass
    clus
vv   DEL PEAK 53(XQ21.33) MUTATED DEL PEAK 53(XQ21.33) WILD-TYPE
  R0                           41                            277
  R1                            3                             13
  R2                            1                             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"
D89V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 53(XQ21.33) MUTATED       9                         0
  DEL PEAK 53(XQ21.33) WILD-TYPE    79                         6
                                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      28
  DEL PEAK 53(XQ21.33) WILD-TYPE   215
D89V12, multiclass
                                           clus
vv                                          DEL PEAK 53(XQ21.33) MUTATED
  ASIAN                                                                9
  BLACK OR AFRICAN AMERICAN                                            0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               28
                                           clus
vv                                          DEL PEAK 53(XQ21.33) WILD-TYPE
  ASIAN                                                                 79
  BLACK OR AFRICAN AMERICAN                                              6
  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"
