[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/10006301/STAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/STAD-TP/10013814/transformed.cor.cli.txt"

nPatients in clinical file=351, in cluster file=369, common to both=346
[1]  81 346
[1] "AMP PEAK  1(1P36.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                            48                            298 
  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                            48                            298 
[1] "AMP PEAK  2(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          126                           220 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          126                           220 
[1] "AMP PEAK  3(1Q42.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                          116                           230 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                          116                           230 
[1] "AMP PEAK  4(3Q26.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                          116                           230 
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                          116                           230 
[1] "AMP PEAK  5(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                            98                            248 
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                            98                            248 
[1] "AMP PEAK  6(5P13.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE 
                           97                           249 
  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE 
                           97                           249 
[1] "AMP PEAK  7(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE 
                           93                           253 
  AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE 
                           93                           253 
[1] "AMP PEAK  8(6Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE 
                         69                         277 
  AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE 
                         69                         277 
[1] "AMP PEAK  9(6Q21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE 
                         62                         284 
  AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE 
                         62                         284 
[1] "AMP PEAK 10(7P22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                          178                           168 
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                          178                           168 
[1] "AMP PEAK 11(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                          161                           185 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                          161                           185 
[1] "AMP PEAK 12(7Q21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                          158                           188 
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                          158                           188 
[1] "AMP PEAK 13(8P23.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE 
                          135                           211 
  AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE 
                          135                           211 
[1] "AMP PEAK 14(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE 
                           235                            111 
  AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE 
                           235                            111 
[1] "AMP PEAK 15(9P24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(9P24.1) MUTATED AMP PEAK 15(9P24.1) WILD-TYPE 
                           54                           292 
  AMP PEAK 15(9P24.1) MUTATED AMP PEAK 15(9P24.1) WILD-TYPE 
                           54                           292 
[1] "AMP PEAK 16(9P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE 
                           64                           282 
  AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE 
                           64                           282 
[1] "AMP PEAK 17(9Q34.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE 
                           90                           256 
  AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE 
                           90                           256 
[1] "AMP PEAK 18(10P11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(10P11.22) MUTATED AMP PEAK 18(10P11.22) WILD-TYPE 
                             91                             255 
  AMP PEAK 18(10P11.22) MUTATED AMP PEAK 18(10P11.22) WILD-TYPE 
                             91                             255 
[1] "AMP PEAK 19(10Q22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(10Q22.2) MUTATED AMP PEAK 19(10Q22.2) WILD-TYPE 
                            66                            280 
  AMP PEAK 19(10Q22.2) MUTATED AMP PEAK 19(10Q22.2) WILD-TYPE 
                            66                            280 
[1] "AMP PEAK 20(10Q26.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(10Q26.13) MUTATED AMP PEAK 20(10Q26.13) WILD-TYPE 
                             69                             277 
  AMP PEAK 20(10Q26.13) MUTATED AMP PEAK 20(10Q26.13) WILD-TYPE 
                             69                             277 
[1] "AMP PEAK 21(11P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(11P13) MUTATED AMP PEAK 21(11P13) WILD-TYPE 
                          65                          281 
  AMP PEAK 21(11P13) MUTATED AMP PEAK 21(11P13) WILD-TYPE 
                          65                          281 
[1] "AMP PEAK 22(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(11Q13.3) MUTATED AMP PEAK 22(11Q13.3) WILD-TYPE 
                            83                            263 
  AMP PEAK 22(11Q13.3) MUTATED AMP PEAK 22(11Q13.3) WILD-TYPE 
                            83                            263 
[1] "AMP PEAK 23(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE 
                            99                            247 
  AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE 
                            99                            247 
[1] "AMP PEAK 24(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE 
                          88                          258 
  AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE 
                          88                          258 
[1] "AMP PEAK 25(13Q12.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(13Q12.3) MUTATED AMP PEAK 25(13Q12.3) WILD-TYPE 
                           133                            213 
  AMP PEAK 25(13Q12.3) MUTATED AMP PEAK 25(13Q12.3) WILD-TYPE 
                           133                            213 
[1] "AMP PEAK 26(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(13Q22.1) MUTATED AMP PEAK 26(13Q22.1) WILD-TYPE 
                           137                            209 
  AMP PEAK 26(13Q22.1) MUTATED AMP PEAK 26(13Q22.1) WILD-TYPE 
                           137                            209 
[1] "AMP PEAK 27(15Q26.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(15Q26.1) MUTATED AMP PEAK 27(15Q26.1) WILD-TYPE 
                            81                            265 
  AMP PEAK 27(15Q26.1) MUTATED AMP PEAK 27(15Q26.1) WILD-TYPE 
                            81                            265 
[1] "AMP PEAK 28(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE 
                         108                          238 
  AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE 
                         108                          238 
[1] "AMP PEAK 29(18Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(18Q11.2) MUTATED AMP PEAK 29(18Q11.2) WILD-TYPE 
                           108                            238 
  AMP PEAK 29(18Q11.2) MUTATED AMP PEAK 29(18Q11.2) WILD-TYPE 
                           108                            238 
[1] "AMP PEAK 30(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 30(19P13.2) MUTATED AMP PEAK 30(19P13.2) WILD-TYPE 
                            39                            307 
  AMP PEAK 30(19P13.2) MUTATED AMP PEAK 30(19P13.2) WILD-TYPE 
                            39                            307 
[1] "AMP PEAK 31(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 31(19Q12) MUTATED AMP PEAK 31(19Q12) WILD-TYPE 
                         103                          243 
  AMP PEAK 31(19Q12) MUTATED AMP PEAK 31(19Q12) WILD-TYPE 
                         103                          243 
[1] "AMP PEAK 32(20Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 32(20Q13.2) MUTATED AMP PEAK 32(20Q13.2) WILD-TYPE 
                           227                            119 
  AMP PEAK 32(20Q13.2) MUTATED AMP PEAK 32(20Q13.2) WILD-TYPE 
                           227                            119 
[1] "AMP PEAK 33(XQ27.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 33(XQ27.3) MUTATED AMP PEAK 33(XQ27.3) WILD-TYPE 
                           64                           282 
  AMP PEAK 33(XQ27.3) MUTATED AMP PEAK 33(XQ27.3) WILD-TYPE 
                           64                           282 
[1] "DEL PEAK  1(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            96                            250 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            96                            250 
[1] "DEL PEAK  2(1P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           66                           280 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           66                           280 
[1] "DEL PEAK  3(1Q25.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q25.1) MUTATED DEL PEAK  3(1Q25.1) WILD-TYPE 
                           12                           334 
  DEL PEAK  3(1Q25.1) MUTATED DEL PEAK  3(1Q25.1) WILD-TYPE 
                           12                           334 
[1] "DEL PEAK  4(1Q44) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE 
                         21                         325 
  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE 
                         21                         325 
[1] "DEL PEAK  5(2Q32.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE 
                           47                           299 
  DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE 
                           47                           299 
[1] "DEL PEAK  6(2Q37.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE 
                           51                           295 
  DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE 
                           51                           295 
[1] "DEL PEAK  7(3P26.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE 
                          104                           242 
  DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE 
                          104                           242 
[1] "DEL PEAK  8(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                          120                           226 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                          120                           226 
[1] "DEL PEAK  9(3Q26.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                            41                            305 
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                            41                            305 
[1] "DEL PEAK 10(4P16.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(4P16.3) MUTATED DEL PEAK 10(4P16.3) WILD-TYPE 
                          131                           215 
  DEL PEAK 10(4P16.3) MUTATED DEL PEAK 10(4P16.3) WILD-TYPE 
                          131                           215 
[1] "DEL PEAK 11(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                          149                           197 
  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                          149                           197 
[1] "DEL PEAK 12(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(4Q34.3) MUTATED DEL PEAK 12(4Q34.3) WILD-TYPE 
                          149                           197 
  DEL PEAK 12(4Q34.3) MUTATED DEL PEAK 12(4Q34.3) WILD-TYPE 
                          149                           197 
[1] "DEL PEAK 13(5Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                          122                           224 
  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                          122                           224 
[1] "DEL PEAK 14(5Q23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(5Q23.2) MUTATED DEL PEAK 14(5Q23.2) WILD-TYPE 
                          109                           237 
  DEL PEAK 14(5Q23.2) MUTATED DEL PEAK 14(5Q23.2) WILD-TYPE 
                          109                           237 
[1] "DEL PEAK 15(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           85                           261 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           85                           261 
[1] "DEL PEAK 16(6Q14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(6Q14.1) MUTATED DEL PEAK 16(6Q14.1) WILD-TYPE 
                           67                           279 
  DEL PEAK 16(6Q14.1) MUTATED DEL PEAK 16(6Q14.1) WILD-TYPE 
                           67                           279 
[1] "DEL PEAK 17(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         76                         270 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         76                         270 
[1] "DEL PEAK 18(7Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                           52                           294 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                           52                           294 
[1] "DEL PEAK 19(7Q36.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE 
                           70                           276 
  DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE 
                           70                           276 
[1] "DEL PEAK 20(8P23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(8P23.3) MUTATED DEL PEAK 20(8P23.3) WILD-TYPE 
                           94                           252 
  DEL PEAK 20(8P23.3) MUTATED DEL PEAK 20(8P23.3) WILD-TYPE 
                           94                           252 
[1] "DEL PEAK 21(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(9P23) MUTATED DEL PEAK 21(9P23) WILD-TYPE 
                        144                         202 
  DEL PEAK 21(9P23) MUTATED DEL PEAK 21(9P23) WILD-TYPE 
                        144                         202 
[1] "DEL PEAK 22(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                          140                           206 
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                          140                           206 
[1] "DEL PEAK 23(9Q21.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(9Q21.11) MUTATED DEL PEAK 23(9Q21.11) WILD-TYPE 
                            84                            262 
  DEL PEAK 23(9Q21.11) MUTATED DEL PEAK 23(9Q21.11) WILD-TYPE 
                            84                            262 
[1] "DEL PEAK 24(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                            54                            292 
  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                            54                            292 
[1] "DEL PEAK 25(10Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(10Q22.3) MUTATED DEL PEAK 25(10Q22.3) WILD-TYPE 
                            53                            293 
  DEL PEAK 25(10Q22.3) MUTATED DEL PEAK 25(10Q22.3) WILD-TYPE 
                            53                            293 
[1] "DEL PEAK 26(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(10Q23.31) MUTATED DEL PEAK 26(10Q23.31) WILD-TYPE 
                             81                             265 
  DEL PEAK 26(10Q23.31) MUTATED DEL PEAK 26(10Q23.31) WILD-TYPE 
                             81                             265 
[1] "DEL PEAK 27(11P15.4) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(11P15.4) MUTATED DEL PEAK 27(11P15.4) WILD-TYPE 
                            72                            274 
  DEL PEAK 27(11P15.4) MUTATED DEL PEAK 27(11P15.4) WILD-TYPE 
                            72                            274 
[1] "DEL PEAK 28(11Q23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(11Q23.2) MUTATED DEL PEAK 28(11Q23.2) WILD-TYPE 
                            74                            272 
  DEL PEAK 28(11Q23.2) MUTATED DEL PEAK 28(11Q23.2) WILD-TYPE 
                            74                            272 
[1] "DEL PEAK 29(12P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE 
                            53                            293 
  DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE 
                            53                            293 
[1] "DEL PEAK 30(13Q12.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(13Q12.11) MUTATED DEL PEAK 30(13Q12.11) WILD-TYPE 
                             49                             297 
  DEL PEAK 30(13Q12.11) MUTATED DEL PEAK 30(13Q12.11) WILD-TYPE 
                             49                             297 
[1] "DEL PEAK 31(14Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(14Q23.3) MUTATED DEL PEAK 31(14Q23.3) WILD-TYPE 
                            99                            247 
  DEL PEAK 31(14Q23.3) MUTATED DEL PEAK 31(14Q23.3) WILD-TYPE 
                            99                            247 
[1] "DEL PEAK 32(14Q32.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(14Q32.33) MUTATED DEL PEAK 32(14Q32.33) WILD-TYPE 
                            100                             246 
  DEL PEAK 32(14Q32.33) MUTATED DEL PEAK 32(14Q32.33) WILD-TYPE 
                            100                             246 
[1] "DEL PEAK 33(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE 
                            94                            252 
  DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE 
                            94                            252 
[1] "DEL PEAK 34(15Q15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(15Q15.1) MUTATED DEL PEAK 34(15Q15.1) WILD-TYPE 
                            97                            249 
  DEL PEAK 34(15Q15.1) MUTATED DEL PEAK 34(15Q15.1) WILD-TYPE 
                            97                            249 
[1] "DEL PEAK 35(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                            68                            278 
  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                            68                            278 
[1] "DEL PEAK 36(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                           135                            211 
  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                           135                            211 
[1] "DEL PEAK 37(17P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE 
                         131                          215 
  DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE 
                         131                          215 
[1] "DEL PEAK 38(17Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE 
                            64                            282 
  DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE 
                            64                            282 
[1] "DEL PEAK 39(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE 
                           156                            190 
  DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE 
                           156                            190 
[1] "DEL PEAK 40(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(19P13.3) MUTATED DEL PEAK 40(19P13.3) WILD-TYPE 
                           114                            232 
  DEL PEAK 40(19P13.3) MUTATED DEL PEAK 40(19P13.3) WILD-TYPE 
                           114                            232 
[1] "DEL PEAK 41(19Q13.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(19Q13.11) MUTATED DEL PEAK 41(19Q13.11) WILD-TYPE 
                             52                             294 
  DEL PEAK 41(19Q13.11) MUTATED DEL PEAK 41(19Q13.11) WILD-TYPE 
                             52                             294 
[1] "DEL PEAK 42(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE 
                            28                            318 
  DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE 
                            28                            318 
[1] "DEL PEAK 43(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE 
                           127                            219 
  DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE 
                           127                            219 
[1] "DEL PEAK 44(21Q22.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(21Q22.13) MUTATED DEL PEAK 44(21Q22.13) WILD-TYPE 
                            136                             210 
  DEL PEAK 44(21Q22.13) MUTATED DEL PEAK 44(21Q22.13) WILD-TYPE 
                            136                             210 
[1] "DEL PEAK 45(22Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(22Q13.31) MUTATED DEL PEAK 45(22Q13.31) WILD-TYPE 
                            117                             229 
  DEL PEAK 45(22Q13.31) MUTATED DEL PEAK 45(22Q13.31) WILD-TYPE 
                            117                             229 
[1] "DEL PEAK 46(XP22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                           65                           281 
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                           65                           281 
[1] "DEL PEAK 47(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 47(XP21.1) MUTATED DEL PEAK 47(XP21.1) WILD-TYPE 
                           61                           285 
  DEL PEAK 47(XP21.1) MUTATED DEL PEAK 47(XP21.1) WILD-TYPE 
                           61                           285 
[1] "DEL PEAK 48(XQ21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE 
                            42                            304 
  DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE 
                            42                            304 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [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 346 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           69 
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            2            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          406          523 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
         312          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-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
         209          169           55           77          169         1842 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
          NA          137           NA           NA           NA           NA 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
        3720         1153         1236         3519         3540         2171 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-ZA-A8F6 
          NA           NA          176          128 
Variable 1:'AGE':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=86,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=210,	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=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'HISTOLOGICAL.TYPE':	nDistinctValues=8,	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=29,	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=19,	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 346 columns, 1 survival variables, and 11 non-survival variables.
AGE, nv=52, 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 
 20  85 146  85 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 20  85 146  85 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
 20  85 146  85 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 20  85 146  85 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
109  92  66  67 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
109  92  66  67 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
109  92  66  67 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
109  92  66  67 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=8, 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=29, 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    31  13
  AMP PEAK  1(1P36.22) WILD-TYPE 191  80
  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                            44                            271 
  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                            13                             80 
$`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         2.27         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        10.26        15.22        16.44 
TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-FP-7829 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-A4GH 
       11.24         2.96        19.53        18.08        26.47        11.77 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RI 
        8.98         6.25        27.42        21.21         3.45        18.38 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A7NU TCGA-IP-7968 TCGA-RD-A7BT TCGA-RD-A7C1 
        1.41         6.44         1.81         2.53         8.61        16.67 
TCGA-RD-A8MW TCGA-RD-A8N1 
       37.91       115.69 

$`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         0.07         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        13.35 
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-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV 
       60.56         3.72         4.50        11.05         4.67       122.30 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-SW-A7EB 
       40.64       116.38        71.38        57.44         8.94         5.79 
TCGA-ZA-A8F6 
        4.21 

  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 
                         10.75                          11.05 
[1] "0.1 - 115.7 (10.8)" "0.1 - 122.3 (11.1)"
[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        3        5        7         3
  AMP PEAK  1(1P36.22) WILD-TYPE       2        9       33       20        29
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  1(1P36.22) MUTATED           7         1          7          5
  AMP PEAK  1(1P36.22) WILD-TYPE        40         2         54         40
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK  1(1P36.22) MUTATED            5        3
  AMP PEAK  1(1P36.22) WILD-TYPE         27       28
D1V3, multiclass
            clus
vv           AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              3                              9
  STAGE IB                              5                             33
  STAGE II                              7                             20
  STAGE IIA                             3                             29
  STAGE IIB                             7                             40
  STAGE III                             1                              2
  STAGE IIIA                            7                             54
  STAGE IIIB                            5                             40
  STAGE IIIC                            5                             27
  STAGE IV                              3                             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  1(1P36.22) MUTATED     5  13  21   8
  AMP PEAK  1(1P36.22) WILD-TYPE  15  72 125  77
D1V4, multiclass
    clus
vv   AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  T1                            5                             15
  T2                           13                             72
  T3                           21                            125
  T4                            8                             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  1(1P36.22) MUTATED   14 15  7 11
  AMP PEAK  1(1P36.22) WILD-TYPE 95 77 59 56
D1V5, multiclass
    clus
vv   AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  N0                           14                             95
  N1                           15                             77
  N2                            7                             59
  N3                           11                             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  1(1P36.22) MUTATED    43   2   3
  AMP PEAK  1(1P36.22) WILD-TYPE 265  19  14
D1V6, multiclass
    clus
vv   AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  M0                           43                            265
  M1                            2                             19
  MX                            3                             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"
D1V7, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.22) MUTATED    12  36
  AMP PEAK  1(1P36.22) WILD-TYPE 125 173
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.22) MUTATED     12   36
  AMP PEAK  1(1P36.22) WILD-TYPE  125  173
        clus
vv       AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  FEMALE                           12                            125
  MALE                             36                            173
[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                                    53
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  1(1P36.22) MUTATED                                                       21
  AMP PEAK  1(1P36.22) WILD-TYPE                                                    133
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  1(1P36.22) MUTATED                                                                   8
  AMP PEAK  1(1P36.22) WILD-TYPE                                                                46
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  1(1P36.22) MUTATED                                                  4
  AMP PEAK  1(1P36.22) WILD-TYPE                                               41
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK  1(1P36.22) MUTATED                                                           1
  AMP PEAK  1(1P36.22) WILD-TYPE                                                         0
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK  1(1P36.22) MUTATED                                                          3
  AMP PEAK  1(1P36.22) WILD-TYPE                                                       16
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK  1(1P36.22) MUTATED                                                           0
  AMP PEAK  1(1P36.22) WILD-TYPE                                                         5
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK  1(1P36.22) MUTATED                                          1
  AMP PEAK  1(1P36.22) WILD-TYPE                                        3
D1V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  1(1P36.22) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      21
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            8
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             4
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     1
                                                                   clus
vv                                                                  AMP PEAK  1(1P36.22) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         53
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             46
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              41
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.22) MUTATED     1  47
  AMP PEAK  1(1P36.22) WILD-TYPE   6 292
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.22) MUTATED      1   47
  AMP PEAK  1(1P36.22) WILD-TYPE    6  292
     clus
vv    AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  NO                             1                              6
  YES                           47                            292
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  1(1P36.22) MUTATED    37   2   1   3
  AMP PEAK  1(1P36.22) WILD-TYPE 240  11  12  22
D1V10, multiclass
    clus
vv   AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  R0                           37                            240
  R1                            2                             11
  R2                            1                             12
  RX                            3                             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  1(1P36.22) MUTATED      10                         0
  AMP PEAK  1(1P36.22) WILD-TYPE    74                         3
                                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      29
  AMP PEAK  1(1P36.22) WILD-TYPE   179
D1V12, multiclass
                                           clus
vv                                          AMP PEAK  1(1P36.22) MUTATED
  ASIAN                                                               10
  BLACK OR AFRICAN AMERICAN                                            0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               29
                                           clus
vv                                          AMP PEAK  1(1P36.22) WILD-TYPE
  ASIAN                                                                 74
  BLACK OR AFRICAN AMERICAN                                              3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                179
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = AMP PEAK  2(1Q21.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  2(1Q21.3) MUTATED    80  30
  AMP PEAK  2(1Q21.3) WILD-TYPE 142  63
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          110                           205 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           30                            63 
$`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         0.07         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 
       10.26        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-A7NU TCGA-KB-A6F7 TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV 
        6.44         1.81        60.56         8.61        16.67       122.30 
TCGA-RD-A8N1 TCGA-RD-A8N6 
      115.69         8.94 

$`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         2.27 
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        13.35        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-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW 
        2.53         5.56         3.72         4.50        11.05         4.67 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-SW-A7EB 
       37.91        40.64       116.38        71.38        57.44         5.79 
TCGA-ZA-A8F6 
        4.21 

  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 
                       10.405                        11.410 
[1] "0.1 - 122.3 (10.4)" "0.1 - 116.4 (11.4)"
[1] "hr=" "1.1"
D2V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  2(1Q21.3) MUTATED         1        5       15        8        13
  AMP PEAK  2(1Q21.3) WILD-TYPE       1        7       23       19        19
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  2(1Q21.3) MUTATED          18         1         22         14
  AMP PEAK  2(1Q21.3) WILD-TYPE        29         2         39         31
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK  2(1Q21.3) MUTATED            8       14
  AMP PEAK  2(1Q21.3) WILD-TYPE         24       17
D2V3, multiclass
            clus
vv           AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             5                             7
  STAGE IB                            15                            23
  STAGE II                             8                            19
  STAGE IIA                           13                            19
  STAGE IIB                           18                            29
  STAGE III                            1                             2
  STAGE IIIA                          22                            39
  STAGE IIIB                          14                            31
  STAGE IIIC                           8                            24
  STAGE IV                            14                            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  2(1Q21.3) MUTATED    9 32 57 25
  AMP PEAK  2(1Q21.3) WILD-TYPE 11 53 89 60
D2V4, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  T1                           9                            11
  T2                          32                            53
  T3                          57                            89
  T4                          25                            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
  AMP PEAK  2(1Q21.3) MUTATED   43 33 19 24
  AMP PEAK  2(1Q21.3) WILD-TYPE 66 59 47 43
D2V5, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  N0                          43                            66
  N1                          33                            59
  N2                          19                            47
  N3                          24                            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
  AMP PEAK  2(1Q21.3) MUTATED   109   8   9
  AMP PEAK  2(1Q21.3) WILD-TYPE 199  13   8
D2V6, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  M0                         109                           199
  M1                           8                            13
  MX                           9                             8
[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    51  75
  AMP PEAK  2(1Q21.3) WILD-TYPE  86 134
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     51   75
  AMP PEAK  2(1Q21.3) WILD-TYPE   86  134
        clus
vv       AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  FEMALE                          51                            86
  MALE                            75                           134
[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                                    47
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  2(1Q21.3) MUTATED                                                       57
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                     97
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  2(1Q21.3) MUTATED                                                                  21
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                                33
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  2(1Q21.3) MUTATED                                                 20
  AMP PEAK  2(1Q21.3) WILD-TYPE                                               25
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK  2(1Q21.3) MUTATED                                                           1
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                         0
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK  2(1Q21.3) MUTATED                                                          5
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                       14
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK  2(1Q21.3) MUTATED                                                           3
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                         2
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK  2(1Q21.3) MUTATED                                          2
  AMP PEAK  2(1Q21.3) WILD-TYPE                                        2
D2V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  2(1Q21.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     57
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          21
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           20
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    2
                                                                   clus
vv                                                                  AMP PEAK  2(1Q21.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       97
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            33
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             25
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V9, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED     6 120
  AMP PEAK  2(1Q21.3) WILD-TYPE   1 219
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED      6  120
  AMP PEAK  2(1Q21.3) WILD-TYPE    1  219
     clus
vv    AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  NO                            6                             1
  YES                         120                           219
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  2(1Q21.3) MUTATED    94   9   5   9
  AMP PEAK  2(1Q21.3) WILD-TYPE 183   4   8  16
D2V10, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  R0                          94                           183
  R1                           9                             4
  R2                           5                             8
  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      33                         2
  AMP PEAK  2(1Q21.3) WILD-TYPE    51                         1
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  2(1Q21.3) MUTATED                                           1    73
  AMP PEAK  2(1Q21.3) WILD-TYPE                                         0   135
D2V12, multiclass
                                           clus
vv                                          AMP PEAK  2(1Q21.3) MUTATED
  ASIAN                                                              33
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              73
                                           clus
vv                                          AMP PEAK  2(1Q21.3) WILD-TYPE
  ASIAN                                                                51
  BLACK OR AFRICAN AMERICAN                                             1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               135
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = AMP PEAK  3(1Q42.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  3(1Q42.3) MUTATED    75  29
  AMP PEAK  3(1Q42.3) WILD-TYPE 147  64
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                          104                           211 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                           29                            64 
$`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         2.27         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         0.07         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        10.26        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 
      122.30       115.69 

$`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 
       13.35        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-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-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW 
        4.50        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-SW-A7EB 
       40.64       116.38        71.38        57.44         8.94         5.79 
TCGA-ZA-A8F6 
        4.21 

  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 
                         7.89                         11.57 
[1] "0.1 - 122.3 (7.9)"  "0.1 - 116.4 (11.6)"
[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       11        8        12
  AMP PEAK  3(1Q42.3) WILD-TYPE       1        6       27       19        20
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  3(1Q42.3) MUTATED          14         2         20         14
  AMP PEAK  3(1Q42.3) WILD-TYPE        33         1         41         31
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK  3(1Q42.3) MUTATED           11       11
  AMP PEAK  3(1Q42.3) WILD-TYPE         21       20
D3V3, multiclass
            clus
vv           AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             6                             6
  STAGE IB                            11                            27
  STAGE II                             8                            19
  STAGE IIA                           12                            20
  STAGE IIB                           14                            33
  STAGE III                            2                             1
  STAGE IIIA                          20                            41
  STAGE IIIB                          14                            31
  STAGE IIIC                          11                            21
  STAGE IV                            11                            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  3(1Q42.3) MUTATED    9 23 50 31
  AMP PEAK  3(1Q42.3) WILD-TYPE 11 62 96 54
D3V4, multiclass
    clus
vv   AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  T1                           9                            11
  T2                          23                            62
  T3                          50                            96
  T4                          31                            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                            N0 N1 N2 N3
  AMP PEAK  3(1Q42.3) MUTATED   40 28 21 21
  AMP PEAK  3(1Q42.3) WILD-TYPE 69 64 45 46
D3V5, multiclass
    clus
vv   AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  N0                          40                            69
  N1                          28                            64
  N2                          21                            45
  N3                          21                            46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  AMP PEAK  3(1Q42.3) MUTATED   101   7   8
  AMP PEAK  3(1Q42.3) WILD-TYPE 207  14   9
D3V6, multiclass
    clus
vv   AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  M0                         101                           207
  M1                           7                            14
  MX                           8                             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"
D3V7, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q42.3) MUTATED    45  71
  AMP PEAK  3(1Q42.3) WILD-TYPE  92 138
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED     45   71
  AMP PEAK  3(1Q42.3) WILD-TYPE   92  138
        clus
vv       AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  FEMALE                          45                            92
  MALE                            71                           138
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  3(1Q42.3) MUTATED                                      10
  AMP PEAK  3(1Q42.3) WILD-TYPE                                    52
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  3(1Q42.3) MUTATED                                                       52
  AMP PEAK  3(1Q42.3) WILD-TYPE                                                    102
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  3(1Q42.3) MUTATED                                                                  19
  AMP PEAK  3(1Q42.3) WILD-TYPE                                                                35
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  3(1Q42.3) MUTATED                                                 23
  AMP PEAK  3(1Q42.3) WILD-TYPE                                               22
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK  3(1Q42.3) MUTATED                                                           1
  AMP PEAK  3(1Q42.3) WILD-TYPE                                                         0
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK  3(1Q42.3) MUTATED                                                          6
  AMP PEAK  3(1Q42.3) WILD-TYPE                                                       13
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK  3(1Q42.3) MUTATED                                                           2
  AMP PEAK  3(1Q42.3) WILD-TYPE                                                         3
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK  3(1Q42.3) MUTATED                                          2
  AMP PEAK  3(1Q42.3) WILD-TYPE                                        2
D3V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  3(1Q42.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      10
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     52
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          19
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           23
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    2
                                                                   clus
vv                                                                  AMP PEAK  3(1Q42.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        52
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      102
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             22
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V9, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q42.3) MUTATED     4 112
  AMP PEAK  3(1Q42.3) WILD-TYPE   3 227
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED      4  112
  AMP PEAK  3(1Q42.3) WILD-TYPE    3  227
     clus
vv    AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  NO                            4                             3
  YES                         112                           227
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  3(1Q42.3) MUTATED    90   6   3   9
  AMP PEAK  3(1Q42.3) WILD-TYPE 187   7  10  16
D3V10, multiclass
    clus
vv   AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  R0                          90                           187
  R1                           6                             7
  R2                           3                            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"
D3V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  3(1Q42.3) MUTATED      31                         2
  AMP PEAK  3(1Q42.3) WILD-TYPE    53                         1
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  3(1Q42.3) MUTATED                                           0    70
  AMP PEAK  3(1Q42.3) WILD-TYPE                                         1   138
D3V12, multiclass
                                           clus
vv                                          AMP PEAK  3(1Q42.3) MUTATED
  ASIAN                                                              31
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              70
                                           clus
vv                                          AMP PEAK  3(1Q42.3) WILD-TYPE
  ASIAN                                                                53
  BLACK OR AFRICAN AMERICAN                                             1
  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(4) Variable = AMP PEAK  4(3Q26.2) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(3Q26.2) MUTATED    77  27
  AMP PEAK  4(3Q26.2) WILD-TYPE 145  66
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                          104                           211 
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                           27                            66 
$`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-6801 TCGA-BR-6802 TCGA-BR-7196 TCGA-BR-7722 
       10.13         0.62        21.11        30.90        12.82         0.16 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8284 
       18.54         0.95        12.76         0.82         1.32         0.72 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8361 TCGA-BR-8367 TCGA-BR-8373 
        0.26         1.55         1.48        19.50        13.74        14.79 
TCGA-BR-8484 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8676 TCGA-BR-8687 TCGA-BR-A452 
        0.72        12.79        15.81         7.53         0.62         0.66 
TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4J4 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PE 
        2.27        13.41         0.53        19.36        20.65        20.42 
TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 
       13.64         3.25        13.18         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-A487 TCGA-CD-A48A 
        0.07         0.10         0.16         0.13         0.13         0.13 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
        0.13         0.10         3.02        15.95         7.99         8.05 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5719 
       47.05        19.07        12.03        12.00        30.97         1.02 
TCGA-CG-5724 TCGA-CG-5725 TCGA-D7-6521 TCGA-D7-6815 TCGA-D7-8570 TCGA-D7-8579 
       12.03        15.02        18.54        15.98        24.72        20.91 
TCGA-D7-A4YU TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-EQ-5647 
       16.44        14.76        11.24         9.76         2.96         0.62 
TCGA-EQ-A4SO TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8211 
       16.24        21.27         0.39         3.02        22.29        13.58 
TCGA-FP-8631 TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-A4G6 TCGA-HU-A4G9 
        0.56         0.23        26.47         5.92        12.30        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4H0 
        3.25        22.75        25.81        11.77         8.98         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RL 
       12.95        19.36        17.69         9.67        27.42         5.19 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F7 
       13.08         1.41         6.44         5.56         1.81        60.56 
TCGA-RD-A7C1 TCGA-RD-A8N1 
       16.67       115.69 

$`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-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        13.84        13.22        16.14         1.25         8.98 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        32.94         9.21        24.76        35.24        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7959 
       15.42        28.01         0.69        12.43         0.69        18.71 
TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 
       17.49         0.69        12.26         0.49        20.55         0.26 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 
       12.95        16.31         7.40         6.18         0.36         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       22.19         2.96         0.95         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-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8590 TCGA-BR-8591 
        5.39         9.21        20.22         1.12         2.14        13.45 
TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        0.20         0.49        11.54        15.81        16.44         0.59 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CS 
       15.68        10.68        12.56         1.15         3.02         0.92 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 
       13.51        12.89         0.79         0.72        14.17        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM 
        0.66        13.51         0.46         1.15        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8529 TCGA-CD-8531 
        2.83        13.15         0.30         0.07         0.13         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A4MG 
        0.10         0.13         0.10         0.07         0.13         0.07 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4438 
        0.10         0.10        20.02        27.02         1.02        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-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 
        7.07        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-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-D7-5578 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-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        20.55        18.84        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        10.26        15.22        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       12.33        16.80        19.50        17.19         0.23         6.97 
TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET 
       21.14        14.27         5.92        15.16        13.78        13.71 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.31        11.44        15.65         4.34         7.40         7.13 
TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7829 
        7.79         6.58        14.47        72.23         8.12        19.53 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HU-8238 
       17.06        59.54         5.03         1.55        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-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GJ TCGA-HU-A4GN 
        0.76        24.30         5.59        11.84        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H5 
        0.10         6.51         6.25        10.19         0.26        12.30 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88         8.81        21.21         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RS TCGA-IP-7968 TCGA-KB-A6F5 TCGA-MX-A5UG 
       18.38         5.36         6.87         2.53         5.56         3.72 
TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
        4.50        11.05         8.61         4.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-SW-A7EB 
       40.64       116.38        71.38        57.44         8.94         5.79 
TCGA-ZA-A8F6 
        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 
                       10.685                        11.050 
[1] "0.1 - 115.7 (10.7)" "0.1 - 122.3 (11.1)"
[1] "hr=" "1.1"
D4V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  4(3Q26.2) MUTATED         0        4       13        9         7
  AMP PEAK  4(3Q26.2) WILD-TYPE       2        8       25       18        25
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  4(3Q26.2) MUTATED          17         1         24         13
  AMP PEAK  4(3Q26.2) WILD-TYPE        30         2         37         32
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK  4(3Q26.2) MUTATED           14        9
  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                             4                             8
  STAGE IB                            13                            25
  STAGE II                             9                            18
  STAGE IIA                            7                            25
  STAGE IIB                           17                            30
  STAGE III                            1                             2
  STAGE IIIA                          24                            37
  STAGE IIIB                          13                            32
  STAGE IIIC                          14                            18
  STAGE IV                             9                            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     7  28  42  35
  AMP PEAK  4(3Q26.2) WILD-TYPE  13  57 104  50
D4V4, multiclass
    clus
vv   AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  T1                           7                            13
  T2                          28                            57
  T3                          42                           104
  T4                          35                            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                            N0 N1 N2 N3
  AMP PEAK  4(3Q26.2) MUTATED   33 36 20 23
  AMP PEAK  4(3Q26.2) WILD-TYPE 76 56 46 44
D4V5, multiclass
    clus
vv   AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  N0                          33                            76
  N1                          36                            56
  N2                          20                            46
  N3                          23                            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  4(3Q26.2) MUTATED    99   7  10
  AMP PEAK  4(3Q26.2) WILD-TYPE 209  14   7
D4V6, multiclass
    clus
vv   AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  M0                          99                           209
  M1                           7                            14
  MX                          10                             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    49  67
  AMP PEAK  4(3Q26.2) WILD-TYPE  88 142
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(3Q26.2) MUTATED     49   67
  AMP PEAK  4(3Q26.2) WILD-TYPE   88  142
        clus
vv       AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  FEMALE                          49                            88
  MALE                            67                           142
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  4(3Q26.2) MUTATED                                      18
  AMP PEAK  4(3Q26.2) WILD-TYPE                                    44
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  4(3Q26.2) MUTATED                                                       57
  AMP PEAK  4(3Q26.2) WILD-TYPE                                                     97
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  4(3Q26.2) MUTATED                                                                  18
  AMP PEAK  4(3Q26.2) WILD-TYPE                                                                36
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  4(3Q26.2) MUTATED                                                 13
  AMP PEAK  4(3Q26.2) WILD-TYPE                                               32
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK  4(3Q26.2) MUTATED                                                           0
  AMP PEAK  4(3Q26.2) WILD-TYPE                                                         1
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK  4(3Q26.2) MUTATED                                                          6
  AMP PEAK  4(3Q26.2) WILD-TYPE                                                       13
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK  4(3Q26.2) MUTATED                                                           1
  AMP PEAK  4(3Q26.2) WILD-TYPE                                                         4
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK  4(3Q26.2) MUTATED                                          2
  AMP PEAK  4(3Q26.2) WILD-TYPE                                        2
D4V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  4(3Q26.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      18
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     57
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          18
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           13
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    2
                                                                   clus
vv                                                                  AMP PEAK  4(3Q26.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        44
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       97
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             32
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V9, binary
                               cls
clus                              0   1
  AMP PEAK  4(3Q26.2) MUTATED     2 114
  AMP PEAK  4(3Q26.2) WILD-TYPE   5 225
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(3Q26.2) MUTATED      2  114
  AMP PEAK  4(3Q26.2) WILD-TYPE    5  225
     clus
vv    AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  NO                            2                             5
  YES                         114                           225
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  4(3Q26.2) MUTATED    92   4   4   9
  AMP PEAK  4(3Q26.2) WILD-TYPE 185   9   9  16
D4V10, multiclass
    clus
vv   AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  R0                          92                           185
  R1                           4                             9
  R2                           4                             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"
D4V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  4(3Q26.2) MUTATED      34                         1
  AMP PEAK  4(3Q26.2) WILD-TYPE    50                         2
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  4(3Q26.2) MUTATED                                           0    64
  AMP PEAK  4(3Q26.2) WILD-TYPE                                         1   144
D4V12, multiclass
                                           clus
vv                                          AMP PEAK  4(3Q26.2) MUTATED
  ASIAN                                                              34
  BLACK OR AFRICAN AMERICAN                                           1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              64
                                           clus
vv                                          AMP PEAK  4(3Q26.2) WILD-TYPE
  ASIAN                                                                50
  BLACK OR AFRICAN AMERICAN                                             2
  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(5) Variable = AMP PEAK  5(5P15.33) MUTATION ANALYSIS
D5V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  5(5P15.33) MUTATED    63  27
  AMP PEAK  5(5P15.33) WILD-TYPE 159  66
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                            90                            225 
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                            27                             66 
$`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 
        0.07         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        10.26 
TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8576 TCGA-D7-A6EX 
       15.22        10.55        11.31        24.72         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-A7NT TCGA-KB-A6F5 TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8N5 TCGA-RD-A8N6 
        5.56         5.56         8.61       122.30        57.44         8.94 

$`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         2.27         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        13.35        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-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS 
        1.81         2.53        60.56         3.72         4.50        11.05 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        4.67        16.67        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-SW-A7EB TCGA-ZA-A8F6 
       71.38         5.79         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 
                        10.405                         11.240 
[1] "0.1 - 122.3 (10.4)" "0.1 - 116.4 (11.2)"
[1] "hr=" "1.1"
D5V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  5(5P15.33) MUTATED         0        3       10        9        10
  AMP PEAK  5(5P15.33) WILD-TYPE       2        9       28       18        22
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  5(5P15.33) MUTATED          14         1         19          7
  AMP PEAK  5(5P15.33) WILD-TYPE        33         2         42         38
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK  5(5P15.33) MUTATED            7       13
  AMP PEAK  5(5P15.33) WILD-TYPE         25       18
D5V3, multiclass
            clus
vv           AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              3                              9
  STAGE IB                             10                             28
  STAGE II                              9                             18
  STAGE IIA                            10                             22
  STAGE IIB                            14                             33
  STAGE III                             1                              2
  STAGE IIIA                           19                             42
  STAGE IIIB                            7                             38
  STAGE IIIC                            7                             25
  STAGE IV                             13                             18
[1] 11  2
[1] TRUE
[1] "dimension of 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 26 49 18
  AMP PEAK  5(5P15.33) WILD-TYPE 18 59 97 67
D5V4, multiclass
    clus
vv   AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  T1                            2                             18
  T2                           26                             59
  T3                           49                             97
  T4                           18                             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
  AMP PEAK  5(5P15.33) MUTATED   31 27 19 17
  AMP PEAK  5(5P15.33) WILD-TYPE 78 65 47 50
D5V5, multiclass
    clus
vv   AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  N0                           31                             78
  N1                           27                             65
  N2                           19                             47
  N3                           17                             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  5(5P15.33) MUTATED    86   7   5
  AMP PEAK  5(5P15.33) WILD-TYPE 222  14  12
D5V6, multiclass
    clus
vv   AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  M0                           86                            222
  M1                            7                             14
  MX                            5                             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    36  62
  AMP PEAK  5(5P15.33) WILD-TYPE 101 147
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(5P15.33) MUTATED     36   62
  AMP PEAK  5(5P15.33) WILD-TYPE  101  147
        clus
vv       AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  FEMALE                           36                            101
  MALE                             62                            147
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  5(5P15.33) MUTATED                                       9
  AMP PEAK  5(5P15.33) WILD-TYPE                                    53
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  5(5P15.33) MUTATED                                                       39
  AMP PEAK  5(5P15.33) WILD-TYPE                                                    115
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  5(5P15.33) MUTATED                                                                  20
  AMP PEAK  5(5P15.33) WILD-TYPE                                                                34
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  5(5P15.33) MUTATED                                                 16
  AMP PEAK  5(5P15.33) WILD-TYPE                                               29
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK  5(5P15.33) MUTATED                                                           1
  AMP PEAK  5(5P15.33) WILD-TYPE                                                         0
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK  5(5P15.33) MUTATED                                                          7
  AMP PEAK  5(5P15.33) WILD-TYPE                                                       12
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK  5(5P15.33) MUTATED                                                           3
  AMP PEAK  5(5P15.33) WILD-TYPE                                                         2
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK  5(5P15.33) MUTATED                                          1
  AMP PEAK  5(5P15.33) WILD-TYPE                                        3
D5V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  5(5P15.33) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      39
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           20
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            16
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     1
                                                                   clus
vv                                                                  AMP PEAK  5(5P15.33) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         53
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       115
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             34
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              29
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, binary
                                cls
clus                               0   1
  AMP PEAK  5(5P15.33) MUTATED     3  95
  AMP PEAK  5(5P15.33) WILD-TYPE   4 244
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(5P15.33) MUTATED      3   95
  AMP PEAK  5(5P15.33) WILD-TYPE    4  244
     clus
vv    AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  NO                             3                              4
  YES                           95                            244
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  5(5P15.33) MUTATED    78   4   5   5
  AMP PEAK  5(5P15.33) WILD-TYPE 199   9   8  20
D5V10, multiclass
    clus
vv   AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  R0                           78                            199
  R1                            4                              9
  R2                            5                              8
  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      24                         2
  AMP PEAK  5(5P15.33) WILD-TYPE    60                         1
                                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      55
  AMP PEAK  5(5P15.33) WILD-TYPE   153
D5V12, multiclass
                                           clus
vv                                          AMP PEAK  5(5P15.33) MUTATED
  ASIAN                                                               24
  BLACK OR AFRICAN AMERICAN                                            2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               55
                                           clus
vv                                          AMP PEAK  5(5P15.33) WILD-TYPE
  ASIAN                                                                 60
  BLACK OR AFRICAN AMERICAN                                              1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                153
[1] 4 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    61  27
  AMP PEAK  6(5P13.1) WILD-TYPE 161  66
  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE 
                           88                           227 
  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE 
                           27                            66 
$`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 
        2.27        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         0.07         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        10.26 
TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8576 TCGA-D7-A6EX 
       15.22        10.55        11.31        24.72         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 
        1.81         5.56        57.44         8.94 

$`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        13.35        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-A6RS TCGA-IP-7968 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS 
        6.87         2.53        60.56         3.72         4.50        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-SW-A7EB TCGA-ZA-A8F6 
      115.69       116.38        71.38         5.79         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 
                       10.405                        11.240 
[1] "0.1 - 72.2 (10.4)"  "0.1 - 122.3 (11.2)"
[1] "hr=" "1.2"
D6V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  6(5P13.1) MUTATED         0        3       10        8        11
  AMP PEAK  6(5P13.1) WILD-TYPE       2        9       28       19        21
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  6(5P13.1) MUTATED          14         1         18          6
  AMP PEAK  6(5P13.1) WILD-TYPE        33         2         43         39
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK  6(5P13.1) MUTATED            9       12
  AMP PEAK  6(5P13.1) WILD-TYPE         23       19
D6V3, multiclass
            clus
vv           AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             3                             9
  STAGE IB                            10                            28
  STAGE II                             8                            19
  STAGE IIA                           11                            21
  STAGE IIB                           14                            33
  STAGE III                            1                             2
  STAGE IIIA                          18                            43
  STAGE IIIB                           6                            39
  STAGE IIIC                           9                            23
  STAGE IV                            12                            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  6(5P13.1) MUTATED    2 24 47 21
  AMP PEAK  6(5P13.1) WILD-TYPE 18 61 99 64
D6V4, multiclass
    clus
vv   AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  T1                           2                            18
  T2                          24                            61
  T3                          47                            99
  T4                          21                            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  6(5P13.1) MUTATED   30 30 15 18
  AMP PEAK  6(5P13.1) WILD-TYPE 79 62 51 49
D6V5, multiclass
    clus
vv   AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  N0                          30                            79
  N1                          30                            62
  N2                          15                            51
  N3                          18                            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  6(5P13.1) MUTATED    85   7   5
  AMP PEAK  6(5P13.1) WILD-TYPE 223  14  12
D6V6, multiclass
    clus
vv   AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  M0                          85                           223
  M1                           7                            14
  MX                           5                            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    37  60
  AMP PEAK  6(5P13.1) WILD-TYPE 100 149
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(5P13.1) MUTATED     37   60
  AMP PEAK  6(5P13.1) WILD-TYPE  100  149
        clus
vv       AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  FEMALE                          37                           100
  MALE                            60                           149
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  6(5P13.1) MUTATED                                       9
  AMP PEAK  6(5P13.1) WILD-TYPE                                    53
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  6(5P13.1) MUTATED                                                       42
  AMP PEAK  6(5P13.1) WILD-TYPE                                                    112
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  6(5P13.1) MUTATED                                                                  19
  AMP PEAK  6(5P13.1) WILD-TYPE                                                                35
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  6(5P13.1) MUTATED                                                 14
  AMP PEAK  6(5P13.1) WILD-TYPE                                               31
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK  6(5P13.1) MUTATED                                                           1
  AMP PEAK  6(5P13.1) WILD-TYPE                                                         0
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK  6(5P13.1) MUTATED                                                          7
  AMP PEAK  6(5P13.1) WILD-TYPE                                                       12
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK  6(5P13.1) MUTATED                                                           2
  AMP PEAK  6(5P13.1) WILD-TYPE                                                         3
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK  6(5P13.1) MUTATED                                          1
  AMP PEAK  6(5P13.1) WILD-TYPE                                        3
D6V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  6(5P13.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     42
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          19
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           14
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    1
                                                                   clus
vv                                                                  AMP PEAK  6(5P13.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        53
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      112
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             31
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V9, binary
                               cls
clus                              0   1
  AMP PEAK  6(5P13.1) MUTATED     3  94
  AMP PEAK  6(5P13.1) WILD-TYPE   4 245
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(5P13.1) MUTATED      3   94
  AMP PEAK  6(5P13.1) WILD-TYPE    4  245
     clus
vv    AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  NO                            3                             4
  YES                          94                           245
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  6(5P13.1) MUTATED    77   4   5   5
  AMP PEAK  6(5P13.1) WILD-TYPE 200   9   8  20
D6V10, multiclass
    clus
vv   AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  R0                          77                           200
  R1                           4                             9
  R2                           5                             8
  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      22                         2
  AMP PEAK  6(5P13.1) WILD-TYPE    62                         1
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  6(5P13.1) MUTATED                                           0    56
  AMP PEAK  6(5P13.1) WILD-TYPE                                         1   152
D6V12, multiclass
                                           clus
vv                                          AMP PEAK  6(5P13.1) MUTATED
  ASIAN                                                              22
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              56
                                           clus
vv                                          AMP PEAK  6(5P13.1) WILD-TYPE
  ASIAN                                                                62
  BLACK OR AFRICAN AMERICAN                                             1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               152
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = AMP PEAK  7(6P21.1) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  7(6P21.1) MUTATED    56  25
  AMP PEAK  7(6P21.1) WILD-TYPE 166  68
  AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE 
                           81                           234 
  AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE 
                           25                            68 
$`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-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI 
       15.68         2.27        13.51        20.65        20.42        13.64 
TCGA-CD-5799 TCGA-CD-5803 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48C TCGA-CG-4436 
        3.25         0.07         0.07         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-D7-6526 TCGA-D7-6527 
       79.07         4.01        55.04        19.13        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8576 
       15.22        15.98        10.55        11.31        12.33         6.97 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-8122 TCGA-FP-7735 
       14.27        16.44         2.96        15.65         7.79         0.39 
TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8249 
       19.53        17.06         0.56         1.55         5.92        14.17 
TCGA-HU-A4GF TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-8663 TCGA-IN-A6RI 
       25.81        17.69        12.30         9.67         3.39        18.38 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NT TCGA-RD-A7BT 
        5.19        13.08         1.41         6.87         5.56         8.61 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 
      122.30        37.91       115.69 

$`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-A4J9 TCGA-BR-A4PF TCGA-BR-A4QL 
       12.82         0.66        19.36         0.46         1.15        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 
        5.13         2.83        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-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A489 
        0.10         0.10         0.13         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-D7-6817 
       18.84        18.54        18.61        17.85        13.35        12.79 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 
       24.72        16.80        19.50        17.19         0.23        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-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74A 
       11.24        11.31        11.44         9.76         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        7.13         0.62        16.24         6.58        14.47        72.23 
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-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 
       13.58         0.23        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-A4G2 
       12.59        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-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-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-A6RJ TCGA-IN-A6RP TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        5.36         6.44         1.81         2.53         5.56        60.56 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N0 
        3.72         4.50        11.05         4.67        16.67        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-ZA-A8F6 
      116.38        71.38        57.44         8.94         5.79         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 
                        11.54                         10.65 
[1] "0.1 - 122.3 (11.5)" "0.1 - 116.4 (10.6)"
[1] "hr=" "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         7
  AMP PEAK  7(6P21.1) WILD-TYPE       1        9       23       17        25
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  7(6P21.1) MUTATED          13         0         15         11
  AMP PEAK  7(6P21.1) WILD-TYPE        34         3         46         34
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK  7(6P21.1) MUTATED            4        9
  AMP PEAK  7(6P21.1) WILD-TYPE         28       22
D7V3, multiclass
            clus
vv           AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             3                             9
  STAGE IB                            15                            23
  STAGE II                            10                            17
  STAGE IIA                            7                            25
  STAGE IIB                           13                            34
  STAGE III                            0                             3
  STAGE IIIA                          15                            46
  STAGE IIIB                          11                            34
  STAGE IIIC                           4                            28
  STAGE IV                             9                            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  7(6P21.1) MUTATED     6  30  38  14
  AMP PEAK  7(6P21.1) WILD-TYPE  14  55 108  71
D7V4, multiclass
    clus
vv   AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE
  T1                           6                            14
  T2                          30                            55
  T3                          38                           108
  T4                          14                            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
  AMP PEAK  7(6P21.1) MUTATED   33 28 15 15
  AMP PEAK  7(6P21.1) WILD-TYPE 76 64 51 52
D7V5, multiclass
    clus
vv   AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE
  N0                          33                            76
  N1                          28                            64
  N2                          15                            51
  N3                          15                            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  7(6P21.1) MUTATED    85   2   6
  AMP PEAK  7(6P21.1) WILD-TYPE 223  19  11
D7V6, multiclass
    clus
vv   AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE
  M0                          85                           223
  M1                           2                            19
  MX                           6                            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"
D7V7, binary
                               cls
clus                              0   1
  AMP PEAK  7(6P21.1) MUTATED    36  57
  AMP PEAK  7(6P21.1) WILD-TYPE 101 152
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(6P21.1) MUTATED     36   57
  AMP PEAK  7(6P21.1) WILD-TYPE  101  152
        clus
vv       AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE
  FEMALE                          36                           101
  MALE                            57                           152
[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                                    58
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  7(6P21.1) MUTATED                                                       48
  AMP PEAK  7(6P21.1) WILD-TYPE                                                    106
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  7(6P21.1) MUTATED                                                                  19
  AMP PEAK  7(6P21.1) WILD-TYPE                                                                35
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  7(6P21.1) MUTATED                                                 16
  AMP PEAK  7(6P21.1) WILD-TYPE                                               29
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK  7(6P21.1) MUTATED                                                           1
  AMP PEAK  7(6P21.1) WILD-TYPE                                                         0
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK  7(6P21.1) MUTATED                                                          3
  AMP PEAK  7(6P21.1) WILD-TYPE                                                       16
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK  7(6P21.1) MUTATED                                                           1
  AMP PEAK  7(6P21.1) WILD-TYPE                                                         4
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK  7(6P21.1) MUTATED                                          1
  AMP PEAK  7(6P21.1) WILD-TYPE                                        3
D7V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  7(6P21.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     48
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          19
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           16
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    1
                                                                   clus
vv                                                                  AMP PEAK  7(6P21.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        58
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      106
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             29
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, binary
                               cls
clus                              0   1
  AMP PEAK  7(6P21.1) MUTATED     4  89
  AMP PEAK  7(6P21.1) WILD-TYPE   3 250
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(6P21.1) MUTATED      4   89
  AMP PEAK  7(6P21.1) WILD-TYPE    3  250
     clus
vv    AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE
  NO                            4                             3
  YES                          89                           250
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  7(6P21.1) MUTATED    71   4   2  10
  AMP PEAK  7(6P21.1) WILD-TYPE 206   9  11  15
D7V10, multiclass
    clus
vv   AMP PEAK  7(6P21.1) MUTATED AMP PEAK  7(6P21.1) WILD-TYPE
  R0                          71                           206
  R1                           4                             9
  R2                           2                            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"
D7V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  7(6P21.1) MUTATED      14                         1
  AMP PEAK  7(6P21.1) WILD-TYPE    70                         2
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  7(6P21.1) MUTATED                                           1    64
  AMP PEAK  7(6P21.1) WILD-TYPE                                         0   144
D7V12, multiclass
                                           clus
vv                                          AMP PEAK  7(6P21.1) MUTATED
  ASIAN                                                              14
  BLACK OR AFRICAN AMERICAN                                           1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              64
                                           clus
vv                                          AMP PEAK  7(6P21.1) WILD-TYPE
  ASIAN                                                                70
  BLACK OR AFRICAN AMERICAN                                             2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               144
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = AMP PEAK  8(6Q12) MUTATION ANALYSIS
D8V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  8(6Q12) MUTATED    39  20
  AMP PEAK  8(6Q12) WILD-TYPE 183  73
  AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE 
                         59                         256 
  AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE 
                         20                          73 
$`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         0.07         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 
       10.26        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-RD-A7BT TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 
       60.56         8.61        37.91       115.69         8.94 

$`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         2.27 
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        13.35        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-A6RS 
        3.45        18.81         5.36        13.08         6.44         6.87 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56         1.81         2.53         5.56         3.72         4.50 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 
       11.05         4.67        16.67       122.30        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-SW-A7EB TCGA-ZA-A8F6 
       71.38        57.44         5.79         4.21 

  AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE 
                       0.07                        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 
                      9.210                      11.505 
[1] "0.1 - 115.7 (9.2)"  "0.1 - 122.3 (11.5)"
[1] "hr=" "1.2"
D8V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  8(6Q12) MUTATED         1        1       11        6         6
  AMP PEAK  8(6Q12) WILD-TYPE       1       11       27       21        26
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  8(6Q12) MUTATED           9         0         13          8
  AMP PEAK  8(6Q12) WILD-TYPE        38         3         48         37
                             vv
clus                          STAGE IIIC STAGE IV
  AMP PEAK  8(6Q12) MUTATED            3        8
  AMP PEAK  8(6Q12) WILD-TYPE         29       23
D8V3, multiclass
            clus
vv           AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE
  STAGE I                            1                           1
  STAGE IA                           1                          11
  STAGE IB                          11                          27
  STAGE II                           6                          21
  STAGE IIA                          6                          26
  STAGE IIB                          9                          38
  STAGE III                          0                           3
  STAGE IIIA                        13                          48
  STAGE IIIB                         8                          37
  STAGE IIIC                         3                          29
  STAGE IV                           8                          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  8(6Q12) MUTATED     4  19  32  12
  AMP PEAK  8(6Q12) WILD-TYPE  16  66 114  73
D8V4, multiclass
    clus
vv   AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE
  T1                         4                          16
  T2                        19                          66
  T3                        32                         114
  T4                        12                          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
  AMP PEAK  8(6Q12) MUTATED   24 21 10 12
  AMP PEAK  8(6Q12) WILD-TYPE 85 71 56 55
D8V5, multiclass
    clus
vv   AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE
  N0                        24                          85
  N1                        21                          71
  N2                        10                          56
  N3                        12                          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                           M0  M1  MX
  AMP PEAK  8(6Q12) MUTATED    61   4   4
  AMP PEAK  8(6Q12) WILD-TYPE 247  17  13
D8V6, multiclass
    clus
vv   AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE
  M0                        61                         247
  M1                         4                          17
  MX                         4                          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"
D8V7, binary
                             cls
clus                            0   1
  AMP PEAK  8(6Q12) MUTATED    30  39
  AMP PEAK  8(6Q12) WILD-TYPE 107 170
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(6Q12) MUTATED     30   39
  AMP PEAK  8(6Q12) WILD-TYPE  107  170
        clus
vv       AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE
  FEMALE                        30                         107
  MALE                          39                         170
[1] 2 2
[1] FALSE
                             vv
clus                          STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  8(6Q12) MUTATED                                       4
  AMP PEAK  8(6Q12) WILD-TYPE                                    58
                             vv
clus                          STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  8(6Q12) MUTATED                                                       35
  AMP PEAK  8(6Q12) WILD-TYPE                                                    119
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  8(6Q12) MUTATED                                                                  18
  AMP PEAK  8(6Q12) WILD-TYPE                                                                36
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  8(6Q12) MUTATED                                                  9
  AMP PEAK  8(6Q12) WILD-TYPE                                               36
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK  8(6Q12) MUTATED                                                           1
  AMP PEAK  8(6Q12) WILD-TYPE                                                         0
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK  8(6Q12) MUTATED                                                          1
  AMP PEAK  8(6Q12) WILD-TYPE                                                       18
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK  8(6Q12) MUTATED                                                           0
  AMP PEAK  8(6Q12) WILD-TYPE                                                         5
                             vv
clus                          STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK  8(6Q12) MUTATED                                          1
  AMP PEAK  8(6Q12) WILD-TYPE                                        3
D8V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  8(6Q12) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                   35
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        18
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                          9
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                  1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                 0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                  1
                                                                   clus
vv                                                                  AMP PEAK  8(6Q12) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      58
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    119
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           36
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, binary
                             cls
clus                            0   1
  AMP PEAK  8(6Q12) MUTATED     3  66
  AMP PEAK  8(6Q12) WILD-TYPE   4 273
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(6Q12) MUTATED      3   66
  AMP PEAK  8(6Q12) WILD-TYPE    4  273
     clus
vv    AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE
  NO                          3                           4
  YES                        66                         273
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  8(6Q12) MUTATED    50   3   3   8
  AMP PEAK  8(6Q12) WILD-TYPE 227  10  10  17
D8V10, multiclass
    clus
vv   AMP PEAK  8(6Q12) MUTATED AMP PEAK  8(6Q12) WILD-TYPE
  R0                        50                         227
  R1                         3                          10
  R2                         3                          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"
D8V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  8(6Q12) MUTATED      12                         1
  AMP PEAK  8(6Q12) WILD-TYPE    72                         2
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  8(6Q12) MUTATED                                           1    44
  AMP PEAK  8(6Q12) WILD-TYPE                                         0   164
D8V12, multiclass
                                           clus
vv                                          AMP PEAK  8(6Q12) MUTATED
  ASIAN                                                            12
  BLACK OR AFRICAN AMERICAN                                         1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         1
  WHITE                                                            44
                                           clus
vv                                          AMP PEAK  8(6Q12) WILD-TYPE
  ASIAN                                                              72
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  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(9) Variable = AMP PEAK  9(6Q21) MUTATION ANALYSIS
D9V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  9(6Q21) MUTATED    36  20
  AMP PEAK  9(6Q21) WILD-TYPE 186  73
  AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE 
                         56                         259 
  AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE 
                         20                          73 
$`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         2.27         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        10.26        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-RD-A7BT TCGA-RD-A7C1 
       18.81         3.39         1.81         5.56         8.61        16.67 
TCGA-RD-A8MW TCGA-RD-A8N6 
       37.91         8.94 

$`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         0.07         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        13.35        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-A6RS TCGA-IN-A7NT TCGA-IP-7968 
       13.08         1.41         6.44         6.87         5.56         2.53 
TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV 
       60.56         3.72         4.50        11.05         4.67       122.30 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-SW-A7EB 
       40.64       115.69       116.38        71.38        57.44         5.79 
TCGA-ZA-A8F6 
        4.21 

  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 
                       9.44                       11.44 
[1] "0.1 - 54.1 (9.4)"   "0.1 - 122.3 (11.4)"
[1] "hr=" "1.4"
D9V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  9(6Q21) MUTATED         0        1        7        5         3
  AMP PEAK  9(6Q21) WILD-TYPE       2       11       31       22        29
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  9(6Q21) MUTATED           8         1         17          5
  AMP PEAK  9(6Q21) WILD-TYPE        39         2         44         40
                             vv
clus                          STAGE IIIC STAGE IV
  AMP PEAK  9(6Q21) MUTATED            4        9
  AMP PEAK  9(6Q21) WILD-TYPE         28       22
D9V3, multiclass
            clus
vv           AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE
  STAGE I                            0                           2
  STAGE IA                           1                          11
  STAGE IB                           7                          31
  STAGE II                           5                          22
  STAGE IIA                          3                          29
  STAGE IIB                          8                          39
  STAGE III                          1                           2
  STAGE IIIA                        17                          44
  STAGE IIIB                         5                          40
  STAGE IIIC                         4                          28
  STAGE IV                           9                          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  9(6Q21) MUTATED     1  18  24  17
  AMP PEAK  9(6Q21) WILD-TYPE  19  67 122  68
D9V4, multiclass
    clus
vv   AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE
  T1                         1                          19
  T2                        18                          67
  T3                        24                         122
  T4                        17                          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  9(6Q21) MUTATED   15 21 11 13
  AMP PEAK  9(6Q21) WILD-TYPE 94 71 55 54
D9V5, multiclass
    clus
vv   AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE
  N0                        15                          94
  N1                        21                          71
  N2                        11                          55
  N3                        13                          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  9(6Q21) MUTATED    54   5   3
  AMP PEAK  9(6Q21) WILD-TYPE 254  16  14
D9V6, multiclass
    clus
vv   AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE
  M0                        54                         254
  M1                         5                          16
  MX                         3                          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"
D9V7, binary
                             cls
clus                            0   1
  AMP PEAK  9(6Q21) MUTATED    24  38
  AMP PEAK  9(6Q21) WILD-TYPE 113 171
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q21) MUTATED     24   38
  AMP PEAK  9(6Q21) WILD-TYPE  113  171
        clus
vv       AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE
  FEMALE                        24                         113
  MALE                          38                         171
[1] 2 2
[1] FALSE
                             vv
clus                          STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  9(6Q21) MUTATED                                       7
  AMP PEAK  9(6Q21) WILD-TYPE                                    55
                             vv
clus                          STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  9(6Q21) MUTATED                                                       27
  AMP PEAK  9(6Q21) WILD-TYPE                                                    127
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  9(6Q21) MUTATED                                                                  14
  AMP PEAK  9(6Q21) WILD-TYPE                                                                40
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  9(6Q21) MUTATED                                                 10
  AMP PEAK  9(6Q21) WILD-TYPE                                               35
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK  9(6Q21) MUTATED                                                           1
  AMP PEAK  9(6Q21) WILD-TYPE                                                         0
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK  9(6Q21) MUTATED                                                          1
  AMP PEAK  9(6Q21) WILD-TYPE                                                       18
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK  9(6Q21) MUTATED                                                           1
  AMP PEAK  9(6Q21) WILD-TYPE                                                         4
                             vv
clus                          STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK  9(6Q21) MUTATED                                          1
  AMP PEAK  9(6Q21) WILD-TYPE                                        3
D9V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  9(6Q21) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                   27
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                         10
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                  1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                 1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                  1
                                                                   clus
vv                                                                  AMP PEAK  9(6Q21) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      55
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           35
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V9, binary
                             cls
clus                            0   1
  AMP PEAK  9(6Q21) MUTATED     3  59
  AMP PEAK  9(6Q21) WILD-TYPE   4 280
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q21) MUTATED      3   59
  AMP PEAK  9(6Q21) WILD-TYPE    4  280
     clus
vv    AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE
  NO                          3                           4
  YES                        59                         280
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  9(6Q21) MUTATED    45   2   4   6
  AMP PEAK  9(6Q21) WILD-TYPE 232  11   9  19
D9V10, multiclass
    clus
vv   AMP PEAK  9(6Q21) MUTATED AMP PEAK  9(6Q21) WILD-TYPE
  R0                        45                         232
  R1                         2                          11
  R2                         4                           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"
D9V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  9(6Q21) MUTATED      13                         0
  AMP PEAK  9(6Q21) WILD-TYPE    71                         3
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  9(6Q21) MUTATED                                           1    38
  AMP PEAK  9(6Q21) WILD-TYPE                                         0   170
D9V12, multiclass
                                           clus
vv                                          AMP PEAK  9(6Q21) MUTATED
  ASIAN                                                            13
  BLACK OR AFRICAN AMERICAN                                         0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         1
  WHITE                                                            38
                                           clus
vv                                          AMP PEAK  9(6Q21) WILD-TYPE
  ASIAN                                                              71
  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(10) Variable = AMP PEAK 10(7P22.1) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(7P22.1) MUTATED   113  49
  AMP PEAK 10(7P22.1) WILD-TYPE 109  44
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                          162                           153 
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                           49                            44 
$`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-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-8364 TCGA-BR-8366 
        7.40         6.18        19.50         0.36        22.19         0.95 
TCGA-BR-8370 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 
        3.32        14.79         0.26         5.39         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U 
        1.12        16.44         0.59         0.62        10.68         1.15 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J4 
        0.66         2.27         0.92        12.89         0.72         0.53 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 
       19.36        13.51        20.42         1.15        13.64         3.25 
TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8535 
       13.18         0.07         0.10         0.16         0.13         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        0.10         0.07         0.13         0.13         0.13         0.07 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
        0.10        20.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       54.08         4.01        21.99        18.97         7.07        12.00 
TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 
       22.98         1.02        12.03        28.96        79.07         4.01 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 
       21.07         7.99        12.66        11.93        19.13        18.84 
TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 
       18.54        17.19        15.22        15.98        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       12.33        24.72        17.19         0.23         6.97        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EX TCGA-D7-A6F0 
       20.91        14.27        16.44        15.16        11.31         2.96 
TCGA-D7-A6F2 TCGA-F1-6177 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-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX 
        3.02        22.29        17.06         0.56         1.55         0.23 
TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD 
       26.47        12.59        14.17        12.30         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       25.81        11.77         8.98         0.10         6.25        10.19 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD 
        2.10        12.95        17.69        12.30         9.67        27.42 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO 
        3.45        18.81         3.39        18.38         5.19         1.41 
TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-RD-A7BT 
        6.44         6.87         1.81         5.56        60.56         8.61 
TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-ZA-A8F6 
      122.30       115.69        57.44         8.94         5.79         4.21 

$`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-8291 TCGA-BR-8363 
       17.49        12.26         0.49        20.55        16.31         0.26 
TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 
        2.96        13.74         4.31        14.04         0.36        19.17 
TCGA-BR-8380 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8588 TCGA-BR-8589 
        0.69        15.85         3.72         0.72        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-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
       15.81        15.68        12.56         3.02        13.41        13.51 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-BR-A4PD 
        0.79        14.17        12.82         0.66         0.46        20.65 
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-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.07         0.07         0.13         0.10         0.10 
TCGA-CD-A487 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4441 
        0.13         0.10         0.10         3.02         1.02        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-5732 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6522 
       15.02        65.10        55.04        12.36        20.55        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-8572 TCGA-D7-8573 
       17.85        13.35        10.26        12.79        16.80        19.50 
TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
        5.92        13.78        14.76        13.71        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-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-8209 TCGA-FP-8210 TCGA-FP-8211 
       16.24        21.27         8.12        59.54         5.03        13.58 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 
       18.08         1.51         5.92        14.27        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 
       10.62         0.76        24.30         5.59        11.84        24.20 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H8 
       21.37        29.98         6.51         0.26        19.36         8.88 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A7NT TCGA-IP-7968 
        8.81        21.21         5.36        13.08         5.56         2.53 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW 
        3.72         4.50        11.05         4.67        16.67        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
       40.64       116.38        71.38 

  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 
                         9.90                         11.54 
[1] "0.1 - 122.3 (9.9)"  "0.1 - 116.4 (11.5)"
[1] "hr=" "1.1"
D10V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 10(7P22.1) MUTATED         2        8       19       13        17
  AMP PEAK 10(7P22.1) WILD-TYPE       0        4       19       14        15
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 10(7P22.1) MUTATED          24         2         33         19
  AMP PEAK 10(7P22.1) WILD-TYPE        23         1         28         26
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 10(7P22.1) MUTATED           19       14
  AMP PEAK 10(7P22.1) WILD-TYPE         13       17
D10V3, multiclass
            clus
vv           AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  STAGE I                              2                             0
  STAGE IA                             8                             4
  STAGE IB                            19                            19
  STAGE II                            13                            14
  STAGE IIA                           17                            15
  STAGE IIB                           24                            23
  STAGE III                            2                             1
  STAGE IIIA                          33                            28
  STAGE IIIB                          19                            26
  STAGE IIIC                          19                            13
  STAGE IV                            14                            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 10(7P22.1) MUTATED   12 41 76 42
  AMP PEAK 10(7P22.1) WILD-TYPE  8 44 70 43
D10V4, multiclass
    clus
vv   AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  T1                          12                             8
  T2                          41                            44
  T3                          76                            70
  T4                          42                            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                            N0 N1 N2 N3
  AMP PEAK 10(7P22.1) MUTATED   58 44 38 32
  AMP PEAK 10(7P22.1) WILD-TYPE 51 48 28 35
D10V5, multiclass
    clus
vv   AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  N0                          58                            51
  N1                          44                            48
  N2                          38                            28
  N3                          32                            35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  AMP PEAK 10(7P22.1) MUTATED   160   7  11
  AMP PEAK 10(7P22.1) WILD-TYPE 148  14   6
D10V6, multiclass
    clus
vv   AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  M0                         160                           148
  M1                           7                            14
  MX                          11                             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"
D10V7, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P22.1) MUTATED    59 119
  AMP PEAK 10(7P22.1) WILD-TYPE  78  90
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P22.1) MUTATED     59  119
  AMP PEAK 10(7P22.1) WILD-TYPE   78   90
        clus
vv       AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  FEMALE                          59                            78
  MALE                           119                            90
[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                                    39
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 10(7P22.1) MUTATED                                                       79
  AMP PEAK 10(7P22.1) WILD-TYPE                                                     75
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 10(7P22.1) MUTATED                                                                  36
  AMP PEAK 10(7P22.1) WILD-TYPE                                                                18
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 10(7P22.1) MUTATED                                                 24
  AMP PEAK 10(7P22.1) WILD-TYPE                                               21
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK 10(7P22.1) MUTATED                                                           0
  AMP PEAK 10(7P22.1) WILD-TYPE                                                         1
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 10(7P22.1) MUTATED                                                          7
  AMP PEAK 10(7P22.1) WILD-TYPE                                                       12
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 10(7P22.1) MUTATED                                                           4
  AMP PEAK 10(7P22.1) WILD-TYPE                                                         1
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 10(7P22.1) MUTATED                                          3
  AMP PEAK 10(7P22.1) WILD-TYPE                                        1
D10V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 10(7P22.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      23
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     79
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           24
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    3
                                                                   clus
vv                                                                  AMP PEAK 10(7P22.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        39
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       75
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            18
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             21
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P22.1) MUTATED     3 175
  AMP PEAK 10(7P22.1) WILD-TYPE   4 164
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P22.1) MUTATED      3  175
  AMP PEAK 10(7P22.1) WILD-TYPE    4  164
     clus
vv    AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  NO                            3                             4
  YES                         175                           164
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 10(7P22.1) MUTATED   145   7   6  11
  AMP PEAK 10(7P22.1) WILD-TYPE 132   6   7  14
D10V10, multiclass
    clus
vv   AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  R0                         145                           132
  R1                           7                             6
  R2                           6                             7
  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"
D10V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 10(7P22.1) MUTATED      42                         3
  AMP PEAK 10(7P22.1) WILD-TYPE    42                         0
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 10(7P22.1) MUTATED                                           1   106
  AMP PEAK 10(7P22.1) WILD-TYPE                                         0   102
D10V12, multiclass
                                           clus
vv                                          AMP PEAK 10(7P22.1) MUTATED
  ASIAN                                                              42
  BLACK OR AFRICAN AMERICAN                                           3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             106
                                           clus
vv                                          AMP PEAK 10(7P22.1) WILD-TYPE
  ASIAN                                                                42
  BLACK OR AFRICAN AMERICAN                                             0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = AMP PEAK 11(7P11.2) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 11(7P11.2) MUTATED    96  49
  AMP PEAK 11(7P11.2) WILD-TYPE 126  44
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                          145                           170 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                           49                            44 
$`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         2.27 
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         0.07 
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-A6RS TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 
        1.41         6.44         6.87         1.81         5.56        60.56 
TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 
        8.61        16.67       122.30       115.69        57.44         8.94 
TCGA-ZA-A8F6 
        4.21 

$`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        13.35        10.26        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 
        4.50        11.05         4.67        37.91        40.64       116.38 
TCGA-RD-A8N4 TCGA-SW-A7EB 
       71.38         5.79 

  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 
                       10.190                        11.325 
[1] "0.1 - 122.3 (10.2)" "0.1 - 116.4 (11.3)"
[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       19       10        14
  AMP PEAK 11(7P11.2) WILD-TYPE       0        4       19       17        18
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 11(7P11.2) MUTATED          23         2         30         18
  AMP PEAK 11(7P11.2) WILD-TYPE        24         1         31         27
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 11(7P11.2) MUTATED           17       10
  AMP PEAK 11(7P11.2) WILD-TYPE         15       21
D11V3, multiclass
            clus
vv           AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  STAGE I                              2                             0
  STAGE IA                             8                             4
  STAGE IB                            19                            19
  STAGE II                            10                            17
  STAGE IIA                           14                            18
  STAGE IIB                           23                            24
  STAGE III                            2                             1
  STAGE IIIA                          30                            31
  STAGE IIIB                          18                            27
  STAGE IIIC                          17                            15
  STAGE IV                            10                            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 11(7P11.2) MUTATED   12 36 69 37
  AMP PEAK 11(7P11.2) WILD-TYPE  8 49 77 48
D11V4, multiclass
    clus
vv   AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  T1                          12                             8
  T2                          36                            49
  T3                          69                            77
  T4                          37                            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                            N0 N1 N2 N3
  AMP PEAK 11(7P11.2) MUTATED   54 41 31 29
  AMP PEAK 11(7P11.2) WILD-TYPE 55 51 35 38
D11V5, multiclass
    clus
vv   AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  N0                          54                            55
  N1                          41                            51
  N2                          31                            35
  N3                          29                            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                             M0  M1  MX
  AMP PEAK 11(7P11.2) MUTATED   146   5  10
  AMP PEAK 11(7P11.2) WILD-TYPE 162  16   7
D11V6, multiclass
    clus
vv   AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  M0                         146                           162
  M1                           5                            16
  MX                          10                             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    54 107
  AMP PEAK 11(7P11.2) WILD-TYPE  83 102
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED     54  107
  AMP PEAK 11(7P11.2) WILD-TYPE   83  102
        clus
vv       AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  FEMALE                          54                            83
  MALE                           107                           102
[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                                    39
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 11(7P11.2) MUTATED                                                       73
  AMP PEAK 11(7P11.2) WILD-TYPE                                                     81
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 11(7P11.2) MUTATED                                                                  31
  AMP PEAK 11(7P11.2) WILD-TYPE                                                                23
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 11(7P11.2) MUTATED                                                 21
  AMP PEAK 11(7P11.2) WILD-TYPE                                               24
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK 11(7P11.2) MUTATED                                                           0
  AMP PEAK 11(7P11.2) WILD-TYPE                                                         1
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 11(7P11.2) MUTATED                                                          6
  AMP PEAK 11(7P11.2) WILD-TYPE                                                       13
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 11(7P11.2) MUTATED                                                           2
  AMP PEAK 11(7P11.2) WILD-TYPE                                                         3
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 11(7P11.2) MUTATED                                          3
  AMP PEAK 11(7P11.2) WILD-TYPE                                        1
D11V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 11(7P11.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      23
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     73
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          31
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           21
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    3
                                                                   clus
vv                                                                  AMP PEAK 11(7P11.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        39
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       81
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            23
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             24
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V9, binary
                               cls
clus                              0   1
  AMP PEAK 11(7P11.2) MUTATED     2 159
  AMP PEAK 11(7P11.2) WILD-TYPE   5 180
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED      2  159
  AMP PEAK 11(7P11.2) WILD-TYPE    5  180
     clus
vv    AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  NO                            2                             5
  YES                         159                           180
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 11(7P11.2) MUTATED   131   7   5  11
  AMP PEAK 11(7P11.2) WILD-TYPE 146   6   8  14
D11V10, multiclass
    clus
vv   AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  R0                         131                           146
  R1                           7                             6
  R2                           5                             8
  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      39                         3
  AMP PEAK 11(7P11.2) WILD-TYPE    45                         0
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 11(7P11.2) MUTATED                                           1    95
  AMP PEAK 11(7P11.2) WILD-TYPE                                         0   113
D11V12, multiclass
                                           clus
vv                                          AMP PEAK 11(7P11.2) MUTATED
  ASIAN                                                              39
  BLACK OR AFRICAN AMERICAN                                           3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              95
                                           clus
vv                                          AMP PEAK 11(7P11.2) WILD-TYPE
  ASIAN                                                                45
  BLACK OR AFRICAN AMERICAN                                             0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = AMP PEAK 12(7Q21.2) MUTATION ANALYSIS
D12V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 12(7Q21.2) MUTATED    97  45
  AMP PEAK 12(7Q21.2) WILD-TYPE 125  48
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                          142                           173 
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                           45                            48 
$`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-A487 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         0.10         0.07         0.13         0.13         0.13 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.07         0.10        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4466 
        7.99        54.08         4.01        14.01        12.03        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5725 
        7.07        12.00        22.98         1.02        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5733 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       28.96        79.07        21.07        12.66        11.93        19.13 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.84        18.54        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 
       15.98        12.79        24.72        19.50        17.19         6.97 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EV TCGA-D7-A6EX 
       21.14        20.91        16.44        15.16        11.24        11.31 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        2.96        15.65         6.58        14.47        72.23         0.39 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HJ-7597 
       19.53        22.29        17.06         0.56         0.23        26.47 
TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GF TCGA-HU-A4GP 
        5.92        14.17        24.30        12.30        25.81         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        0.10         6.25        10.19         2.10        12.95        19.36 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A7NT 
        3.45         3.39         5.19         1.41         6.44         5.56 
TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW 
        1.81         5.56        60.56         8.61       122.30        37.91 
TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-ZA-A8F6 
      115.69        57.44         8.94         4.21 

$`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         2.27         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-A489 
        0.07         0.07         0.07         0.10         0.10         0.13 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4443 TCGA-CG-4444 
        0.10         0.10         1.02         8.05        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 
       19.07        21.99         9.01        30.97         6.97         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5730 
        0.99         6.02         0.99       105.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 
       55.04         7.99        12.36        20.55        18.61        17.85 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8575 TCGA-D7-A4YT 
       10.55        11.31        12.33        16.80         0.23        14.27 
TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ 
        5.92        13.78        14.76        13.71        11.44         9.76 
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-A448 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       21.27         8.12         3.02        59.54         5.03        13.58 
TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
        1.55        18.08         1.51        14.27        12.59        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 
       12.10        10.62         0.76         5.59        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT 
        3.25        22.75        11.77        21.37        29.98         6.51 
TCGA-HU-A4GY TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
        0.26        17.69        12.30         9.67         8.88         8.81 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
       27.42        21.21        18.81        18.38         5.36        13.08 
TCGA-IN-A6RS TCGA-IP-7968 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW 
        6.87         2.53         3.72         4.50        11.05         4.67 
TCGA-RD-A7C1 TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-SW-A7EB 
       16.67        40.64       116.38        71.38         5.79 

  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 
                        10.96                         11.05 
[1] "0.1 - 122.3 (11.0)" "0.1 - 116.4 (11.1)"
[1] "hr=" "1.1"
D12V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 12(7Q21.2) MUTATED         2        6       17       13        15
  AMP PEAK 12(7Q21.2) WILD-TYPE       0        6       21       14        17
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 12(7Q21.2) MUTATED          22         2         28         18
  AMP PEAK 12(7Q21.2) WILD-TYPE        25         1         33         27
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 12(7Q21.2) MUTATED           15       11
  AMP PEAK 12(7Q21.2) WILD-TYPE         17       20
D12V3, multiclass
            clus
vv           AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  STAGE I                              2                             0
  STAGE IA                             6                             6
  STAGE IB                            17                            21
  STAGE II                            13                            14
  STAGE IIA                           15                            17
  STAGE IIB                           22                            25
  STAGE III                            2                             1
  STAGE IIIA                          28                            33
  STAGE IIIB                          18                            27
  STAGE IIIC                          15                            17
  STAGE IV                            11                            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 12(7Q21.2) MUTATED    9 40 67 35
  AMP PEAK 12(7Q21.2) WILD-TYPE 11 45 79 50
D12V4, multiclass
    clus
vv   AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  T1                           9                            11
  T2                          40                            45
  T3                          67                            79
  T4                          35                            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                            N0 N1 N2 N3
  AMP PEAK 12(7Q21.2) MUTATED   53 37 33 29
  AMP PEAK 12(7Q21.2) WILD-TYPE 56 55 33 38
D12V5, multiclass
    clus
vv   AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  N0                          53                            56
  N1                          37                            55
  N2                          33                            33
  N3                          29                            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                             M0  M1  MX
  AMP PEAK 12(7Q21.2) MUTATED   141   6  11
  AMP PEAK 12(7Q21.2) WILD-TYPE 167  15   6
D12V6, multiclass
    clus
vv   AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  M0                         141                           167
  M1                           6                            15
  MX                          11                             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    54 104
  AMP PEAK 12(7Q21.2) WILD-TYPE  83 105
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7Q21.2) MUTATED     54  104
  AMP PEAK 12(7Q21.2) WILD-TYPE   83  105
        clus
vv       AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  FEMALE                          54                            83
  MALE                           104                           105
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 12(7Q21.2) MUTATED                                      24
  AMP PEAK 12(7Q21.2) WILD-TYPE                                    38
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 12(7Q21.2) MUTATED                                                       72
  AMP PEAK 12(7Q21.2) WILD-TYPE                                                     82
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 12(7Q21.2) MUTATED                                                                  31
  AMP PEAK 12(7Q21.2) WILD-TYPE                                                                23
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 12(7Q21.2) MUTATED                                                 17
  AMP PEAK 12(7Q21.2) WILD-TYPE                                               28
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK 12(7Q21.2) MUTATED                                                           1
  AMP PEAK 12(7Q21.2) WILD-TYPE                                                         0
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 12(7Q21.2) MUTATED                                                          7
  AMP PEAK 12(7Q21.2) WILD-TYPE                                                       12
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 12(7Q21.2) MUTATED                                                           2
  AMP PEAK 12(7Q21.2) WILD-TYPE                                                         3
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 12(7Q21.2) MUTATED                                          2
  AMP PEAK 12(7Q21.2) WILD-TYPE                                        2
D12V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 12(7Q21.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      24
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     72
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          31
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           17
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    2
                                                                   clus
vv                                                                  AMP PEAK 12(7Q21.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        38
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       82
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            23
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             28
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V9, binary
                               cls
clus                              0   1
  AMP PEAK 12(7Q21.2) MUTATED     3 155
  AMP PEAK 12(7Q21.2) WILD-TYPE   4 184
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7Q21.2) MUTATED      3  155
  AMP PEAK 12(7Q21.2) WILD-TYPE    4  184
     clus
vv    AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  NO                            3                             4
  YES                         155                           184
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 12(7Q21.2) MUTATED   130   4   5  11
  AMP PEAK 12(7Q21.2) WILD-TYPE 147   9   8  14
D12V10, multiclass
    clus
vv   AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  R0                         130                           147
  R1                           4                             9
  R2                           5                             8
  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      36                         3
  AMP PEAK 12(7Q21.2) WILD-TYPE    48                         0
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 12(7Q21.2) MUTATED                                           1    93
  AMP PEAK 12(7Q21.2) WILD-TYPE                                         0   115
D12V12, multiclass
                                           clus
vv                                          AMP PEAK 12(7Q21.2) MUTATED
  ASIAN                                                              36
  BLACK OR AFRICAN AMERICAN                                           3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              93
                                           clus
vv                                          AMP PEAK 12(7Q21.2) WILD-TYPE
  ASIAN                                                                48
  BLACK OR AFRICAN AMERICAN                                             0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               115
[1] 4 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(8P23.1) MUTATION ANALYSIS
D13V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 13(8P23.1) MUTATED    87  30
  AMP PEAK 13(8P23.1) WILD-TYPE 135  63
  AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE 
                          117                           198 
  AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE 
                           30                            63 
$`AMP PEAK 13(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 
        2.27         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        10.26        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-MX-A5UJ 
        8.81         5.19         6.87         5.56        60.56         4.50 
TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-ZA-A8F6 
       16.67       115.69         4.21 

$`AMP PEAK 13(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         0.07 
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 
       13.35        17.19        15.22        15.98        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YY 
       19.50        17.19        21.14        14.27        16.44        13.78 
TCGA-D7-A6ET TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       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-A7NU TCGA-IP-7968 TCGA-KB-A6F5 
       13.08         1.41         6.44         1.81         2.53         5.56 
TCGA-MX-A5UG TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
        3.72        11.05         8.61         4.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-SW-A7EB 
       40.64       116.38        71.38        57.44         8.94         5.79 

  AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE 
                         0.07                          0.07 
  AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE 
                       115.69                        122.30 
  AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE 
                        11.84                          9.62 
[1] "0.1 - 115.7 (11.8)" "0.1 - 122.3 (9.6)" 
[1] "hr=" "1.3"
D13V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 13(8P23.1) MUTATED         1        6       17       11        12
  AMP PEAK 13(8P23.1) WILD-TYPE       1        6       21       16        20
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 13(8P23.1) MUTATED          23         0         21         11
  AMP PEAK 13(8P23.1) WILD-TYPE        24         3         40         34
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 13(8P23.1) MUTATED           12       12
  AMP PEAK 13(8P23.1) WILD-TYPE         20       19
D13V3, multiclass
            clus
vv           AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             6                             6
  STAGE IB                            17                            21
  STAGE II                            11                            16
  STAGE IIA                           12                            20
  STAGE IIB                           23                            24
  STAGE III                            0                             3
  STAGE IIIA                          21                            40
  STAGE IIIB                          11                            34
  STAGE IIIC                          12                            20
  STAGE IV                            12                            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 13(8P23.1) MUTATED   10 38 50 31
  AMP PEAK 13(8P23.1) WILD-TYPE 10 47 96 54
D13V4, multiclass
    clus
vv   AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE
  T1                          10                            10
  T2                          38                            47
  T3                          50                            96
  T4                          31                            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                            N0 N1 N2 N3
  AMP PEAK 13(8P23.1) MUTATED   41 37 23 26
  AMP PEAK 13(8P23.1) WILD-TYPE 68 55 43 41
D13V5, multiclass
    clus
vv   AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE
  N0                          41                            68
  N1                          37                            55
  N2                          23                            43
  N3                          26                            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 13(8P23.1) MUTATED   123   7   5
  AMP PEAK 13(8P23.1) WILD-TYPE 185  14  12
D13V6, multiclass
    clus
vv   AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE
  M0                         123                           185
  M1                           7                            14
  MX                           5                            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"
D13V7, binary
                               cls
clus                              0   1
  AMP PEAK 13(8P23.1) MUTATED    63  72
  AMP PEAK 13(8P23.1) WILD-TYPE  74 137
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(8P23.1) MUTATED     63   72
  AMP PEAK 13(8P23.1) WILD-TYPE   74  137
        clus
vv       AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE
  FEMALE                          63                            74
  MALE                            72                           137
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 13(8P23.1) MUTATED                                      25
  AMP PEAK 13(8P23.1) WILD-TYPE                                    37
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 13(8P23.1) MUTATED                                                       56
  AMP PEAK 13(8P23.1) WILD-TYPE                                                     98
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 13(8P23.1) MUTATED                                                                  22
  AMP PEAK 13(8P23.1) WILD-TYPE                                                                32
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 13(8P23.1) MUTATED                                                 17
  AMP PEAK 13(8P23.1) WILD-TYPE                                               28
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK 13(8P23.1) MUTATED                                                           1
  AMP PEAK 13(8P23.1) WILD-TYPE                                                         0
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 13(8P23.1) MUTATED                                                          9
  AMP PEAK 13(8P23.1) WILD-TYPE                                                       10
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 13(8P23.1) MUTATED                                                           2
  AMP PEAK 13(8P23.1) WILD-TYPE                                                         3
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 13(8P23.1) MUTATED                                          2
  AMP PEAK 13(8P23.1) WILD-TYPE                                        2
D13V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 13(8P23.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      25
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     56
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          22
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           17
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    2
                                                                   clus
vv                                                                  AMP PEAK 13(8P23.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        37
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       98
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            32
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             28
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V9, binary
                               cls
clus                              0   1
  AMP PEAK 13(8P23.1) MUTATED     5 130
  AMP PEAK 13(8P23.1) WILD-TYPE   2 209
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(8P23.1) MUTATED      5  130
  AMP PEAK 13(8P23.1) WILD-TYPE    2  209
     clus
vv    AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE
  NO                            5                             2
  YES                         130                           209
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 13(8P23.1) MUTATED   104   6   4  14
  AMP PEAK 13(8P23.1) WILD-TYPE 173   7   9  11
D13V10, multiclass
    clus
vv   AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE
  R0                         104                           173
  R1                           6                             7
  R2                           4                             9
  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"
D13V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 13(8P23.1) MUTATED      32                         0
  AMP PEAK 13(8P23.1) WILD-TYPE    52                         3
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 13(8P23.1) MUTATED                                           0    83
  AMP PEAK 13(8P23.1) WILD-TYPE                                         1   125
D13V12, multiclass
                                           clus
vv                                          AMP PEAK 13(8P23.1) MUTATED
  ASIAN                                                              32
  BLACK OR AFRICAN AMERICAN                                           0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              83
                                           clus
vv                                          AMP PEAK 13(8P23.1) WILD-TYPE
  ASIAN                                                                52
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               125
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = AMP PEAK 14(8Q24.21) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 14(8Q24.21) MUTATED   149  63
  AMP PEAK 14(8Q24.21) WILD-TYPE  73  30
  AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE 
                           212                            103 
  AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE 
                            63                             30 
$`AMP PEAK 14(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         2.27         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         0.07         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        13.35        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-A6RS TCGA-IN-A7NT 
        5.19        13.08         1.41         6.44         6.87         5.56 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ 
        1.81         2.53         5.56        60.56         3.72         4.50 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N4 TCGA-RD-A8N6 
       11.05         8.61        16.67       115.69        71.38         8.94 
TCGA-SW-A7EB TCGA-ZA-A8F6 
        5.79         4.21 

$`AMP PEAK 14(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        10.26        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YY TCGA-D7-A6ET 
       19.50        17.19         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 
       57.44 

  AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE 
                        115.69                         122.30 
  AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE 
                        11.145                         10.620 
[1] "0.1 - 115.7 (11.1)" "0.1 - 122.3 (10.6)"
[1] "hr=" "1.1"
D14V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 14(8Q24.21) MUTATED         2       11       25       20        20
  AMP PEAK 14(8Q24.21) WILD-TYPE       0        1       13        7        12
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 14(8Q24.21) MUTATED          32         2         43         23
  AMP PEAK 14(8Q24.21) WILD-TYPE        15         1         18         22
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 14(8Q24.21) MUTATED           23       20
  AMP PEAK 14(8Q24.21) WILD-TYPE          9       11
D14V3, multiclass
            clus
vv           AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE
  STAGE I                               2                              0
  STAGE IA                             11                              1
  STAGE IB                             25                             13
  STAGE II                             20                              7
  STAGE IIA                            20                             12
  STAGE IIB                            32                             15
  STAGE III                             2                              1
  STAGE IIIA                           43                             18
  STAGE IIIB                           23                             22
  STAGE IIIC                           23                              9
  STAGE IV                             20                             11
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK 14(8Q24.21) MUTATED   19 58 98 51
  AMP PEAK 14(8Q24.21) WILD-TYPE  1 27 48 34
D14V4, multiclass
    clus
vv   AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE
  T1                           19                              1
  T2                           58                             27
  T3                           98                             48
  T4                           51                             34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 14(8Q24.21) MUTATED   73 65 39 48
  AMP PEAK 14(8Q24.21) WILD-TYPE 36 27 27 19
D14V5, multiclass
    clus
vv   AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE
  N0                           73                             36
  N1                           65                             27
  N2                           39                             27
  N3                           48                             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  AMP PEAK 14(8Q24.21) MUTATED   209  12  14
  AMP PEAK 14(8Q24.21) WILD-TYPE  99   9   3
D14V6, multiclass
    clus
vv   AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE
  M0                          209                             99
  M1                           12                              9
  MX                           14                              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"
D14V7, binary
                                cls
clus                               0   1
  AMP PEAK 14(8Q24.21) MUTATED    92 143
  AMP PEAK 14(8Q24.21) WILD-TYPE  45  66
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(8Q24.21) MUTATED     92  143
  AMP PEAK 14(8Q24.21) WILD-TYPE   45   66
        clus
vv       AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE
  FEMALE                           92                             45
  MALE                            143                             66
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 14(8Q24.21) MUTATED                                      33
  AMP PEAK 14(8Q24.21) WILD-TYPE                                    29
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 14(8Q24.21) MUTATED                                                      106
  AMP PEAK 14(8Q24.21) WILD-TYPE                                                     48
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 14(8Q24.21) MUTATED                                                                  41
  AMP PEAK 14(8Q24.21) WILD-TYPE                                                                13
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 14(8Q24.21) MUTATED                                                 32
  AMP PEAK 14(8Q24.21) WILD-TYPE                                               13
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK 14(8Q24.21) MUTATED                                                           0
  AMP PEAK 14(8Q24.21) WILD-TYPE                                                         1
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 14(8Q24.21) MUTATED                                                         14
  AMP PEAK 14(8Q24.21) WILD-TYPE                                                        5
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 14(8Q24.21) MUTATED                                                           4
  AMP PEAK 14(8Q24.21) WILD-TYPE                                                         1
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 14(8Q24.21) MUTATED                                          3
  AMP PEAK 14(8Q24.21) WILD-TYPE                                        1
D14V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 14(8Q24.21) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       33
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     106
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           41
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            32
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     3
                                                                   clus
vv                                                                  AMP PEAK 14(8Q24.21) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         29
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        48
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              13
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V9, binary
                                cls
clus                               0   1
  AMP PEAK 14(8Q24.21) MUTATED     5 230
  AMP PEAK 14(8Q24.21) WILD-TYPE   2 109
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(8Q24.21) MUTATED      5  230
  AMP PEAK 14(8Q24.21) WILD-TYPE    2  109
     clus
vv    AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE
  NO                             5                              2
  YES                          230                            109
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 14(8Q24.21) MUTATED   185  10   9  20
  AMP PEAK 14(8Q24.21) WILD-TYPE  92   3   4   5
D14V10, multiclass
    clus
vv   AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE
  R0                          185                             92
  R1                           10                              3
  R2                            9                              4
  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"
D14V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 14(8Q24.21) MUTATED      53                         3
  AMP PEAK 14(8Q24.21) WILD-TYPE    31                         0
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 14(8Q24.21) MUTATED                                           1
  AMP PEAK 14(8Q24.21) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 14(8Q24.21) MUTATED     141
  AMP PEAK 14(8Q24.21) WILD-TYPE    67
D14V12, multiclass
                                           clus
vv                                          AMP PEAK 14(8Q24.21) MUTATED
  ASIAN                                                               53
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              141
                                           clus
vv                                          AMP PEAK 14(8Q24.21) WILD-TYPE
  ASIAN                                                                 31
  BLACK OR AFRICAN AMERICAN                                              0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                 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"

Clustering(15) Variable = AMP PEAK 15(9P24.1) MUTATION ANALYSIS
D15V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 15(9P24.1) MUTATED    32  15
  AMP PEAK 15(9P24.1) WILD-TYPE 190  78
  AMP PEAK 15(9P24.1) MUTATED AMP PEAK 15(9P24.1) WILD-TYPE 
                           47                           268 
  AMP PEAK 15(9P24.1) MUTATED AMP PEAK 15(9P24.1) WILD-TYPE 
                           15                            78 
$`AMP PEAK 15(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 
        2.10        12.95        12.30         3.39        60.56 

$`AMP PEAK 15(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         2.27 
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         0.07         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        13.35        17.19        10.26        15.98 
TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       12.79        11.31        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV 
        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-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-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        3.72         4.50        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-SW-A7EB TCGA-ZA-A8F6 
       57.44         8.94         5.79         4.21 

  AMP PEAK 15(9P24.1) MUTATED AMP PEAK 15(9P24.1) WILD-TYPE 
                         0.10                          0.07 
  AMP PEAK 15(9P24.1) MUTATED AMP PEAK 15(9P24.1) WILD-TYPE 
                        72.23                        122.30 
  AMP PEAK 15(9P24.1) MUTATED AMP PEAK 15(9P24.1) WILD-TYPE 
                        11.54                         10.47 
[1] "0.1 - 72.2 (11.5)"  "0.1 - 122.3 (10.5)"
[1] "hr=" "1.1"
D15V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 15(9P24.1) MUTATED         1        3        9        3         6
  AMP PEAK 15(9P24.1) WILD-TYPE       1        9       29       24        26
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 15(9P24.1) MUTATED           5         1          6          7
  AMP PEAK 15(9P24.1) WILD-TYPE        42         2         55         38
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 15(9P24.1) MUTATED            6        4
  AMP PEAK 15(9P24.1) WILD-TYPE         26       27
D15V3, multiclass
            clus
vv           AMP PEAK 15(9P24.1) MUTATED AMP PEAK 15(9P24.1) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             3                             9
  STAGE IB                             9                            29
  STAGE II                             3                            24
  STAGE IIA                            6                            26
  STAGE IIB                            5                            42
  STAGE III                            1                             2
  STAGE IIIA                           6                            55
  STAGE IIIB                           7                            38
  STAGE IIIC                           6                            26
  STAGE IV                             4                            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 15(9P24.1) MUTATED     5  15  17  16
  AMP PEAK 15(9P24.1) WILD-TYPE  15  70 129  69
D15V4, multiclass
    clus
vv   AMP PEAK 15(9P24.1) MUTATED AMP PEAK 15(9P24.1) WILD-TYPE
  T1                           5                            15
  T2                          15                            70
  T3                          17                           129
  T4                          16                            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 15(9P24.1) MUTATED   21 13  4 14
  AMP PEAK 15(9P24.1) WILD-TYPE 88 79 62 53
D15V5, multiclass
    clus
vv   AMP PEAK 15(9P24.1) MUTATED AMP PEAK 15(9P24.1) WILD-TYPE
  N0                          21                            88
  N1                          13                            79
  N2                           4                            62
  N3                          14                            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 15(9P24.1) MUTATED    48   3   3
  AMP PEAK 15(9P24.1) WILD-TYPE 260  18  14
D15V6, multiclass
    clus
vv   AMP PEAK 15(9P24.1) MUTATED AMP PEAK 15(9P24.1) WILD-TYPE
  M0                          48                           260
  M1                           3                            18
  MX                           3                            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"
D15V7, binary
                               cls
clus                              0   1
  AMP PEAK 15(9P24.1) MUTATED    22  32
  AMP PEAK 15(9P24.1) WILD-TYPE 115 177
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(9P24.1) MUTATED     22   32
  AMP PEAK 15(9P24.1) WILD-TYPE  115  177
        clus
vv       AMP PEAK 15(9P24.1) MUTATED AMP PEAK 15(9P24.1) WILD-TYPE
  FEMALE                          22                           115
  MALE                            32                           177
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 15(9P24.1) MUTATED                                       4
  AMP PEAK 15(9P24.1) WILD-TYPE                                    58
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 15(9P24.1) MUTATED                                                       24
  AMP PEAK 15(9P24.1) WILD-TYPE                                                    130
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 15(9P24.1) MUTATED                                                                   9
  AMP PEAK 15(9P24.1) WILD-TYPE                                                                45
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 15(9P24.1) MUTATED                                                  9
  AMP PEAK 15(9P24.1) WILD-TYPE                                               36
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK 15(9P24.1) MUTATED                                                           0
  AMP PEAK 15(9P24.1) WILD-TYPE                                                         1
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 15(9P24.1) MUTATED                                                          5
  AMP PEAK 15(9P24.1) WILD-TYPE                                                       14
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 15(9P24.1) MUTATED                                                           2
  AMP PEAK 15(9P24.1) WILD-TYPE                                                         3
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 15(9P24.1) MUTATED                                          1
  AMP PEAK 15(9P24.1) WILD-TYPE                                        3
D15V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 15(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                                            9
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    1
                                                                   clus
vv                                                                  AMP PEAK 15(9P24.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        58
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            45
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             36
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V9, binary
                               cls
clus                              0   1
  AMP PEAK 15(9P24.1) MUTATED     3  51
  AMP PEAK 15(9P24.1) WILD-TYPE   4 288
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(9P24.1) MUTATED      3   51
  AMP PEAK 15(9P24.1) WILD-TYPE    4  288
     clus
vv    AMP PEAK 15(9P24.1) MUTATED AMP PEAK 15(9P24.1) WILD-TYPE
  NO                            3                             4
  YES                          51                           288
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 15(9P24.1) MUTATED    42   3   2   4
  AMP PEAK 15(9P24.1) WILD-TYPE 235  10  11  21
D15V10, multiclass
    clus
vv   AMP PEAK 15(9P24.1) MUTATED AMP PEAK 15(9P24.1) WILD-TYPE
  R0                          42                           235
  R1                           3                            10
  R2                           2                            11
  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"
D15V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 15(9P24.1) MUTATED      17                         1
  AMP PEAK 15(9P24.1) WILD-TYPE    67                         2
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 15(9P24.1) MUTATED                                           0    27
  AMP PEAK 15(9P24.1) WILD-TYPE                                         1   181
D15V12, multiclass
                                           clus
vv                                          AMP PEAK 15(9P24.1) MUTATED
  ASIAN                                                              17
  BLACK OR AFRICAN AMERICAN                                           1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              27
                                           clus
vv                                          AMP PEAK 15(9P24.1) WILD-TYPE
  ASIAN                                                                67
  BLACK OR AFRICAN AMERICAN                                             2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               181
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = AMP PEAK 16(9P13.3) MUTATION ANALYSIS
D16V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 16(9P13.3) MUTATED    43  16
  AMP PEAK 16(9P13.3) WILD-TYPE 179  77
  AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE 
                           59                           256 
  AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE 
                           16                            77 
$`AMP PEAK 16(9P13.3) 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-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8486 TCGA-BR-8588 
        0.49         0.26        16.31         1.55        20.22        12.79 
TCGA-BR-8678 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4J4 TCGA-BR-A4PE 
       11.54         1.15         0.66         2.27         0.53        20.42 
TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-8526 TCGA-CD-8535 TCGA-CD-A4MH 
       13.64         2.83        13.18         0.07         0.13         0.10 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4477 
        7.99         8.05        47.05        21.99        18.97        30.97 
TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 
       11.93        17.19        10.26        15.22        10.55        12.33 
TCGA-D7-8575 TCGA-D7-A4YT TCGA-D7-A4Z0 TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 
        0.23        14.27        14.76        11.31        11.44         2.96 
TCGA-EQ-5647 TCGA-F1-A448 TCGA-FP-7829 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8249 
        0.62        21.27        19.53         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 
        9.67         3.39        60.56       122.30       115.69 

$`AMP PEAK 16(9P13.3) 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-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-8286 
        0.69        12.26        20.55         0.72         0.26        12.95 
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-8487 
       15.85         3.72         5.39         0.72         9.21         1.12 
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-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       12.56         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-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM 
       13.51         0.46        20.65         1.15        11.57         5.13 
TCGA-CD-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-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-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         0.07         0.13         0.13         0.13 
TCGA-CD-A48C 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-4438 TCGA-CG-4440 TCGA-CG-4441 
       27.02        15.95         1.02        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 
       29.98        19.07        12.03         9.01         7.07        12.00 
TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       22.98         6.97         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-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.66        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8570 
       17.85        13.35        15.98        12.79        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-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44         5.92        15.16        13.78        13.71        11.24 
TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 
        9.76        15.65         4.34         7.40         7.13         7.79 
TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 
       16.24         6.58        14.47        72.23         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-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-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-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BT 
        2.53         5.56         3.72         4.50        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-SW-A7EB TCGA-ZA-A8F6 
       57.44         8.94         5.79         4.21 

  AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE 
                         0.07                          0.07 
  AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE 
                       122.30                        116.38 
  AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE 
                        11.93                         10.16 
[1] "0.1 - 122.3 (11.9)" "0.1 - 116.4 (10.2)"
[1] "hr=" "1.2"
D16V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 16(9P13.3) MUTATED         1        3       12        4         4
  AMP PEAK 16(9P13.3) WILD-TYPE       1        9       26       23        28
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 16(9P13.3) MUTATED           8         0         13          9
  AMP PEAK 16(9P13.3) WILD-TYPE        39         3         48         36
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 16(9P13.3) MUTATED            3        5
  AMP PEAK 16(9P13.3) WILD-TYPE         29       26
D16V3, multiclass
            clus
vv           AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             3                             9
  STAGE IB                            12                            26
  STAGE II                             4                            23
  STAGE IIA                            4                            28
  STAGE IIB                            8                            39
  STAGE III                            0                             3
  STAGE IIIA                          13                            48
  STAGE IIIB                           9                            36
  STAGE IIIC                           3                            29
  STAGE IV                             5                            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 16(9P13.3) MUTATED     6  20  24  13
  AMP PEAK 16(9P13.3) WILD-TYPE  14  65 122  72
D16V4, multiclass
    clus
vv   AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE
  T1                           6                            14
  T2                          20                            65
  T3                          24                           122
  T4                          13                            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
  AMP PEAK 16(9P13.3) MUTATED   21 18 12 12
  AMP PEAK 16(9P13.3) WILD-TYPE 88 74 54 55
D16V5, multiclass
    clus
vv   AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE
  N0                          21                            88
  N1                          18                            74
  N2                          12                            54
  N3                          12                            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                             M0  M1  MX
  AMP PEAK 16(9P13.3) MUTATED    59   3   2
  AMP PEAK 16(9P13.3) WILD-TYPE 249  18  15
D16V6, multiclass
    clus
vv   AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE
  M0                          59                           249
  M1                           3                            18
  MX                           2                            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(9P13.3) MUTATED    29  35
  AMP PEAK 16(9P13.3) WILD-TYPE 108 174
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(9P13.3) MUTATED     29   35
  AMP PEAK 16(9P13.3) WILD-TYPE  108  174
        clus
vv       AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE
  FEMALE                          29                           108
  MALE                            35                           174
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 16(9P13.3) MUTATED                                       5
  AMP PEAK 16(9P13.3) WILD-TYPE                                    57
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 16(9P13.3) MUTATED                                                       23
  AMP PEAK 16(9P13.3) WILD-TYPE                                                    131
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 16(9P13.3) MUTATED                                                                  11
  AMP PEAK 16(9P13.3) WILD-TYPE                                                                43
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 16(9P13.3) MUTATED                                                 12
  AMP PEAK 16(9P13.3) WILD-TYPE                                               33
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK 16(9P13.3) MUTATED                                                           1
  AMP PEAK 16(9P13.3) WILD-TYPE                                                         0
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 16(9P13.3) MUTATED                                                          9
  AMP PEAK 16(9P13.3) WILD-TYPE                                                       10
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 16(9P13.3) MUTATED                                                           2
  AMP PEAK 16(9P13.3) WILD-TYPE                                                         3
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 16(9P13.3) MUTATED                                          1
  AMP PEAK 16(9P13.3) WILD-TYPE                                        3
D16V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 16(9P13.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     23
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           12
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    1
                                                                   clus
vv                                                                  AMP PEAK 16(9P13.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        57
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            43
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             33
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V9, binary
                               cls
clus                              0   1
  AMP PEAK 16(9P13.3) MUTATED     4  60
  AMP PEAK 16(9P13.3) WILD-TYPE   3 279
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(9P13.3) MUTATED      4   60
  AMP PEAK 16(9P13.3) WILD-TYPE    3  279
     clus
vv    AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE
  NO                            4                             3
  YES                          60                           279
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 16(9P13.3) MUTATED    53   4   2   3
  AMP PEAK 16(9P13.3) WILD-TYPE 224   9  11  22
D16V10, multiclass
    clus
vv   AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE
  R0                          53                           224
  R1                           4                             9
  R2                           2                            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"
D16V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 16(9P13.3) MUTATED      15                         0
  AMP PEAK 16(9P13.3) WILD-TYPE    69                         3
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 16(9P13.3) MUTATED                                           0    38
  AMP PEAK 16(9P13.3) WILD-TYPE                                         1   170
D16V12, multiclass
                                           clus
vv                                          AMP PEAK 16(9P13.3) MUTATED
  ASIAN                                                              15
  BLACK OR AFRICAN AMERICAN                                           0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              38
                                           clus
vv                                          AMP PEAK 16(9P13.3) WILD-TYPE
  ASIAN                                                                69
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  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(17) Variable = AMP PEAK 17(9Q34.3) MUTATION ANALYSIS
D17V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 17(9Q34.3) MUTATED    57  23
  AMP PEAK 17(9Q34.3) WILD-TYPE 165  70
  AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE 
                           80                           235 
  AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE 
                           23                            70 
$`AMP PEAK 17(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         2.27         0.53         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-8535 TCGA-CD-A487 
       20.65        20.42        13.15        13.18         0.13         0.13 
TCGA-CD-A48A TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4449 TCGA-CG-4466 
        0.13         3.02        27.02         7.99        19.07        18.97 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5718 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6526 
       22.98        30.97         1.02        12.66        11.93        17.19 
TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-A4YT TCGA-D7-A4YX TCGA-D7-A4Z0 
       15.22        10.55        11.31        14.27        15.16        14.76 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 
       11.31        11.44         9.76         2.96        15.65         4.34 
TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-A4BF TCGA-HF-A5NB 
        0.62        16.24        72.23        21.27         1.55        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4GF 
       26.47         1.51        14.17         0.76        12.30        25.81 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 
        8.98         6.25        12.30        27.42         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RO TCGA-IN-A6RS TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-RD-A7BS 
        3.39         1.41         6.87         5.56        60.56        11.05 
TCGA-RD-A8MV TCGA-RD-A8N1 
      122.30       115.69 

$`AMP PEAK 17(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-A486 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG 
        0.13         0.10         0.07         0.13         0.13         0.07 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4305 TCGA-CG-4306 
        0.10         0.10         0.10        20.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 
       12.03        21.99         9.01         7.07        12.00         6.97 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-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-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       21.07         7.99        12.36        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 
       18.54        18.61        17.85        13.35        10.26        15.98 
TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       12.79        12.33        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-A4YY TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 
       13.78        13.71        11.24         7.40         7.13         7.79 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
        6.58        14.47         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-A8CX TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 
        0.23         5.92        14.27        12.59        11.41        12.10 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       10.62        24.30         5.59        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT 
       22.75        11.77        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-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-A6RI TCGA-IN-A6RJ 
        9.67         8.88         8.81        21.21        18.38         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 
        5.19        13.08         6.44         5.56         1.81         2.53 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW 
        3.72         4.50         8.61         4.67        16.67        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-SW-A7EB 
       40.64       116.38        71.38        57.44         8.94         5.79 
TCGA-ZA-A8F6 
        4.21 

  AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE 
                         0.13                          0.07 
  AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE 
                       122.30                        116.38 
  AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE 
                       12.115                         9.670 
[1] "0.1 - 122.3 (12.1)" "0.1 - 116.4 (9.7)" 
[1] "hr=" "1.2"
D17V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 17(9Q34.3) MUTATED         1        6       12        6         7
  AMP PEAK 17(9Q34.3) WILD-TYPE       1        6       26       21        25
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 17(9Q34.3) MUTATED          16         1         16          8
  AMP PEAK 17(9Q34.3) WILD-TYPE        31         2         45         37
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 17(9Q34.3) MUTATED            4        7
  AMP PEAK 17(9Q34.3) WILD-TYPE         28       24
D17V3, multiclass
            clus
vv           AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             6                             6
  STAGE IB                            12                            26
  STAGE II                             6                            21
  STAGE IIA                            7                            25
  STAGE IIB                           16                            31
  STAGE III                            1                             2
  STAGE IIIA                          16                            45
  STAGE IIIB                           8                            37
  STAGE IIIC                           4                            28
  STAGE IV                             7                            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 17(9Q34.3) MUTATED     8  24  37  17
  AMP PEAK 17(9Q34.3) WILD-TYPE  12  61 109  68
D17V4, multiclass
    clus
vv   AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE
  T1                           8                            12
  T2                          24                            61
  T3                          37                           109
  T4                          17                            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 17(9Q34.3) MUTATED   31 25 18 13
  AMP PEAK 17(9Q34.3) WILD-TYPE 78 67 48 54
D17V5, multiclass
    clus
vv   AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE
  N0                          31                            78
  N1                          25                            67
  N2                          18                            48
  N3                          13                            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 17(9Q34.3) MUTATED    82   5   3
  AMP PEAK 17(9Q34.3) WILD-TYPE 226  16  14
D17V6, multiclass
    clus
vv   AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE
  M0                          82                           226
  M1                           5                            16
  MX                           3                            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"
D17V7, binary
                               cls
clus                              0   1
  AMP PEAK 17(9Q34.3) MUTATED    33  57
  AMP PEAK 17(9Q34.3) WILD-TYPE 104 152
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9Q34.3) MUTATED     33   57
  AMP PEAK 17(9Q34.3) WILD-TYPE  104  152
        clus
vv       AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE
  FEMALE                          33                           104
  MALE                            57                           152
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 17(9Q34.3) MUTATED                                      10
  AMP PEAK 17(9Q34.3) WILD-TYPE                                    52
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 17(9Q34.3) MUTATED                                                       39
  AMP PEAK 17(9Q34.3) WILD-TYPE                                                    115
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 17(9Q34.3) MUTATED                                                                  13
  AMP PEAK 17(9Q34.3) WILD-TYPE                                                                41
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 17(9Q34.3) MUTATED                                                 12
  AMP PEAK 17(9Q34.3) WILD-TYPE                                               33
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK 17(9Q34.3) MUTATED                                                           0
  AMP PEAK 17(9Q34.3) WILD-TYPE                                                         1
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 17(9Q34.3) MUTATED                                                         10
  AMP PEAK 17(9Q34.3) WILD-TYPE                                                        9
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 17(9Q34.3) MUTATED                                                           3
  AMP PEAK 17(9Q34.3) WILD-TYPE                                                         2
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 17(9Q34.3) MUTATED                                          2
  AMP PEAK 17(9Q34.3) WILD-TYPE                                        2
D17V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 17(9Q34.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      10
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     39
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           12
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    2
                                                                   clus
vv                                                                  AMP PEAK 17(9Q34.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        52
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      115
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            41
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             33
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V9, binary
                               cls
clus                              0   1
  AMP PEAK 17(9Q34.3) MUTATED     3  87
  AMP PEAK 17(9Q34.3) WILD-TYPE   4 252
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9Q34.3) MUTATED      3   87
  AMP PEAK 17(9Q34.3) WILD-TYPE    4  252
     clus
vv    AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE
  NO                            3                             4
  YES                          87                           252
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 17(9Q34.3) MUTATED    73   5   2   7
  AMP PEAK 17(9Q34.3) WILD-TYPE 204   8  11  18
D17V10, multiclass
    clus
vv   AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE
  R0                          73                           204
  R1                           5                             8
  R2                           2                            11
  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"
D17V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 17(9Q34.3) MUTATED      18                         1
  AMP PEAK 17(9Q34.3) WILD-TYPE    66                         2
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 17(9Q34.3) MUTATED                                           0    56
  AMP PEAK 17(9Q34.3) WILD-TYPE                                         1   152
D17V12, multiclass
                                           clus
vv                                          AMP PEAK 17(9Q34.3) MUTATED
  ASIAN                                                              18
  BLACK OR AFRICAN AMERICAN                                           1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              56
                                           clus
vv                                          AMP PEAK 17(9Q34.3) WILD-TYPE
  ASIAN                                                                66
  BLACK OR AFRICAN AMERICAN                                             2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               152
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = AMP PEAK 18(10P11.22) MUTATION ANALYSIS
D18V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 18(10P11.22) MUTATED    60  24
  AMP PEAK 18(10P11.22) WILD-TYPE 162  69
  AMP PEAK 18(10P11.22) MUTATED AMP PEAK 18(10P11.22) WILD-TYPE 
                             84                             231 
  AMP PEAK 18(10P11.22) MUTATED AMP PEAK 18(10P11.22) WILD-TYPE 
                             24                              69 
$`AMP PEAK 18(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-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV 
        3.39        18.38        11.05         8.61        16.67       122.30 

$`AMP PEAK 18(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         2.27         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         0.07 
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        13.35 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       10.26        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         4.50         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-SW-A7EB TCGA-ZA-A8F6 
        8.94         5.79         4.21 

  AMP PEAK 18(10P11.22) MUTATED AMP PEAK 18(10P11.22) WILD-TYPE 
                           0.07                            0.07 
  AMP PEAK 18(10P11.22) MUTATED AMP PEAK 18(10P11.22) WILD-TYPE 
                         122.30                          116.38 
  AMP PEAK 18(10P11.22) MUTATED AMP PEAK 18(10P11.22) WILD-TYPE 
                          11.36                           10.26 
[1] "0.1 - 122.3 (11.4)" "0.1 - 116.4 (10.3)"
[1] "hr=" "1.1"
D18V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 18(10P11.22) MUTATED         0        6        8        4         9
  AMP PEAK 18(10P11.22) WILD-TYPE       2        6       30       23        23
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 18(10P11.22) MUTATED          18         1         15         11
  AMP PEAK 18(10P11.22) WILD-TYPE        29         2         46         34
                                 vv
clus                              STAGE IIIC STAGE IV
  AMP PEAK 18(10P11.22) MUTATED            6       11
  AMP PEAK 18(10P11.22) WILD-TYPE         26       20
D18V3, multiclass
            clus
vv           AMP PEAK 18(10P11.22) MUTATED AMP PEAK 18(10P11.22) WILD-TYPE
  STAGE I                                0                               2
  STAGE IA                               6                               6
  STAGE IB                               8                              30
  STAGE II                               4                              23
  STAGE IIA                              9                              23
  STAGE IIB                             18                              29
  STAGE III                              1                               2
  STAGE IIIA                            15                              46
  STAGE IIIB                            11                              34
  STAGE IIIC                             6                              26
  STAGE IV                              11                              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 18(10P11.22) MUTATED     6  17  44  23
  AMP PEAK 18(10P11.22) WILD-TYPE  14  68 102  62
D18V4, multiclass
    clus
vv   AMP PEAK 18(10P11.22) MUTATED AMP PEAK 18(10P11.22) WILD-TYPE
  T1                             6                              14
  T2                            17                              68
  T3                            44                             102
  T4                            23                              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 18(10P11.22) MUTATED   32 23 18 16
  AMP PEAK 18(10P11.22) WILD-TYPE 77 69 48 51
D18V5, multiclass
    clus
vv   AMP PEAK 18(10P11.22) MUTATED AMP PEAK 18(10P11.22) WILD-TYPE
  N0                            32                              77
  N1                            23                              69
  N2                            18                              48
  N3                            16                              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 18(10P11.22) MUTATED    79   6   6
  AMP PEAK 18(10P11.22) WILD-TYPE 229  15  11
D18V6, multiclass
    clus
vv   AMP PEAK 18(10P11.22) MUTATED AMP PEAK 18(10P11.22) WILD-TYPE
  M0                            79                             229
  M1                             6                              15
  MX                             6                              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"
D18V7, binary
                                 cls
clus                                0   1
  AMP PEAK 18(10P11.22) MUTATED    37  54
  AMP PEAK 18(10P11.22) WILD-TYPE 100 155
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(10P11.22) MUTATED     37   54
  AMP PEAK 18(10P11.22) WILD-TYPE  100  155
        clus
vv       AMP PEAK 18(10P11.22) MUTATED AMP PEAK 18(10P11.22) WILD-TYPE
  FEMALE                            37                             100
  MALE                              54                             155
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 18(10P11.22) MUTATED                                      14
  AMP PEAK 18(10P11.22) WILD-TYPE                                    48
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 18(10P11.22) MUTATED                                                       39
  AMP PEAK 18(10P11.22) WILD-TYPE                                                    115
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 18(10P11.22) MUTATED                                                                  14
  AMP PEAK 18(10P11.22) WILD-TYPE                                                                40
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 18(10P11.22) MUTATED                                                 18
  AMP PEAK 18(10P11.22) WILD-TYPE                                               27
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK 18(10P11.22) MUTATED                                                           0
  AMP PEAK 18(10P11.22) WILD-TYPE                                                         1
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 18(10P11.22) MUTATED                                                          3
  AMP PEAK 18(10P11.22) WILD-TYPE                                                       16
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 18(10P11.22) MUTATED                                                           1
  AMP PEAK 18(10P11.22) WILD-TYPE                                                         4
                                 vv
clus                              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 18(10P11.22) MUTATED                                          1
  AMP PEAK 18(10P11.22) WILD-TYPE                                        3
D18V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 18(10P11.22) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        14
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       39
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             18
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      1
                                                                   clus
vv                                                                  AMP PEAK 18(10P11.22) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        115
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               27
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                        3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V9, binary
                                 cls
clus                                0   1
  AMP PEAK 18(10P11.22) MUTATED     3  88
  AMP PEAK 18(10P11.22) WILD-TYPE   4 251
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(10P11.22) MUTATED      3   88
  AMP PEAK 18(10P11.22) WILD-TYPE    4  251
     clus
vv    AMP PEAK 18(10P11.22) MUTATED AMP PEAK 18(10P11.22) WILD-TYPE
  NO                              3                               4
  YES                            88                             251
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 18(10P11.22) MUTATED    73   2   5   5
  AMP PEAK 18(10P11.22) WILD-TYPE 204  11   8  20
D18V10, multiclass
    clus
vv   AMP PEAK 18(10P11.22) MUTATED AMP PEAK 18(10P11.22) WILD-TYPE
  R0                            73                             204
  R1                             2                              11
  R2                             5                               8
  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"
D18V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 18(10P11.22) MUTATED      29                         2
  AMP PEAK 18(10P11.22) WILD-TYPE    55                         1
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 18(10P11.22) MUTATED                                           1
  AMP PEAK 18(10P11.22) WILD-TYPE                                         0
                                 vv
clus                              WHITE
  AMP PEAK 18(10P11.22) MUTATED      49
  AMP PEAK 18(10P11.22) WILD-TYPE   159
D18V12, multiclass
                                           clus
vv                                          AMP PEAK 18(10P11.22) MUTATED
  ASIAN                                                                29
  BLACK OR AFRICAN AMERICAN                                             2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                49
                                           clus
vv                                          AMP PEAK 18(10P11.22) WILD-TYPE
  ASIAN                                                                  55
  BLACK OR AFRICAN AMERICAN                                               1
  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(19) Variable = AMP PEAK 19(10Q22.2) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 19(10Q22.2) MUTATED    42  21
  AMP PEAK 19(10Q22.2) WILD-TYPE 180  72
  AMP PEAK 19(10Q22.2) MUTATED AMP PEAK 19(10Q22.2) WILD-TYPE 
                            63                            252 
  AMP PEAK 19(10Q22.2) MUTATED AMP PEAK 19(10Q22.2) WILD-TYPE 
                            21                             72 
$`AMP PEAK 19(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-A4H6 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RP TCGA-IN-A7NU 
        9.67        27.42         3.45         3.39         6.44         1.81 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A8MV 
       11.05         8.61       122.30 

$`AMP PEAK 19(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         2.27         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         0.07         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        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       15.98        12.79        11.31        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       17.19         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-A4H2 
        0.10         6.51        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       19.36        17.69        12.30         8.88         8.81        21.21 
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-A6RS TCGA-IN-A7NT TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG 
        6.87         5.56         2.53         5.56        60.56         3.72 
TCGA-MX-A5UJ TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        4.50         4.67        16.67        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-ZA-A8F6 
      116.38        71.38        57.44         8.94         5.79         4.21 

  AMP PEAK 19(10Q22.2) MUTATED AMP PEAK 19(10Q22.2) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 19(10Q22.2) MUTATED AMP PEAK 19(10Q22.2) WILD-TYPE 
                        122.30                         116.38 
  AMP PEAK 19(10Q22.2) MUTATED AMP PEAK 19(10Q22.2) WILD-TYPE 
                         10.13                          11.49 
[1] "0.1 - 122.3 (10.1)" "0.1 - 116.4 (11.5)"
[1] "hr=" "1.1"
D19V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 19(10Q22.2) MUTATED         0        4        3        7         2
  AMP PEAK 19(10Q22.2) WILD-TYPE       2        8       35       20        30
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 19(10Q22.2) MUTATED          10         2         16          9
  AMP PEAK 19(10Q22.2) WILD-TYPE        37         1         45         36
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 19(10Q22.2) MUTATED            5        7
  AMP PEAK 19(10Q22.2) WILD-TYPE         27       24
D19V3, multiclass
            clus
vv           AMP PEAK 19(10Q22.2) MUTATED AMP PEAK 19(10Q22.2) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              4                              8
  STAGE IB                              3                             35
  STAGE II                              7                             20
  STAGE IIA                             2                             30
  STAGE IIB                            10                             37
  STAGE III                             2                              1
  STAGE IIIA                           16                             45
  STAGE IIIB                            9                             36
  STAGE IIIC                            5                             27
  STAGE IV                              7                             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 19(10Q22.2) MUTATED     4  13  30  18
  AMP PEAK 19(10Q22.2) WILD-TYPE  16  72 116  67
D19V4, multiclass
    clus
vv   AMP PEAK 19(10Q22.2) MUTATED AMP PEAK 19(10Q22.2) WILD-TYPE
  T1                            4                             16
  T2                           13                             72
  T3                           30                            116
  T4                           18                             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
  AMP PEAK 19(10Q22.2) MUTATED   18 17 19 11
  AMP PEAK 19(10Q22.2) WILD-TYPE 91 75 47 56
D19V5, multiclass
    clus
vv   AMP PEAK 19(10Q22.2) MUTATED AMP PEAK 19(10Q22.2) WILD-TYPE
  N0                           18                             91
  N1                           17                             75
  N2                           19                             47
  N3                           11                             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 19(10Q22.2) MUTATED    60   3   3
  AMP PEAK 19(10Q22.2) WILD-TYPE 248  18  14
D19V6, multiclass
    clus
vv   AMP PEAK 19(10Q22.2) MUTATED AMP PEAK 19(10Q22.2) WILD-TYPE
  M0                           60                            248
  M1                            3                             18
  MX                            3                             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"
D19V7, binary
                                cls
clus                               0   1
  AMP PEAK 19(10Q22.2) MUTATED    25  41
  AMP PEAK 19(10Q22.2) WILD-TYPE 112 168
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(10Q22.2) MUTATED     25   41
  AMP PEAK 19(10Q22.2) WILD-TYPE  112  168
        clus
vv       AMP PEAK 19(10Q22.2) MUTATED AMP PEAK 19(10Q22.2) WILD-TYPE
  FEMALE                           25                            112
  MALE                             41                            168
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 19(10Q22.2) MUTATED                                      11
  AMP PEAK 19(10Q22.2) WILD-TYPE                                    51
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 19(10Q22.2) MUTATED                                                       27
  AMP PEAK 19(10Q22.2) WILD-TYPE                                                    127
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 19(10Q22.2) MUTATED                                                                  13
  AMP PEAK 19(10Q22.2) WILD-TYPE                                                                41
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 19(10Q22.2) MUTATED                                                 11
  AMP PEAK 19(10Q22.2) WILD-TYPE                                               34
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK 19(10Q22.2) MUTATED                                                           0
  AMP PEAK 19(10Q22.2) WILD-TYPE                                                         1
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 19(10Q22.2) MUTATED                                                          3
  AMP PEAK 19(10Q22.2) WILD-TYPE                                                       16
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 19(10Q22.2) MUTATED                                                           1
  AMP PEAK 19(10Q22.2) WILD-TYPE                                                         4
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 19(10Q22.2) MUTATED                                          0
  AMP PEAK 19(10Q22.2) WILD-TYPE                                        4
D19V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 19(10Q22.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       11
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      27
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            11
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     0
                                                                   clus
vv                                                                  AMP PEAK 19(10Q22.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         51
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             41
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              34
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       4
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V9, binary
                                cls
clus                               0   1
  AMP PEAK 19(10Q22.2) MUTATED     2  64
  AMP PEAK 19(10Q22.2) WILD-TYPE   5 275
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(10Q22.2) MUTATED      2   64
  AMP PEAK 19(10Q22.2) WILD-TYPE    5  275
     clus
vv    AMP PEAK 19(10Q22.2) MUTATED AMP PEAK 19(10Q22.2) WILD-TYPE
  NO                             2                              5
  YES                           64                            275
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 19(10Q22.2) MUTATED    59   0   2   4
  AMP PEAK 19(10Q22.2) WILD-TYPE 218  13  11  21
D19V10, multiclass
    clus
vv   AMP PEAK 19(10Q22.2) MUTATED AMP PEAK 19(10Q22.2) WILD-TYPE
  R0                           59                            218
  R1                            0                             13
  R2                            2                             11
  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"
D19V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 19(10Q22.2) MUTATED      18                         1
  AMP PEAK 19(10Q22.2) WILD-TYPE    66                         2
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 19(10Q22.2) MUTATED                                           1
  AMP PEAK 19(10Q22.2) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 19(10Q22.2) MUTATED      39
  AMP PEAK 19(10Q22.2) WILD-TYPE   169
D19V12, multiclass
                                           clus
vv                                          AMP PEAK 19(10Q22.2) MUTATED
  ASIAN                                                               18
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               39
                                           clus
vv                                          AMP PEAK 19(10Q22.2) WILD-TYPE
  ASIAN                                                                 66
  BLACK OR AFRICAN AMERICAN                                              2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                169
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = AMP PEAK 20(10Q26.13) MUTATION ANALYSIS
D20V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 20(10Q26.13) MUTATED    45  20
  AMP PEAK 20(10Q26.13) WILD-TYPE 177  73
  AMP PEAK 20(10Q26.13) MUTATED AMP PEAK 20(10Q26.13) WILD-TYPE 
                             65                             250 
  AMP PEAK 20(10Q26.13) MUTATED AMP PEAK 20(10Q26.13) WILD-TYPE 
                             20                              73 
$`AMP PEAK 20(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 
        3.39        18.38         6.44         5.56        11.05 

$`AMP PEAK 20(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         2.27 
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         0.07 
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 
       13.35        10.26        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-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 
       13.08         1.41         6.87         5.56         1.81         2.53 
TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
       60.56         3.72         4.50         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-SW-A7EB TCGA-ZA-A8F6 
       57.44         8.94         5.79         4.21 

  AMP PEAK 20(10Q26.13) MUTATED AMP PEAK 20(10Q26.13) WILD-TYPE 
                           0.07                            0.07 
  AMP PEAK 20(10Q26.13) MUTATED AMP PEAK 20(10Q26.13) WILD-TYPE 
                          72.23                          122.30 
  AMP PEAK 20(10Q26.13) MUTATED AMP PEAK 20(10Q26.13) WILD-TYPE 
                          11.24                           10.65 
[1] "0.1 - 72.2 (11.2)"  "0.1 - 122.3 (10.6)"
[1] "hr=" "1"  
D20V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 20(10Q26.13) MUTATED         0        5        7        8         4
  AMP PEAK 20(10Q26.13) WILD-TYPE       2        7       31       19        28
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 20(10Q26.13) MUTATED           9         0         15          6
  AMP PEAK 20(10Q26.13) WILD-TYPE        38         3         46         39
                                 vv
clus                              STAGE IIIC STAGE IV
  AMP PEAK 20(10Q26.13) MUTATED            4        8
  AMP PEAK 20(10Q26.13) WILD-TYPE         28       23
D20V3, multiclass
            clus
vv           AMP PEAK 20(10Q26.13) MUTATED AMP PEAK 20(10Q26.13) WILD-TYPE
  STAGE I                                0                               2
  STAGE IA                               5                               7
  STAGE IB                               7                              31
  STAGE II                               8                              19
  STAGE IIA                              4                              28
  STAGE IIB                              9                              38
  STAGE III                              0                               3
  STAGE IIIA                            15                              46
  STAGE IIIB                             6                              39
  STAGE IIIC                             4                              28
  STAGE IV                               8                              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 20(10Q26.13) MUTATED     6  19  27  14
  AMP PEAK 20(10Q26.13) WILD-TYPE  14  66 119  71
D20V4, multiclass
    clus
vv   AMP PEAK 20(10Q26.13) MUTATED AMP PEAK 20(10Q26.13) WILD-TYPE
  T1                             6                              14
  T2                            19                              66
  T3                            27                             119
  T4                            14                              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
  AMP PEAK 20(10Q26.13) MUTATED   23 18 15 10
  AMP PEAK 20(10Q26.13) WILD-TYPE 86 74 51 57
D20V5, multiclass
    clus
vv   AMP PEAK 20(10Q26.13) MUTATED AMP PEAK 20(10Q26.13) WILD-TYPE
  N0                            23                              86
  N1                            18                              74
  N2                            15                              51
  N3                            10                              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 20(10Q26.13) MUTATED    62   3   4
  AMP PEAK 20(10Q26.13) WILD-TYPE 246  18  13
D20V6, multiclass
    clus
vv   AMP PEAK 20(10Q26.13) MUTATED AMP PEAK 20(10Q26.13) WILD-TYPE
  M0                            62                             246
  M1                             3                              18
  MX                             4                              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"
D20V7, binary
                                 cls
clus                                0   1
  AMP PEAK 20(10Q26.13) MUTATED    28  41
  AMP PEAK 20(10Q26.13) WILD-TYPE 109 168
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(10Q26.13) MUTATED     28   41
  AMP PEAK 20(10Q26.13) WILD-TYPE  109  168
        clus
vv       AMP PEAK 20(10Q26.13) MUTATED AMP PEAK 20(10Q26.13) WILD-TYPE
  FEMALE                            28                             109
  MALE                              41                             168
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 20(10Q26.13) MUTATED                                       9
  AMP PEAK 20(10Q26.13) WILD-TYPE                                    53
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 20(10Q26.13) MUTATED                                                       29
  AMP PEAK 20(10Q26.13) WILD-TYPE                                                    125
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 20(10Q26.13) MUTATED                                                                  14
  AMP PEAK 20(10Q26.13) WILD-TYPE                                                                40
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 20(10Q26.13) MUTATED                                                  9
  AMP PEAK 20(10Q26.13) WILD-TYPE                                               36
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK 20(10Q26.13) MUTATED                                                           0
  AMP PEAK 20(10Q26.13) WILD-TYPE                                                         1
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 20(10Q26.13) MUTATED                                                          5
  AMP PEAK 20(10Q26.13) WILD-TYPE                                                       14
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 20(10Q26.13) MUTATED                                                           2
  AMP PEAK 20(10Q26.13) WILD-TYPE                                                         3
                                 vv
clus                              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 20(10Q26.13) MUTATED                                          0
  AMP PEAK 20(10Q26.13) WILD-TYPE                                        4
D20V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 20(10Q26.13) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       29
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              9
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      0
                                                                   clus
vv                                                                  AMP PEAK 20(10Q26.13) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          53
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               36
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                        4
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V9, binary
                                 cls
clus                                0   1
  AMP PEAK 20(10Q26.13) MUTATED     2  67
  AMP PEAK 20(10Q26.13) WILD-TYPE   5 272
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(10Q26.13) MUTATED      2   67
  AMP PEAK 20(10Q26.13) WILD-TYPE    5  272
     clus
vv    AMP PEAK 20(10Q26.13) MUTATED AMP PEAK 20(10Q26.13) WILD-TYPE
  NO                              2                               5
  YES                            67                             272
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 20(10Q26.13) MUTATED    59   1   2   6
  AMP PEAK 20(10Q26.13) WILD-TYPE 218  12  11  19
D20V10, multiclass
    clus
vv   AMP PEAK 20(10Q26.13) MUTATED AMP PEAK 20(10Q26.13) WILD-TYPE
  R0                            59                             218
  R1                             1                              12
  R2                             2                              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"
D20V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 20(10Q26.13) MUTATED      16                         2
  AMP PEAK 20(10Q26.13) WILD-TYPE    68                         1
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 20(10Q26.13) MUTATED                                           0
  AMP PEAK 20(10Q26.13) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  AMP PEAK 20(10Q26.13) MUTATED      39
  AMP PEAK 20(10Q26.13) WILD-TYPE   169
D20V12, multiclass
                                           clus
vv                                          AMP PEAK 20(10Q26.13) MUTATED
  ASIAN                                                                16
  BLACK OR AFRICAN AMERICAN                                             2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                39
                                           clus
vv                                          AMP PEAK 20(10Q26.13) WILD-TYPE
  ASIAN                                                                  68
  BLACK OR AFRICAN AMERICAN                                               1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 169
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = AMP PEAK 21(11P13) MUTATION ANALYSIS
D21V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 21(11P13) MUTATED    34  23
  AMP PEAK 21(11P13) WILD-TYPE 188  70
  AMP PEAK 21(11P13) MUTATED AMP PEAK 21(11P13) WILD-TYPE 
                          57                          258 
  AMP PEAK 21(11P13) MUTATED AMP PEAK 21(11P13) WILD-TYPE 
                          23                           70 
$`AMP PEAK 21(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 
        2.27        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-RD-A7BT 
        5.36         1.41         5.56         1.81         5.56         8.61 
TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N5 
       16.67       115.69        57.44 

$`AMP PEAK 21(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         0.07 
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        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 
       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-A6RS TCGA-IP-7968 TCGA-KB-A6F7 
        5.19        13.08         6.44         6.87         2.53        60.56 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
        3.72         4.50        11.05         4.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-ZA-A8F6 
       40.64       116.38        71.38         8.94         5.79         4.21 

  AMP PEAK 21(11P13) MUTATED AMP PEAK 21(11P13) WILD-TYPE 
                        0.07                         0.07 
  AMP PEAK 21(11P13) MUTATED AMP PEAK 21(11P13) WILD-TYPE 
                      115.69                       122.30 
  AMP PEAK 21(11P13) MUTATED AMP PEAK 21(11P13) WILD-TYPE 
                       6.970                       11.805 
[1] "0.1 - 115.7 (7.0)"  "0.1 - 122.3 (11.8)"
[1] "hr=" "1.9"
D21V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 21(11P13) MUTATED         0        1        7        4         3
  AMP PEAK 21(11P13) WILD-TYPE       2       11       31       23        29
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 21(11P13) MUTATED          10         1         11          6
  AMP PEAK 21(11P13) WILD-TYPE        37         2         50         39
                              vv
clus                           STAGE IIIC STAGE IV
  AMP PEAK 21(11P13) MUTATED            9        9
  AMP PEAK 21(11P13) WILD-TYPE         23       22
D21V3, multiclass
            clus
vv           AMP PEAK 21(11P13) MUTATED AMP PEAK 21(11P13) WILD-TYPE
  STAGE I                             0                            2
  STAGE IA                            1                           11
  STAGE IB                            7                           31
  STAGE II                            4                           23
  STAGE IIA                           3                           29
  STAGE IIB                          10                           37
  STAGE III                           1                            2
  STAGE IIIA                         11                           50
  STAGE IIIB                          6                           39
  STAGE IIIC                          9                           23
  STAGE IV                            9                           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 21(11P13) MUTATED     3   9  30  20
  AMP PEAK 21(11P13) WILD-TYPE  17  76 116  65
D21V4, multiclass
    clus
vv   AMP PEAK 21(11P13) MUTATED AMP PEAK 21(11P13) WILD-TYPE
  T1                          3                           17
  T2                          9                           76
  T3                         30                          116
  T4                         20                           65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2 N3
  AMP PEAK 21(11P13) MUTATED   16 19 13 14
  AMP PEAK 21(11P13) WILD-TYPE 93 73 53 53
D21V5, multiclass
    clus
vv   AMP PEAK 21(11P13) MUTATED AMP PEAK 21(11P13) WILD-TYPE
  N0                         16                           93
  N1                         19                           73
  N2                         13                           53
  N3                         14                           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 21(11P13) MUTATED    55   4   6
  AMP PEAK 21(11P13) WILD-TYPE 253  17  11
D21V6, multiclass
    clus
vv   AMP PEAK 21(11P13) MUTATED AMP PEAK 21(11P13) WILD-TYPE
  M0                         55                          253
  M1                          4                           17
  MX                          6                           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"
D21V7, binary
                              cls
clus                             0   1
  AMP PEAK 21(11P13) MUTATED    22  43
  AMP PEAK 21(11P13) WILD-TYPE 115 166
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(11P13) MUTATED     22   43
  AMP PEAK 21(11P13) WILD-TYPE  115  166
        clus
vv       AMP PEAK 21(11P13) MUTATED AMP PEAK 21(11P13) WILD-TYPE
  FEMALE                         22                          115
  MALE                           43                          166
[1] 2 2
[1] FALSE
                              vv
clus                           STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 21(11P13) MUTATED                                      12
  AMP PEAK 21(11P13) WILD-TYPE                                    50
                              vv
clus                           STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 21(11P13) MUTATED                                                       31
  AMP PEAK 21(11P13) WILD-TYPE                                                    123
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 21(11P13) MUTATED                                                                   8
  AMP PEAK 21(11P13) WILD-TYPE                                                                46
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 21(11P13) MUTATED                                                  6
  AMP PEAK 21(11P13) WILD-TYPE                                               39
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK 21(11P13) MUTATED                                                           0
  AMP PEAK 21(11P13) WILD-TYPE                                                         1
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 21(11P13) MUTATED                                                          5
  AMP PEAK 21(11P13) WILD-TYPE                                                       14
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 21(11P13) MUTATED                                                           0
  AMP PEAK 21(11P13) WILD-TYPE                                                         5
                              vv
clus                           STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 21(11P13) MUTATED                                          2
  AMP PEAK 21(11P13) WILD-TYPE                                        2
D21V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 21(11P13) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    31
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          8
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           6
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                  0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                  0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   2
                                                                   clus
vv                                                                  AMP PEAK 21(11P13) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     123
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           46
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            39
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V9, binary
                              cls
clus                             0   1
  AMP PEAK 21(11P13) MUTATED     2  63
  AMP PEAK 21(11P13) WILD-TYPE   5 276
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(11P13) MUTATED      2   63
  AMP PEAK 21(11P13) WILD-TYPE    5  276
     clus
vv    AMP PEAK 21(11P13) MUTATED AMP PEAK 21(11P13) WILD-TYPE
  NO                           2                            5
  YES                         63                          276
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 21(11P13) MUTATED    49   3   3   5
  AMP PEAK 21(11P13) WILD-TYPE 228  10  10  20
D21V10, multiclass
    clus
vv   AMP PEAK 21(11P13) MUTATED AMP PEAK 21(11P13) WILD-TYPE
  R0                         49                          228
  R1                          3                           10
  R2                          3                           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"
D21V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 21(11P13) MUTATED      16                         0
  AMP PEAK 21(11P13) WILD-TYPE    68                         3
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 21(11P13) MUTATED                                           1    39
  AMP PEAK 21(11P13) WILD-TYPE                                         0   169
D21V12, multiclass
                                           clus
vv                                          AMP PEAK 21(11P13) MUTATED
  ASIAN                                                             16
  BLACK OR AFRICAN AMERICAN                                          0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                             39
                                           clus
vv                                          AMP PEAK 21(11P13) WILD-TYPE
  ASIAN                                                               68
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              169
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = AMP PEAK 22(11Q13.3) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 22(11Q13.3) MUTATED    48  22
  AMP PEAK 22(11Q13.3) WILD-TYPE 174  71
  AMP PEAK 22(11Q13.3) MUTATED AMP PEAK 22(11Q13.3) WILD-TYPE 
                            70                            245 
  AMP PEAK 22(11Q13.3) MUTATED AMP PEAK 22(11Q13.3) WILD-TYPE 
                            22                             71 
$`AMP PEAK 22(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         2.27 
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-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-RD-A7BT TCGA-RD-A7C1 
        6.44         5.56         1.81         5.56         8.61        16.67 
TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 
      122.30       115.69        57.44         8.94 

$`AMP PEAK 22(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         0.07         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 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       17.19        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-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         4.50        11.05         4.67        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-SW-A7EB TCGA-ZA-A8F6 
       40.64       116.38        71.38         5.79         4.21 

  AMP PEAK 22(11Q13.3) MUTATED AMP PEAK 22(11Q13.3) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 22(11Q13.3) MUTATED AMP PEAK 22(11Q13.3) WILD-TYPE 
                        122.30                         116.38 
  AMP PEAK 22(11Q13.3) MUTATED AMP PEAK 22(11Q13.3) WILD-TYPE 
                         6.705                         11.700 
[1] "0.1 - 122.3 (6.7)"  "0.1 - 116.4 (11.7)"
[1] "hr=" "1.2"
D22V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 22(11Q13.3) MUTATED         1        3        7        7         6
  AMP PEAK 22(11Q13.3) WILD-TYPE       1        9       31       20        26
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 22(11Q13.3) MUTATED          11         0         15         10
  AMP PEAK 22(11Q13.3) WILD-TYPE        36         3         46         35
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 22(11Q13.3) MUTATED           10        8
  AMP PEAK 22(11Q13.3) WILD-TYPE         22       23
D22V3, multiclass
            clus
vv           AMP PEAK 22(11Q13.3) MUTATED AMP PEAK 22(11Q13.3) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                              3                              9
  STAGE IB                              7                             31
  STAGE II                              7                             20
  STAGE IIA                             6                             26
  STAGE IIB                            11                             36
  STAGE III                             0                              3
  STAGE IIIA                           15                             46
  STAGE IIIB                           10                             35
  STAGE IIIC                           10                             22
  STAGE IV                              8                             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 22(11Q13.3) MUTATED     5  18  34  22
  AMP PEAK 22(11Q13.3) WILD-TYPE  15  67 112  63
D22V4, multiclass
    clus
vv   AMP PEAK 22(11Q13.3) MUTATED AMP PEAK 22(11Q13.3) WILD-TYPE
  T1                            5                             15
  T2                           18                             67
  T3                           34                            112
  T4                           22                             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 22(11Q13.3) MUTATED   23 22 23 11
  AMP PEAK 22(11Q13.3) WILD-TYPE 86 70 43 56
D22V5, multiclass
    clus
vv   AMP PEAK 22(11Q13.3) MUTATED AMP PEAK 22(11Q13.3) WILD-TYPE
  N0                           23                             86
  N1                           22                             70
  N2                           23                             43
  N3                           11                             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 22(11Q13.3) MUTATED    77   2   4
  AMP PEAK 22(11Q13.3) WILD-TYPE 231  19  13
D22V6, multiclass
    clus
vv   AMP PEAK 22(11Q13.3) MUTATED AMP PEAK 22(11Q13.3) WILD-TYPE
  M0                           77                            231
  M1                            2                             19
  MX                            4                             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"
D22V7, binary
                                cls
clus                               0   1
  AMP PEAK 22(11Q13.3) MUTATED    29  54
  AMP PEAK 22(11Q13.3) WILD-TYPE 108 155
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(11Q13.3) MUTATED     29   54
  AMP PEAK 22(11Q13.3) WILD-TYPE  108  155
        clus
vv       AMP PEAK 22(11Q13.3) MUTATED AMP PEAK 22(11Q13.3) WILD-TYPE
  FEMALE                           29                            108
  MALE                             54                            155
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 22(11Q13.3) MUTATED                                      10
  AMP PEAK 22(11Q13.3) WILD-TYPE                                    52
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 22(11Q13.3) MUTATED                                                       42
  AMP PEAK 22(11Q13.3) WILD-TYPE                                                    112
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 22(11Q13.3) MUTATED                                                                  14
  AMP PEAK 22(11Q13.3) WILD-TYPE                                                                40
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 22(11Q13.3) MUTATED                                                  9
  AMP PEAK 22(11Q13.3) WILD-TYPE                                               36
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK 22(11Q13.3) MUTATED                                                           0
  AMP PEAK 22(11Q13.3) WILD-TYPE                                                         1
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 22(11Q13.3) MUTATED                                                          6
  AMP PEAK 22(11Q13.3) WILD-TYPE                                                       13
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 22(11Q13.3) MUTATED                                                           1
  AMP PEAK 22(11Q13.3) WILD-TYPE                                                         4
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 22(11Q13.3) MUTATED                                          0
  AMP PEAK 22(11Q13.3) WILD-TYPE                                        4
D22V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 22(11Q13.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       10
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      42
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             9
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     0
                                                                   clus
vv                                                                  AMP PEAK 22(11Q13.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         52
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       112
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              36
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       4
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V9, binary
                                cls
clus                               0   1
  AMP PEAK 22(11Q13.3) MUTATED     2  81
  AMP PEAK 22(11Q13.3) WILD-TYPE   5 258
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(11Q13.3) MUTATED      2   81
  AMP PEAK 22(11Q13.3) WILD-TYPE    5  258
     clus
vv    AMP PEAK 22(11Q13.3) MUTATED AMP PEAK 22(11Q13.3) WILD-TYPE
  NO                             2                              5
  YES                           81                            258
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 22(11Q13.3) MUTATED    65   4   3   6
  AMP PEAK 22(11Q13.3) WILD-TYPE 212   9  10  19
D22V10, multiclass
    clus
vv   AMP PEAK 22(11Q13.3) MUTATED AMP PEAK 22(11Q13.3) WILD-TYPE
  R0                           65                            212
  R1                            4                              9
  R2                            3                             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"
D22V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 22(11Q13.3) MUTATED      21                         1
  AMP PEAK 22(11Q13.3) WILD-TYPE    63                         2
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 22(11Q13.3) MUTATED                                           1
  AMP PEAK 22(11Q13.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 22(11Q13.3) MUTATED      47
  AMP PEAK 22(11Q13.3) WILD-TYPE   161
D22V12, multiclass
                                           clus
vv                                          AMP PEAK 22(11Q13.3) MUTATED
  ASIAN                                                               21
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               47
                                           clus
vv                                          AMP PEAK 22(11Q13.3) WILD-TYPE
  ASIAN                                                                 63
  BLACK OR AFRICAN AMERICAN                                              2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                161
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = AMP PEAK 23(12P12.1) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 23(12P12.1) MUTATED    67  24
  AMP PEAK 23(12P12.1) WILD-TYPE 155  69
  AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE 
                            91                            224 
  AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE 
                            24                             69 
$`AMP PEAK 23(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 
        2.27         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-A7NU TCGA-IP-7968 TCGA-KB-A6F7 TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8N6 
        1.81         2.53        60.56        11.05        16.67         8.94 
TCGA-SW-A7EB 
        5.79 

$`AMP PEAK 23(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 
        0.07         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 
       13.35        10.26        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-RD-A7BT TCGA-RD-A7BW 
        5.56         5.56         3.72         4.50         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-ZA-A8F6 
       57.44         4.21 

  AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE 
                         79.07                         122.30 
  AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE 
                         8.120                         11.735 
[1] "0.1 - 79.1 (8.1)"   "0.1 - 122.3 (11.7)"
[1] "hr=" "1"  
D23V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 23(12P12.1) MUTATED         0        1        9        7        11
  AMP PEAK 23(12P12.1) WILD-TYPE       2       11       29       20        21
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 23(12P12.1) MUTATED          16         1         22         13
  AMP PEAK 23(12P12.1) WILD-TYPE        31         2         39         32
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 23(12P12.1) MUTATED           10        8
  AMP PEAK 23(12P12.1) WILD-TYPE         22       23
D23V3, multiclass
            clus
vv           AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              1                             11
  STAGE IB                              9                             29
  STAGE II                              7                             20
  STAGE IIA                            11                             21
  STAGE IIB                            16                             31
  STAGE III                             1                              2
  STAGE IIIA                           22                             39
  STAGE IIIB                           13                             32
  STAGE IIIC                           10                             22
  STAGE IV                              8                             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 23(12P12.1) MUTATED    4 19 51 24
  AMP PEAK 23(12P12.1) WILD-TYPE 16 66 95 61
D23V4, multiclass
    clus
vv   AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE
  T1                            4                             16
  T2                           19                             66
  T3                           51                             95
  T4                           24                             61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 23(12P12.1) MUTATED   27 30 25 17
  AMP PEAK 23(12P12.1) WILD-TYPE 82 62 41 50
D23V5, multiclass
    clus
vv   AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE
  N0                           27                             82
  N1                           30                             62
  N2                           25                             41
  N3                           17                             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 23(12P12.1) MUTATED    89   6   4
  AMP PEAK 23(12P12.1) WILD-TYPE 219  15  13
D23V6, multiclass
    clus
vv   AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE
  M0                           89                            219
  M1                            6                             15
  MX                            4                             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"
D23V7, binary
                                cls
clus                               0   1
  AMP PEAK 23(12P12.1) MUTATED    38  61
  AMP PEAK 23(12P12.1) WILD-TYPE  99 148
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(12P12.1) MUTATED     38   61
  AMP PEAK 23(12P12.1) WILD-TYPE   99  148
        clus
vv       AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE
  FEMALE                           38                             99
  MALE                             61                            148
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 23(12P12.1) MUTATED                                      21
  AMP PEAK 23(12P12.1) WILD-TYPE                                    41
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 23(12P12.1) MUTATED                                                       44
  AMP PEAK 23(12P12.1) WILD-TYPE                                                    110
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 23(12P12.1) MUTATED                                                                  11
  AMP PEAK 23(12P12.1) WILD-TYPE                                                                43
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 23(12P12.1) MUTATED                                                 17
  AMP PEAK 23(12P12.1) WILD-TYPE                                               28
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK 23(12P12.1) MUTATED                                                           0
  AMP PEAK 23(12P12.1) WILD-TYPE                                                         1
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 23(12P12.1) MUTATED                                                          4
  AMP PEAK 23(12P12.1) WILD-TYPE                                                       15
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 23(12P12.1) MUTATED                                                           0
  AMP PEAK 23(12P12.1) WILD-TYPE                                                         5
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 23(12P12.1) MUTATED                                          1
  AMP PEAK 23(12P12.1) WILD-TYPE                                        3
D23V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 23(12P12.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       21
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      44
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            17
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     1
                                                                   clus
vv                                                                  AMP PEAK 23(12P12.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         41
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       110
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             43
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              28
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V9, binary
                                cls
clus                               0   1
  AMP PEAK 23(12P12.1) MUTATED     2  97
  AMP PEAK 23(12P12.1) WILD-TYPE   5 242
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(12P12.1) MUTATED      2   97
  AMP PEAK 23(12P12.1) WILD-TYPE    5  242
     clus
vv    AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE
  NO                             2                              5
  YES                           97                            242
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 23(12P12.1) MUTATED    79   5   5   4
  AMP PEAK 23(12P12.1) WILD-TYPE 198   8   8  21
D23V10, multiclass
    clus
vv   AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE
  R0                           79                            198
  R1                            5                              8
  R2                            5                              8
  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"
D23V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 23(12P12.1) MUTATED      27                         1
  AMP PEAK 23(12P12.1) WILD-TYPE    57                         2
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 23(12P12.1) MUTATED                                           0
  AMP PEAK 23(12P12.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 23(12P12.1) MUTATED      61
  AMP PEAK 23(12P12.1) WILD-TYPE   147
D23V12, multiclass
                                           clus
vv                                          AMP PEAK 23(12P12.1) MUTATED
  ASIAN                                                               27
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               61
                                           clus
vv                                          AMP PEAK 23(12P12.1) WILD-TYPE
  ASIAN                                                                 57
  BLACK OR AFRICAN AMERICAN                                              2
  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(24) Variable = AMP PEAK 24(12Q15) MUTATION ANALYSIS
D24V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 24(12Q15) MUTATED    59  24
  AMP PEAK 24(12Q15) WILD-TYPE 163  69
  AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE 
                          83                          232 
  AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE 
                          24                           69 
$`AMP PEAK 24(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        10.26        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 
        1.41         6.44        60.56         4.67        16.67 

$`AMP PEAK 24(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         2.27        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         0.07         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 
       13.35        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-A6RS TCGA-IN-A7NT TCGA-IN-A7NU 
       18.81        18.38         5.19         6.87         5.56         1.81 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BT 
        2.53         5.56         3.72         4.50        11.05         8.61 
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-SW-A7EB TCGA-ZA-A8F6 
       57.44         8.94         5.79         4.21 

  AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE 
                        0.07                         0.07 
  AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE 
                       79.07                       122.30 
  AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE 
                       6.610                       11.555 
[1] "0.1 - 79.1 (6.6)"   "0.1 - 122.3 (11.6)"
[1] "hr=" "1.1"
D24V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 24(12Q15) MUTATED         0        1        9        7        11
  AMP PEAK 24(12Q15) WILD-TYPE       2       11       29       20        21
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 24(12Q15) MUTATED          14         1         16          9
  AMP PEAK 24(12Q15) WILD-TYPE        33         2         45         36
                              vv
clus                           STAGE IIIC STAGE IV
  AMP PEAK 24(12Q15) MUTATED            9        9
  AMP PEAK 24(12Q15) WILD-TYPE         23       22
D24V3, multiclass
            clus
vv           AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE
  STAGE I                             0                            2
  STAGE IA                            1                           11
  STAGE IB                            9                           29
  STAGE II                            7                           20
  STAGE IIA                          11                           21
  STAGE IIB                          14                           33
  STAGE III                           1                            2
  STAGE IIIA                         16                           45
  STAGE IIIB                          9                           36
  STAGE IIIC                          9                           23
  STAGE IV                            9                           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 24(12Q15) MUTATED     5  20  37  24
  AMP PEAK 24(12Q15) WILD-TYPE  15  65 109  61
D24V4, multiclass
    clus
vv   AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE
  T1                          5                           15
  T2                         20                           65
  T3                         37                          109
  T4                         24                           61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2 N3
  AMP PEAK 24(12Q15) MUTATED   25 29 19 14
  AMP PEAK 24(12Q15) WILD-TYPE 84 63 47 53
D24V5, multiclass
    clus
vv   AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE
  N0                         25                           84
  N1                         29                           63
  N2                         19                           47
  N3                         14                           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 24(12Q15) MUTATED    78   6   4
  AMP PEAK 24(12Q15) WILD-TYPE 230  15  13
D24V6, multiclass
    clus
vv   AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE
  M0                         78                          230
  M1                          6                           15
  MX                          4                           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(12Q15) MUTATED    33  55
  AMP PEAK 24(12Q15) WILD-TYPE 104 154
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(12Q15) MUTATED     33   55
  AMP PEAK 24(12Q15) WILD-TYPE  104  154
        clus
vv       AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE
  FEMALE                         33                          104
  MALE                           55                          154
[1] 2 2
[1] FALSE
                              vv
clus                           STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 24(12Q15) MUTATED                                      20
  AMP PEAK 24(12Q15) WILD-TYPE                                    42
                              vv
clus                           STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 24(12Q15) MUTATED                                                       35
  AMP PEAK 24(12Q15) WILD-TYPE                                                    119
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 24(12Q15) MUTATED                                                                   9
  AMP PEAK 24(12Q15) WILD-TYPE                                                                45
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 24(12Q15) MUTATED                                                 16
  AMP PEAK 24(12Q15) WILD-TYPE                                               29
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK 24(12Q15) MUTATED                                                           1
  AMP PEAK 24(12Q15) WILD-TYPE                                                         0
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 24(12Q15) MUTATED                                                          3
  AMP PEAK 24(12Q15) WILD-TYPE                                                       16
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 24(12Q15) MUTATED                                                           0
  AMP PEAK 24(12Q15) WILD-TYPE                                                         5
                              vv
clus                           STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 24(12Q15) MUTATED                                          2
  AMP PEAK 24(12Q15) WILD-TYPE                                        2
D24V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 24(12Q15) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     20
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    35
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          9
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                          16
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                  1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                  0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   2
                                                                   clus
vv                                                                  AMP PEAK 24(12Q15) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       42
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     119
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           45
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            29
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V9, binary
                              cls
clus                             0   1
  AMP PEAK 24(12Q15) MUTATED     3  85
  AMP PEAK 24(12Q15) WILD-TYPE   4 254
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(12Q15) MUTATED      3   85
  AMP PEAK 24(12Q15) WILD-TYPE    4  254
     clus
vv    AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE
  NO                           3                            4
  YES                         85                          254
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 24(12Q15) MUTATED    68   3   5   5
  AMP PEAK 24(12Q15) WILD-TYPE 209  10   8  20
D24V10, multiclass
    clus
vv   AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE
  R0                         68                          209
  R1                          3                           10
  R2                          5                            8
  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"
D24V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 24(12Q15) MUTATED      27                         0
  AMP PEAK 24(12Q15) WILD-TYPE    57                         3
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 24(12Q15) MUTATED                                           0    48
  AMP PEAK 24(12Q15) WILD-TYPE                                         1   160
D24V12, multiclass
                                           clus
vv                                          AMP PEAK 24(12Q15) MUTATED
  ASIAN                                                             27
  BLACK OR AFRICAN AMERICAN                                          0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          0
  WHITE                                                             48
                                           clus
vv                                          AMP PEAK 24(12Q15) WILD-TYPE
  ASIAN                                                               57
  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(25) Variable = AMP PEAK 25(13Q12.3) MUTATION ANALYSIS
D25V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 25(13Q12.3) MUTATED    90  30
  AMP PEAK 25(13Q12.3) WILD-TYPE 132  63
  AMP PEAK 25(13Q12.3) MUTATED AMP PEAK 25(13Q12.3) WILD-TYPE 
                           120                            195 
  AMP PEAK 25(13Q12.3) MUTATED AMP PEAK 25(13Q12.3) WILD-TYPE 
                            30                             63 
$`AMP PEAK 25(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         2.27         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 
        0.07         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-RD-A7BT 
        1.41         6.44         6.87         1.81         5.56         8.61 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-SW-A7EB 
      122.30        37.91       115.69        57.44         8.94         5.79 

$`AMP PEAK 25(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        13.35        10.26        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-A7NT TCGA-IP-7968 TCGA-KB-A6F7 
        5.36         5.19        13.08         5.56         2.53        60.56 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N0 
        3.72         4.50        11.05         4.67        16.67        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-ZA-A8F6 
      116.38        71.38         4.21 

  AMP PEAK 25(13Q12.3) MUTATED AMP PEAK 25(13Q12.3) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 25(13Q12.3) MUTATED AMP PEAK 25(13Q12.3) WILD-TYPE 
                        122.30                         116.38 
  AMP PEAK 25(13Q12.3) MUTATED AMP PEAK 25(13Q12.3) WILD-TYPE 
                        12.015                          9.760 
[1] "0.1 - 122.3 (12.0)" "0.1 - 116.4 (9.8)" 
[1] "hr=" "1.4"
D25V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 25(13Q12.3) MUTATED         1        5       10       11        14
  AMP PEAK 25(13Q12.3) WILD-TYPE       1        7       28       16        18
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 25(13Q12.3) MUTATED          18         2         26         14
  AMP PEAK 25(13Q12.3) WILD-TYPE        29         1         35         31
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 25(13Q12.3) MUTATED           10       15
  AMP PEAK 25(13Q12.3) WILD-TYPE         22       16
D25V3, multiclass
            clus
vv           AMP PEAK 25(13Q12.3) MUTATED AMP PEAK 25(13Q12.3) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                              5                              7
  STAGE IB                             10                             28
  STAGE II                             11                             16
  STAGE IIA                            14                             18
  STAGE IIB                            18                             29
  STAGE III                             2                              1
  STAGE IIIA                           26                             35
  STAGE IIIB                           14                             31
  STAGE IIIC                           10                             22
  STAGE IV                             15                             16
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK 25(13Q12.3) MUTATED    7 37 54 30
  AMP PEAK 25(13Q12.3) WILD-TYPE 13 48 92 55
D25V4, multiclass
    clus
vv   AMP PEAK 25(13Q12.3) MUTATED AMP PEAK 25(13Q12.3) WILD-TYPE
  T1                            7                             13
  T2                           37                             48
  T3                           54                             92
  T4                           30                             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 25(13Q12.3) MUTATED   42 32 25 28
  AMP PEAK 25(13Q12.3) WILD-TYPE 67 60 41 39
D25V5, multiclass
    clus
vv   AMP PEAK 25(13Q12.3) MUTATED AMP PEAK 25(13Q12.3) WILD-TYPE
  N0                           42                             67
  N1                           32                             60
  N2                           25                             41
  N3                           28                             39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  AMP PEAK 25(13Q12.3) MUTATED   122   7   4
  AMP PEAK 25(13Q12.3) WILD-TYPE 186  14  13
D25V6, multiclass
    clus
vv   AMP PEAK 25(13Q12.3) MUTATED AMP PEAK 25(13Q12.3) WILD-TYPE
  M0                          122                            186
  M1                            7                             14
  MX                            4                             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"
D25V7, binary
                                cls
clus                               0   1
  AMP PEAK 25(13Q12.3) MUTATED    50  83
  AMP PEAK 25(13Q12.3) WILD-TYPE  87 126
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(13Q12.3) MUTATED     50   83
  AMP PEAK 25(13Q12.3) WILD-TYPE   87  126
        clus
vv       AMP PEAK 25(13Q12.3) MUTATED AMP PEAK 25(13Q12.3) WILD-TYPE
  FEMALE                           50                             87
  MALE                             83                            126
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 25(13Q12.3) MUTATED                                      16
  AMP PEAK 25(13Q12.3) WILD-TYPE                                    46
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 25(13Q12.3) MUTATED                                                       61
  AMP PEAK 25(13Q12.3) WILD-TYPE                                                     93
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 25(13Q12.3) MUTATED                                                                  23
  AMP PEAK 25(13Q12.3) WILD-TYPE                                                                31
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 25(13Q12.3) MUTATED                                                 18
  AMP PEAK 25(13Q12.3) WILD-TYPE                                               27
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK 25(13Q12.3) MUTATED                                                           0
  AMP PEAK 25(13Q12.3) WILD-TYPE                                                         1
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 25(13Q12.3) MUTATED                                                          9
  AMP PEAK 25(13Q12.3) WILD-TYPE                                                       10
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 25(13Q12.3) MUTATED                                                           4
  AMP PEAK 25(13Q12.3) WILD-TYPE                                                         1
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 25(13Q12.3) MUTATED                                          1
  AMP PEAK 25(13Q12.3) WILD-TYPE                                        3
D25V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 25(13Q12.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       16
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      61
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           23
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            18
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     1
                                                                   clus
vv                                                                  AMP PEAK 25(13Q12.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        93
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             31
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              27
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V9, binary
                                cls
clus                               0   1
  AMP PEAK 25(13Q12.3) MUTATED     3 130
  AMP PEAK 25(13Q12.3) WILD-TYPE   4 209
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(13Q12.3) MUTATED      3  130
  AMP PEAK 25(13Q12.3) WILD-TYPE    4  209
     clus
vv    AMP PEAK 25(13Q12.3) MUTATED AMP PEAK 25(13Q12.3) WILD-TYPE
  NO                             3                              4
  YES                          130                            209
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 25(13Q12.3) MUTATED   103   7   6   9
  AMP PEAK 25(13Q12.3) WILD-TYPE 174   6   7  16
D25V10, multiclass
    clus
vv   AMP PEAK 25(13Q12.3) MUTATED AMP PEAK 25(13Q12.3) WILD-TYPE
  R0                          103                            174
  R1                            7                              6
  R2                            6                              7
  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"
D25V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 25(13Q12.3) MUTATED      30                         2
  AMP PEAK 25(13Q12.3) WILD-TYPE    54                         1
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 25(13Q12.3) MUTATED                                           1
  AMP PEAK 25(13Q12.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 25(13Q12.3) MUTATED      80
  AMP PEAK 25(13Q12.3) WILD-TYPE   128
D25V12, multiclass
                                           clus
vv                                          AMP PEAK 25(13Q12.3) MUTATED
  ASIAN                                                               30
  BLACK OR AFRICAN AMERICAN                                            2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               80
                                           clus
vv                                          AMP PEAK 25(13Q12.3) WILD-TYPE
  ASIAN                                                                 54
  BLACK OR AFRICAN AMERICAN                                              1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                128
[1] 4 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(13Q22.1) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 26(13Q22.1) MUTATED    94  32
  AMP PEAK 26(13Q22.1) WILD-TYPE 128  61
  AMP PEAK 26(13Q22.1) MUTATED AMP PEAK 26(13Q22.1) WILD-TYPE 
                           126                            189 
  AMP PEAK 26(13Q22.1) MUTATED AMP PEAK 26(13Q22.1) WILD-TYPE 
                            32                             61 
$`AMP PEAK 26(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-6707 TCGA-BR-6801 TCGA-BR-7197 
       39.12         0.62        32.78        16.14        21.11         9.21 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 
       35.24        15.42        28.01         0.69        18.54         0.95 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8362 TCGA-BR-8373 TCGA-BR-8381 
        0.69        12.26         0.49         0.36        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8678 TCGA-BR-8682 
       15.85         5.39         9.21        12.79        11.54        16.44 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4IY 
       15.68         0.62        10.68         1.15         2.27        12.89 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
        0.72        14.17        12.82        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
       20.42         1.15         5.13         3.25        13.15         0.30 
TCGA-CD-8525 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A4MG 
        0.07         0.13         0.13         0.07         0.13         0.07 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 
        0.10        20.02        15.95         1.02         7.99        54.08 
TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 
        4.01        29.98        19.07         7.07        12.00         1.02 
TCGA-CG-5719 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
        1.02       105.07        15.02         4.01        55.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6524 
       12.36        12.66        11.93        19.13        18.54        17.85 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       17.19        10.26        15.98        10.55        11.31        12.33 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-A4YT TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6F0 
       19.50        17.19        14.27        14.76        11.24         2.96 
TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-8631 
       15.65         0.62         7.79        72.23        19.53         0.56 
TCGA-FP-A4BF TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G6 TCGA-HU-A4G8 
        1.55        12.59        14.17        12.10        12.30        11.84 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H3 
       22.75        25.81         6.51         6.25         0.26        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL 
       17.69        12.30        27.42         3.39        18.38         5.19 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-RD-A7BT 
        1.41         6.44         1.81         2.53         5.56         8.61 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-SW-A7EB 
      122.30        37.91       115.69        57.44         8.94         5.79 

$`AMP PEAK 26(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-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 
       13.84        13.22         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-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-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-8363 
        1.55         1.48         7.40         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-8380 TCGA-BR-8384 TCGA-BR-8484 
        3.32         0.36        19.17         0.69         3.72         0.72 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22         1.12        15.81         2.14        13.45         0.20 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-A44T TCGA-BR-A452 
        7.53         0.49        15.81         0.59        12.56         0.66 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J4 
        3.02         0.92        13.41        13.51         0.79         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5801 
        0.66        19.36        13.64        11.57         2.83        13.18 
TCGA-CD-5803 TCGA-CD-8524 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-8536 TCGA-CD-A487 TCGA-CD-A489 
        0.16         0.10         0.10         0.10         0.13         0.13 
TCGA-CD-A48C TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4437 
        0.13         0.10         0.10         3.02        27.02         8.05 
TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 
       14.01        47.05        12.03        21.99         9.01        18.97 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       22.98        30.97         6.97         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-6519 
       12.03        28.96        79.07        65.10        21.07        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-8570 
       18.84        18.61        13.35        15.22        12.79        24.72 
TCGA-D7-8572 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU 
       16.80         0.23         6.97        21.14        20.91        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY 
        5.92        15.16        13.78        13.71        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6177 
        9.76         4.34         7.40         7.13        16.24         6.58 
TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
       14.47        21.27         8.12         0.39         3.02        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A8CX TCGA-HF-A5NB 
       17.06        59.54         5.03        13.58         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 
       26.47         1.51         5.92        14.27        11.41        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH 
        0.76        24.30         5.59        24.20         3.25        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4H0 
       21.37        29.98         8.98         0.10        10.19         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       12.95         9.67         8.88         8.81        21.21         3.45 
TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NT TCGA-KB-A6F7 
       18.81         5.36        13.08         6.87         5.56        60.56 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N0 
        3.72         4.50        11.05         4.67        16.67        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-ZA-A8F6 
      116.38        71.38         4.21 

  AMP PEAK 26(13Q22.1) MUTATED AMP PEAK 26(13Q22.1) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 26(13Q22.1) MUTATED AMP PEAK 26(13Q22.1) WILD-TYPE 
                        122.30                         116.38 
  AMP PEAK 26(13Q22.1) MUTATED AMP PEAK 26(13Q22.1) WILD-TYPE 
                         11.77                           9.76 
[1] "0.1 - 122.3 (11.8)" "0.1 - 116.4 (9.8)" 
[1] "hr=" "1.4"
D26V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 26(13Q22.1) MUTATED         1        4       11       13        15
  AMP PEAK 26(13Q22.1) WILD-TYPE       1        8       27       14        17
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 26(13Q22.1) MUTATED          23         1         24         13
  AMP PEAK 26(13Q22.1) WILD-TYPE        24         2         37         32
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 26(13Q22.1) MUTATED           10       14
  AMP PEAK 26(13Q22.1) WILD-TYPE         22       17
D26V3, multiclass
            clus
vv           AMP PEAK 26(13Q22.1) MUTATED AMP PEAK 26(13Q22.1) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                              4                              8
  STAGE IB                             11                             27
  STAGE II                             13                             14
  STAGE IIA                            15                             17
  STAGE IIB                            23                             24
  STAGE III                             1                              2
  STAGE IIIA                           24                             37
  STAGE IIIB                           13                             32
  STAGE IIIC                           10                             22
  STAGE IV                             14                             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 26(13Q22.1) MUTATED    6 38 58 29
  AMP PEAK 26(13Q22.1) WILD-TYPE 14 47 88 56
D26V4, multiclass
    clus
vv   AMP PEAK 26(13Q22.1) MUTATED AMP PEAK 26(13Q22.1) WILD-TYPE
  T1                            6                             14
  T2                           38                             47
  T3                           58                             88
  T4                           29                             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                             N0 N1 N2 N3
  AMP PEAK 26(13Q22.1) MUTATED   43 38 28 23
  AMP PEAK 26(13Q22.1) WILD-TYPE 66 54 38 44
D26V5, multiclass
    clus
vv   AMP PEAK 26(13Q22.1) MUTATED AMP PEAK 26(13Q22.1) WILD-TYPE
  N0                           43                             66
  N1                           38                             54
  N2                           28                             38
  N3                           23                             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 26(13Q22.1) MUTATED   127   6   4
  AMP PEAK 26(13Q22.1) WILD-TYPE 181  15  13
D26V6, multiclass
    clus
vv   AMP PEAK 26(13Q22.1) MUTATED AMP PEAK 26(13Q22.1) WILD-TYPE
  M0                          127                            181
  M1                            6                             15
  MX                            4                             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"
D26V7, binary
                                cls
clus                               0   1
  AMP PEAK 26(13Q22.1) MUTATED    46  91
  AMP PEAK 26(13Q22.1) WILD-TYPE  91 118
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(13Q22.1) MUTATED     46   91
  AMP PEAK 26(13Q22.1) WILD-TYPE   91  118
        clus
vv       AMP PEAK 26(13Q22.1) MUTATED AMP PEAK 26(13Q22.1) WILD-TYPE
  FEMALE                           46                             91
  MALE                             91                            118
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 26(13Q22.1) MUTATED                                      14
  AMP PEAK 26(13Q22.1) WILD-TYPE                                    48
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 26(13Q22.1) MUTATED                                                       65
  AMP PEAK 26(13Q22.1) WILD-TYPE                                                     89
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 26(13Q22.1) MUTATED                                                                  24
  AMP PEAK 26(13Q22.1) WILD-TYPE                                                                30
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 26(13Q22.1) MUTATED                                                 17
  AMP PEAK 26(13Q22.1) WILD-TYPE                                               28
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK 26(13Q22.1) MUTATED                                                           1
  AMP PEAK 26(13Q22.1) WILD-TYPE                                                         0
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 26(13Q22.1) MUTATED                                                         10
  AMP PEAK 26(13Q22.1) WILD-TYPE                                                        9
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 26(13Q22.1) MUTATED                                                           4
  AMP PEAK 26(13Q22.1) WILD-TYPE                                                         1
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 26(13Q22.1) MUTATED                                          1
  AMP PEAK 26(13Q22.1) WILD-TYPE                                        3
D26V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 26(13Q22.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       14
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      65
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           24
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            17
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     1
                                                                   clus
vv                                                                  AMP PEAK 26(13Q22.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        89
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             30
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              28
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V9, binary
                                cls
clus                               0   1
  AMP PEAK 26(13Q22.1) MUTATED     2 135
  AMP PEAK 26(13Q22.1) WILD-TYPE   5 204
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(13Q22.1) MUTATED      2  135
  AMP PEAK 26(13Q22.1) WILD-TYPE    5  204
     clus
vv    AMP PEAK 26(13Q22.1) MUTATED AMP PEAK 26(13Q22.1) WILD-TYPE
  NO                             2                              5
  YES                          135                            204
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 26(13Q22.1) MUTATED   106   7   6  10
  AMP PEAK 26(13Q22.1) WILD-TYPE 171   6   7  15
D26V10, multiclass
    clus
vv   AMP PEAK 26(13Q22.1) MUTATED AMP PEAK 26(13Q22.1) WILD-TYPE
  R0                          106                            171
  R1                            7                              6
  R2                            6                              7
  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"
D26V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 26(13Q22.1) MUTATED      31                         1
  AMP PEAK 26(13Q22.1) WILD-TYPE    53                         2
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 26(13Q22.1) MUTATED                                           1
  AMP PEAK 26(13Q22.1) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 26(13Q22.1) MUTATED      83
  AMP PEAK 26(13Q22.1) WILD-TYPE   125
D26V12, multiclass
                                           clus
vv                                          AMP PEAK 26(13Q22.1) MUTATED
  ASIAN                                                               31
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               83
                                           clus
vv                                          AMP PEAK 26(13Q22.1) WILD-TYPE
  ASIAN                                                                 53
  BLACK OR AFRICAN AMERICAN                                              2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                125
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = AMP PEAK 27(15Q26.1) MUTATION ANALYSIS
D27V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 27(15Q26.1) MUTATED    52  22
  AMP PEAK 27(15Q26.1) WILD-TYPE 170  71
  AMP PEAK 27(15Q26.1) MUTATED AMP PEAK 27(15Q26.1) WILD-TYPE 
                            74                            241 
  AMP PEAK 27(15Q26.1) MUTATED AMP PEAK 27(15Q26.1) WILD-TYPE 
                            22                             71 
$`AMP PEAK 27(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-A4CQ TCGA-BR-A4J4 TCGA-BR-A4PF 
       22.19         0.59         0.62         2.27         0.53         1.15 
TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 
       13.64         3.25        13.15         0.07         0.10         0.13 
TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A4MG TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4475 
        0.13         0.07         0.07        47.05        19.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5730 
       30.97         6.97         1.02        12.03        79.07         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6525 
       55.04         7.99        11.93        20.55        18.84        13.35 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A4YT 
       15.22        15.98        10.55        12.33         0.23        14.27 
TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-8099 
       15.65         0.62        72.23         8.12        19.53        17.06 
TCGA-FP-8211 TCGA-FP-8631 TCGA-HU-A4G8 TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GY 
       13.58         0.56        11.84        25.81        11.77         0.26 
TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       12.30        27.42         3.45        18.81         3.39        18.38 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-RD-A7BT 
       13.08         1.41         2.53         5.56        60.56         8.61 
TCGA-RD-A8MV TCGA-RD-A8N6 
      122.30         8.94 

$`AMP PEAK 27(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-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-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM 
       13.51         0.46        20.65        20.42        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 
        2.83        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.07         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        0.13         0.13         0.13         0.13         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-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
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-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 
        1.02         0.99         6.02         0.99       105.07        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 
       28.96        65.10        21.07        12.36        12.66        19.13 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6817 
       18.54        18.61        17.85        17.19        10.26        12.79 
TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 
       11.31        24.72        16.80        19.50        17.19         6.97 
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-A6F0 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO 
        2.96         4.34         7.40         7.13         7.79        16.24 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
        6.58        14.47        21.27         0.39         3.02        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 
       59.54         5.03         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-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-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       24.20         3.25        22.75        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.25        10.19         2.10        12.95 
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-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU 
        5.36         5.19         6.44         6.87         5.56         1.81 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW 
        3.72         4.50        11.05         4.67        16.67        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-SW-A7EB 
       40.64       115.69       116.38        71.38        57.44         5.79 
TCGA-ZA-A8F6 
        4.21 

  AMP PEAK 27(15Q26.1) MUTATED AMP PEAK 27(15Q26.1) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 27(15Q26.1) MUTATED AMP PEAK 27(15Q26.1) WILD-TYPE 
                        122.30                         116.38 
  AMP PEAK 27(15Q26.1) MUTATED AMP PEAK 27(15Q26.1) WILD-TYPE 
                         11.16                          11.05 
[1] "0.1 - 122.3 (11.2)" "0.1 - 116.4 (11.1)"
[1] "hr=" "1"  
D27V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 27(15Q26.1) MUTATED         0        3        8        8         8
  AMP PEAK 27(15Q26.1) WILD-TYPE       2        9       30       19        24
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 27(15Q26.1) MUTATED           9         1         17          8
  AMP PEAK 27(15Q26.1) WILD-TYPE        38         2         44         37
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 27(15Q26.1) MUTATED            5       11
  AMP PEAK 27(15Q26.1) WILD-TYPE         27       20
D27V3, multiclass
            clus
vv           AMP PEAK 27(15Q26.1) MUTATED AMP PEAK 27(15Q26.1) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              3                              9
  STAGE IB                              8                             30
  STAGE II                              8                             19
  STAGE IIA                             8                             24
  STAGE IIB                             9                             38
  STAGE III                             1                              2
  STAGE IIIA                           17                             44
  STAGE IIIB                            8                             37
  STAGE IIIC                            5                             27
  STAGE IV                             11                             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 27(15Q26.1) MUTATED     5  24  33  17
  AMP PEAK 27(15Q26.1) WILD-TYPE  15  61 113  68
D27V4, multiclass
    clus
vv   AMP PEAK 27(15Q26.1) MUTATED AMP PEAK 27(15Q26.1) WILD-TYPE
  T1                            5                             15
  T2                           24                             61
  T3                           33                            113
  T4                           17                             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(15Q26.1) MUTATED   26 21 21 11
  AMP PEAK 27(15Q26.1) WILD-TYPE 83 71 45 56
D27V5, multiclass
    clus
vv   AMP PEAK 27(15Q26.1) MUTATED AMP PEAK 27(15Q26.1) WILD-TYPE
  N0                           26                             83
  N1                           21                             71
  N2                           21                             45
  N3                           11                             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 27(15Q26.1) MUTATED    69   7   5
  AMP PEAK 27(15Q26.1) WILD-TYPE 239  14  12
D27V6, multiclass
    clus
vv   AMP PEAK 27(15Q26.1) MUTATED AMP PEAK 27(15Q26.1) WILD-TYPE
  M0                           69                            239
  M1                            7                             14
  MX                            5                             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"
D27V7, binary
                                cls
clus                               0   1
  AMP PEAK 27(15Q26.1) MUTATED    26  55
  AMP PEAK 27(15Q26.1) WILD-TYPE 111 154
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(15Q26.1) MUTATED     26   55
  AMP PEAK 27(15Q26.1) WILD-TYPE  111  154
        clus
vv       AMP PEAK 27(15Q26.1) MUTATED AMP PEAK 27(15Q26.1) WILD-TYPE
  FEMALE                           26                            111
  MALE                             55                            154
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 27(15Q26.1) MUTATED                                      13
  AMP PEAK 27(15Q26.1) WILD-TYPE                                    49
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 27(15Q26.1) MUTATED                                                       32
  AMP PEAK 27(15Q26.1) WILD-TYPE                                                    122
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 27(15Q26.1) MUTATED                                                                  15
  AMP PEAK 27(15Q26.1) WILD-TYPE                                                                39
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 27(15Q26.1) MUTATED                                                 11
  AMP PEAK 27(15Q26.1) WILD-TYPE                                               34
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK 27(15Q26.1) MUTATED                                                           0
  AMP PEAK 27(15Q26.1) WILD-TYPE                                                         1
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 27(15Q26.1) MUTATED                                                          7
  AMP PEAK 27(15Q26.1) WILD-TYPE                                                       12
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 27(15Q26.1) MUTATED                                                           2
  AMP PEAK 27(15Q26.1) WILD-TYPE                                                         3
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 27(15Q26.1) MUTATED                                          0
  AMP PEAK 27(15Q26.1) WILD-TYPE                                        4
D27V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 27(15Q26.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       13
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      32
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           15
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            11
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     0
                                                                   clus
vv                                                                  AMP PEAK 27(15Q26.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       122
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              34
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       4
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V9, binary
                                cls
clus                               0   1
  AMP PEAK 27(15Q26.1) MUTATED     2  79
  AMP PEAK 27(15Q26.1) WILD-TYPE   5 260
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(15Q26.1) MUTATED      2   79
  AMP PEAK 27(15Q26.1) WILD-TYPE    5  260
     clus
vv    AMP PEAK 27(15Q26.1) MUTATED AMP PEAK 27(15Q26.1) WILD-TYPE
  NO                             2                              5
  YES                           79                            260
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 27(15Q26.1) MUTATED    61   5   5   5
  AMP PEAK 27(15Q26.1) WILD-TYPE 216   8   8  20
D27V10, multiclass
    clus
vv   AMP PEAK 27(15Q26.1) MUTATED AMP PEAK 27(15Q26.1) WILD-TYPE
  R0                           61                            216
  R1                            5                              8
  R2                            5                              8
  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"
D27V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 27(15Q26.1) MUTATED      19                         1
  AMP PEAK 27(15Q26.1) WILD-TYPE    65                         2
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 27(15Q26.1) MUTATED                                           1
  AMP PEAK 27(15Q26.1) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 27(15Q26.1) MUTATED      44
  AMP PEAK 27(15Q26.1) WILD-TYPE   164
D27V12, multiclass
                                           clus
vv                                          AMP PEAK 27(15Q26.1) MUTATED
  ASIAN                                                               19
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               44
                                           clus
vv                                          AMP PEAK 27(15Q26.1) WILD-TYPE
  ASIAN                                                                 65
  BLACK OR AFRICAN AMERICAN                                              2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  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(28) Variable = AMP PEAK 28(17Q12) MUTATION ANALYSIS
D28V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 28(17Q12) MUTATED    71  30
  AMP PEAK 28(17Q12) WILD-TYPE 151  63
  AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE 
                         101                          214 
  AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE 
                          30                           63 
$`AMP PEAK 28(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         2.27         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         0.07         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        13.35        17.19        10.26 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8573 TCGA-D7-8576 
       15.98        12.79        11.31        12.33        19.50         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-A6RS 
       18.38         5.19        13.08         1.41         6.44         6.87 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-RD-A7BT TCGA-RD-A8N6 
        5.56         1.81         2.53         8.61         8.94 

$`AMP PEAK 28(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-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW 
        5.56        60.56         3.72         4.50        11.05         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-SW-A7EB TCGA-ZA-A8F6 
       71.38        57.44         5.79         4.21 

  AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE 
                        0.07                         0.07 
  AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE 
                       72.23                       122.30 
  AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE 
                      11.310                       10.585 
[1] "0.1 - 72.2 (11.3)"  "0.1 - 122.3 (10.6)"
[1] "hr=" "1.1"
D28V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 28(17Q12) MUTATED         0        6       12        7         9
  AMP PEAK 28(17Q12) WILD-TYPE       2        6       26       20        23
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 28(17Q12) MUTATED          12         1         19         14
  AMP PEAK 28(17Q12) WILD-TYPE        35         2         42         31
                              vv
clus                           STAGE IIIC STAGE IV
  AMP PEAK 28(17Q12) MUTATED           10       15
  AMP PEAK 28(17Q12) WILD-TYPE         22       16
D28V3, multiclass
            clus
vv           AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE
  STAGE I                             0                            2
  STAGE IA                            6                            6
  STAGE IB                           12                           26
  STAGE II                            7                           20
  STAGE IIA                           9                           23
  STAGE IIB                          12                           35
  STAGE III                           1                            2
  STAGE IIIA                         19                           42
  STAGE IIIB                         14                           31
  STAGE IIIC                         10                           22
  STAGE IV                           15                           16
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK 28(17Q12) MUTATED     8  31  39  28
  AMP PEAK 28(17Q12) WILD-TYPE  12  54 107  57
D28V4, multiclass
    clus
vv   AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE
  T1                          8                           12
  T2                         31                           54
  T3                         39                          107
  T4                         28                           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 28(17Q12) MUTATED   35 26 20 24
  AMP PEAK 28(17Q12) WILD-TYPE 74 66 46 43
D28V5, multiclass
    clus
vv   AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE
  N0                         35                           74
  N1                         26                           66
  N2                         20                           46
  N3                         24                           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
  AMP PEAK 28(17Q12) MUTATED    86  12  10
  AMP PEAK 28(17Q12) WILD-TYPE 222   9   7
D28V6, multiclass
    clus
vv   AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE
  M0                         86                          222
  M1                         12                            9
  MX                         10                            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"
D28V7, binary
                              cls
clus                             0   1
  AMP PEAK 28(17Q12) MUTATED    37  71
  AMP PEAK 28(17Q12) WILD-TYPE 100 138
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 28(17Q12) MUTATED     37   71
  AMP PEAK 28(17Q12) WILD-TYPE  100  138
        clus
vv       AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE
  FEMALE                         37                          100
  MALE                           71                          138
[1] 2 2
[1] FALSE
                              vv
clus                           STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 28(17Q12) MUTATED                                       9
  AMP PEAK 28(17Q12) WILD-TYPE                                    53
                              vv
clus                           STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 28(17Q12) MUTATED                                                       44
  AMP PEAK 28(17Q12) WILD-TYPE                                                    110
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 28(17Q12) MUTATED                                                                  22
  AMP PEAK 28(17Q12) WILD-TYPE                                                                32
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 28(17Q12) MUTATED                                                 20
  AMP PEAK 28(17Q12) WILD-TYPE                                               25
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK 28(17Q12) MUTATED                                                           1
  AMP PEAK 28(17Q12) WILD-TYPE                                                         0
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 28(17Q12) MUTATED                                                          6
  AMP PEAK 28(17Q12) WILD-TYPE                                                       13
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 28(17Q12) MUTATED                                                           3
  AMP PEAK 28(17Q12) WILD-TYPE                                                         2
                              vv
clus                           STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 28(17Q12) MUTATED                                          2
  AMP PEAK 28(17Q12) WILD-TYPE                                        2
D28V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 28(17Q12) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    44
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         22
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                          20
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                  1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                  3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   2
                                                                   clus
vv                                                                  AMP PEAK 28(17Q12) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       53
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     110
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           32
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            25
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V9, binary
                              cls
clus                             0   1
  AMP PEAK 28(17Q12) MUTATED     3 105
  AMP PEAK 28(17Q12) WILD-TYPE   4 234
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 28(17Q12) MUTATED      3  105
  AMP PEAK 28(17Q12) WILD-TYPE    4  234
     clus
vv    AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE
  NO                           3                            4
  YES                        105                          234
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 28(17Q12) MUTATED    91   0   9   3
  AMP PEAK 28(17Q12) WILD-TYPE 186  13   4  22
D28V10, multiclass
    clus
vv   AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE
  R0                         91                          186
  R1                          0                           13
  R2                          9                            4
  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"
D28V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 28(17Q12) MUTATED      25                         2
  AMP PEAK 28(17Q12) WILD-TYPE    59                         1
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 28(17Q12) MUTATED                                           1    62
  AMP PEAK 28(17Q12) WILD-TYPE                                         0   146
D28V12, multiclass
                                           clus
vv                                          AMP PEAK 28(17Q12) MUTATED
  ASIAN                                                             25
  BLACK OR AFRICAN AMERICAN                                          2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                             62
                                           clus
vv                                          AMP PEAK 28(17Q12) WILD-TYPE
  ASIAN                                                               59
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  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(29) Variable = AMP PEAK 29(18Q11.2) MUTATION ANALYSIS
D29V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 29(18Q11.2) MUTATED    63  33
  AMP PEAK 29(18Q11.2) WILD-TYPE 159  60
  AMP PEAK 29(18Q11.2) MUTATED AMP PEAK 29(18Q11.2) WILD-TYPE 
                            96                            219 
  AMP PEAK 29(18Q11.2) MUTATED AMP PEAK 29(18Q11.2) WILD-TYPE 
                            33                             60 
$`AMP PEAK 29(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         2.27 
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         0.07 
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        13.35        17.19        10.26        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-A7NU TCGA-KB-A6F7 TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-SW-A7EB 
        1.81        60.56         4.67        16.67       115.69         5.79 

$`AMP PEAK 29(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         4.50        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-ZA-A8F6 
       57.44         8.94         4.21 

  AMP PEAK 29(18Q11.2) MUTATED AMP PEAK 29(18Q11.2) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 29(18Q11.2) MUTATED AMP PEAK 29(18Q11.2) WILD-TYPE 
                        115.69                         122.30 
  AMP PEAK 29(18Q11.2) MUTATED AMP PEAK 29(18Q11.2) WILD-TYPE 
                         7.415                         11.770 
[1] "0.1 - 115.7 (7.4)"  "0.1 - 122.3 (11.8)"
[1] "hr=" "1.5"
D29V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 29(18Q11.2) MUTATED         0        4       10        6        10
  AMP PEAK 29(18Q11.2) WILD-TYPE       2        8       28       21        22
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 29(18Q11.2) MUTATED          11         0         21         15
  AMP PEAK 29(18Q11.2) WILD-TYPE        36         3         40         30
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 29(18Q11.2) MUTATED           13       11
  AMP PEAK 29(18Q11.2) WILD-TYPE         19       20
D29V3, multiclass
            clus
vv           AMP PEAK 29(18Q11.2) MUTATED AMP PEAK 29(18Q11.2) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              4                              8
  STAGE IB                             10                             28
  STAGE II                              6                             21
  STAGE IIA                            10                             22
  STAGE IIB                            11                             36
  STAGE III                             0                              3
  STAGE IIIA                           21                             40
  STAGE IIIB                           15                             30
  STAGE IIIC                           13                             19
  STAGE IV                             11                             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 29(18Q11.2) MUTATED     7  23  44  28
  AMP PEAK 29(18Q11.2) WILD-TYPE  13  62 102  57
D29V4, multiclass
    clus
vv   AMP PEAK 29(18Q11.2) MUTATED AMP PEAK 29(18Q11.2) WILD-TYPE
  T1                            7                             13
  T2                           23                             62
  T3                           44                            102
  T4                           28                             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 29(18Q11.2) MUTATED   30 27 22 25
  AMP PEAK 29(18Q11.2) WILD-TYPE 79 65 44 42
D29V5, multiclass
    clus
vv   AMP PEAK 29(18Q11.2) MUTATED AMP PEAK 29(18Q11.2) WILD-TYPE
  N0                           30                             79
  N1                           27                             65
  N2                           22                             44
  N3                           25                             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 29(18Q11.2) MUTATED    95   7   6
  AMP PEAK 29(18Q11.2) WILD-TYPE 213  14  11
D29V6, multiclass
    clus
vv   AMP PEAK 29(18Q11.2) MUTATED AMP PEAK 29(18Q11.2) WILD-TYPE
  M0                           95                            213
  M1                            7                             14
  MX                            6                             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"
D29V7, binary
                                cls
clus                               0   1
  AMP PEAK 29(18Q11.2) MUTATED    41  67
  AMP PEAK 29(18Q11.2) WILD-TYPE  96 142
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(18Q11.2) MUTATED     41   67
  AMP PEAK 29(18Q11.2) WILD-TYPE   96  142
        clus
vv       AMP PEAK 29(18Q11.2) MUTATED AMP PEAK 29(18Q11.2) WILD-TYPE
  FEMALE                           41                             96
  MALE                             67                            142
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 29(18Q11.2) MUTATED                                      13
  AMP PEAK 29(18Q11.2) WILD-TYPE                                    49
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 29(18Q11.2) MUTATED                                                       53
  AMP PEAK 29(18Q11.2) WILD-TYPE                                                    101
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 29(18Q11.2) MUTATED                                                                  14
  AMP PEAK 29(18Q11.2) WILD-TYPE                                                                40
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 29(18Q11.2) MUTATED                                                 13
  AMP PEAK 29(18Q11.2) WILD-TYPE                                               32
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK 29(18Q11.2) MUTATED                                                           1
  AMP PEAK 29(18Q11.2) WILD-TYPE                                                         0
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 29(18Q11.2) MUTATED                                                          7
  AMP PEAK 29(18Q11.2) WILD-TYPE                                                       12
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 29(18Q11.2) MUTATED                                                           3
  AMP PEAK 29(18Q11.2) WILD-TYPE                                                         2
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 29(18Q11.2) MUTATED                                          3
  AMP PEAK 29(18Q11.2) WILD-TYPE                                        1
D29V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 29(18Q11.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       13
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      53
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            13
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     3
                                                                   clus
vv                                                                  AMP PEAK 29(18Q11.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       101
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              32
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V9, binary
                                cls
clus                               0   1
  AMP PEAK 29(18Q11.2) MUTATED     5 103
  AMP PEAK 29(18Q11.2) WILD-TYPE   2 236
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(18Q11.2) MUTATED      5  103
  AMP PEAK 29(18Q11.2) WILD-TYPE    2  236
     clus
vv    AMP PEAK 29(18Q11.2) MUTATED AMP PEAK 29(18Q11.2) WILD-TYPE
  NO                             5                              2
  YES                          103                            236
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 29(18Q11.2) MUTATED    81   8   6   8
  AMP PEAK 29(18Q11.2) WILD-TYPE 196   5   7  17
D29V10, multiclass
    clus
vv   AMP PEAK 29(18Q11.2) MUTATED AMP PEAK 29(18Q11.2) WILD-TYPE
  R0                           81                            196
  R1                            8                              5
  R2                            6                              7
  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"
D29V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 29(18Q11.2) MUTATED      23                         1
  AMP PEAK 29(18Q11.2) WILD-TYPE    61                         2
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 29(18Q11.2) MUTATED                                           0
  AMP PEAK 29(18Q11.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 29(18Q11.2) MUTATED      69
  AMP PEAK 29(18Q11.2) WILD-TYPE   139
D29V12, multiclass
                                           clus
vv                                          AMP PEAK 29(18Q11.2) MUTATED
  ASIAN                                                               23
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               69
                                           clus
vv                                          AMP PEAK 29(18Q11.2) WILD-TYPE
  ASIAN                                                                 61
  BLACK OR AFRICAN AMERICAN                                              2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                139
[1] 4 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(19P13.2) MUTATION ANALYSIS
D30V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 30(19P13.2) MUTATED    28   7
  AMP PEAK 30(19P13.2) WILD-TYPE 194  86
  AMP PEAK 30(19P13.2) MUTATED AMP PEAK 30(19P13.2) WILD-TYPE 
                            35                            280 
  AMP PEAK 30(19P13.2) MUTATED AMP PEAK 30(19P13.2) WILD-TYPE 
                             7                             86 
$`AMP PEAK 30(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         0.07 
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 
       13.35        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 
       22.75         3.45         6.44         5.56         8.61 

$`AMP PEAK 30(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 
        2.27         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        10.26        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-A6RS TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 
       13.08         1.41         6.87         1.81         2.53         5.56 
TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
       60.56         3.72         4.50        11.05         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-SW-A7EB TCGA-ZA-A8F6 
       57.44         8.94         5.79         4.21 

  AMP PEAK 30(19P13.2) MUTATED AMP PEAK 30(19P13.2) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 30(19P13.2) MUTATED AMP PEAK 30(19P13.2) WILD-TYPE 
                         79.07                         122.30 
  AMP PEAK 30(19P13.2) MUTATED AMP PEAK 30(19P13.2) WILD-TYPE 
                        13.180                         10.585 
[1] "0.1 - 79.1 (13.2)"  "0.1 - 122.3 (10.6)"
[1] "hr=" "1.6"
D30V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 30(19P13.2) MUTATED         0        0        2        2         5
  AMP PEAK 30(19P13.2) WILD-TYPE       2       12       36       25        27
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 30(19P13.2) MUTATED           4         1         11          6
  AMP PEAK 30(19P13.2) WILD-TYPE        43         2         50         39
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 30(19P13.2) MUTATED            2        5
  AMP PEAK 30(19P13.2) WILD-TYPE         30       26
D30V3, multiclass
            clus
vv           AMP PEAK 30(19P13.2) MUTATED AMP PEAK 30(19P13.2) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              0                             12
  STAGE IB                              2                             36
  STAGE II                              2                             25
  STAGE IIA                             5                             27
  STAGE IIB                             4                             43
  STAGE III                             1                              2
  STAGE IIIA                           11                             50
  STAGE IIIB                            6                             39
  STAGE IIIC                            2                             30
  STAGE IV                              5                             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 30(19P13.2) MUTATED     1   9  22   7
  AMP PEAK 30(19P13.2) WILD-TYPE  19  76 124  78
D30V4, multiclass
    clus
vv   AMP PEAK 30(19P13.2) MUTATED AMP PEAK 30(19P13.2) WILD-TYPE
  T1                            1                             19
  T2                            9                             76
  T3                           22                            124
  T4                            7                             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 30(19P13.2) MUTATED   11  8 10  9
  AMP PEAK 30(19P13.2) WILD-TYPE 98 84 56 58
D30V5, multiclass
    clus
vv   AMP PEAK 30(19P13.2) MUTATED AMP PEAK 30(19P13.2) WILD-TYPE
  N0                           11                             98
  N1                            8                             84
  N2                           10                             56
  N3                            9                             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
  AMP PEAK 30(19P13.2) MUTATED    33   4   2
  AMP PEAK 30(19P13.2) WILD-TYPE 275  17  15
D30V6, multiclass
    clus
vv   AMP PEAK 30(19P13.2) MUTATED AMP PEAK 30(19P13.2) WILD-TYPE
  M0                           33                            275
  M1                            4                             17
  MX                            2                             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"
D30V7, binary
                                cls
clus                               0   1
  AMP PEAK 30(19P13.2) MUTATED    17  22
  AMP PEAK 30(19P13.2) WILD-TYPE 120 187
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 30(19P13.2) MUTATED     17   22
  AMP PEAK 30(19P13.2) WILD-TYPE  120  187
        clus
vv       AMP PEAK 30(19P13.2) MUTATED AMP PEAK 30(19P13.2) WILD-TYPE
  FEMALE                           17                            120
  MALE                             22                            187
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 30(19P13.2) MUTATED                                       7
  AMP PEAK 30(19P13.2) WILD-TYPE                                    55
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 30(19P13.2) MUTATED                                                       16
  AMP PEAK 30(19P13.2) WILD-TYPE                                                    138
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 30(19P13.2) MUTATED                                                                   6
  AMP PEAK 30(19P13.2) WILD-TYPE                                                                48
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 30(19P13.2) MUTATED                                                  7
  AMP PEAK 30(19P13.2) WILD-TYPE                                               38
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK 30(19P13.2) MUTATED                                                           0
  AMP PEAK 30(19P13.2) WILD-TYPE                                                         1
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 30(19P13.2) MUTATED                                                          1
  AMP PEAK 30(19P13.2) WILD-TYPE                                                       18
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 30(19P13.2) MUTATED                                                           0
  AMP PEAK 30(19P13.2) WILD-TYPE                                                         5
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 30(19P13.2) MUTATED                                          2
  AMP PEAK 30(19P13.2) WILD-TYPE                                        2
D30V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 30(19P13.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      16
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             7
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
                                                                   clus
vv                                                                  AMP PEAK 30(19P13.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         55
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       138
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             48
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              38
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V9, binary
                                cls
clus                               0   1
  AMP PEAK 30(19P13.2) MUTATED     0  39
  AMP PEAK 30(19P13.2) WILD-TYPE   7 300
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 30(19P13.2) MUTATED      0   39
  AMP PEAK 30(19P13.2) WILD-TYPE    7  300
     clus
vv    AMP PEAK 30(19P13.2) MUTATED AMP PEAK 30(19P13.2) WILD-TYPE
  NO                             0                              7
  YES                           39                            300
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 30(19P13.2) MUTATED    30   2   3   2
  AMP PEAK 30(19P13.2) WILD-TYPE 247  11  10  23
D30V10, multiclass
    clus
vv   AMP PEAK 30(19P13.2) MUTATED AMP PEAK 30(19P13.2) WILD-TYPE
  R0                           30                            247
  R1                            2                             11
  R2                            3                             10
  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"
D30V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 30(19P13.2) MUTATED       9                         0
  AMP PEAK 30(19P13.2) WILD-TYPE    75                         3
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 30(19P13.2) MUTATED                                           1
  AMP PEAK 30(19P13.2) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 30(19P13.2) MUTATED      25
  AMP PEAK 30(19P13.2) WILD-TYPE   183
D30V12, multiclass
                                           clus
vv                                          AMP PEAK 30(19P13.2) MUTATED
  ASIAN                                                                9
  BLACK OR AFRICAN AMERICAN                                            0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               25
                                           clus
vv                                          AMP PEAK 30(19P13.2) WILD-TYPE
  ASIAN                                                                 75
  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(31) Variable = AMP PEAK 31(19Q12) MUTATION ANALYSIS
D31V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 31(19Q12) MUTATED    67  24
  AMP PEAK 31(19Q12) WILD-TYPE 155  69
  AMP PEAK 31(19Q12) MUTATED AMP PEAK 31(19Q12) WILD-TYPE 
                          91                          224 
  AMP PEAK 31(19Q12) MUTATED AMP PEAK 31(19Q12) WILD-TYPE 
                          24                           69 
$`AMP PEAK 31(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         0.07         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        10.26        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-SW-A7EB 
        5.79 

$`AMP PEAK 31(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         2.27         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        13.35 
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-A6RS TCGA-IN-A7NT TCGA-IN-A7NU 
        3.39         5.36        13.08         6.87         5.56         1.81 
TCGA-IP-7968 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MV 
        2.53         3.72         4.50        11.05        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-ZA-A8F6 
        8.94         4.21 

  AMP PEAK 31(19Q12) MUTATED AMP PEAK 31(19Q12) WILD-TYPE 
                        0.07                         0.07 
  AMP PEAK 31(19Q12) MUTATED AMP PEAK 31(19Q12) WILD-TYPE 
                       72.23                       122.30 
  AMP PEAK 31(19Q12) MUTATED AMP PEAK 31(19Q12) WILD-TYPE 
                      10.550                       11.275 
[1] "0.1 - 72.2 (10.6)"  "0.1 - 122.3 (11.3)"
[1] "hr=" "1.1"
D31V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 31(19Q12) MUTATED         0        4       11        8        10
  AMP PEAK 31(19Q12) WILD-TYPE       2        8       27       19        22
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 31(19Q12) MUTATED          15         1         20         11
  AMP PEAK 31(19Q12) WILD-TYPE        32         2         41         34
                              vv
clus                           STAGE IIIC STAGE IV
  AMP PEAK 31(19Q12) MUTATED            6       12
  AMP PEAK 31(19Q12) WILD-TYPE         26       19
D31V3, multiclass
            clus
vv           AMP PEAK 31(19Q12) MUTATED AMP PEAK 31(19Q12) WILD-TYPE
  STAGE I                             0                            2
  STAGE IA                            4                            8
  STAGE IB                           11                           27
  STAGE II                            8                           19
  STAGE IIA                          10                           22
  STAGE IIB                          15                           32
  STAGE III                           1                            2
  STAGE IIIA                         20                           41
  STAGE IIIB                         11                           34
  STAGE IIIC                          6                           26
  STAGE IV                           12                           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 31(19Q12) MUTATED    6 23 53 18
  AMP PEAK 31(19Q12) WILD-TYPE 14 62 93 67
D31V4, multiclass
    clus
vv   AMP PEAK 31(19Q12) MUTATED AMP PEAK 31(19Q12) WILD-TYPE
  T1                          6                           14
  T2                         23                           62
  T3                         53                           93
  T4                         18                           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
  AMP PEAK 31(19Q12) MUTATED   32 29 16 22
  AMP PEAK 31(19Q12) WILD-TYPE 77 63 50 45
D31V5, multiclass
    clus
vv   AMP PEAK 31(19Q12) MUTATED AMP PEAK 31(19Q12) WILD-TYPE
  N0                         32                           77
  N1                         29                           63
  N2                         16                           50
  N3                         22                           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 31(19Q12) MUTATED    88   8   7
  AMP PEAK 31(19Q12) WILD-TYPE 220  13  10
D31V6, multiclass
    clus
vv   AMP PEAK 31(19Q12) MUTATED AMP PEAK 31(19Q12) WILD-TYPE
  M0                         88                          220
  M1                          8                           13
  MX                          7                           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"
D31V7, binary
                              cls
clus                             0   1
  AMP PEAK 31(19Q12) MUTATED    40  63
  AMP PEAK 31(19Q12) WILD-TYPE  97 146
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 31(19Q12) MUTATED     40   63
  AMP PEAK 31(19Q12) WILD-TYPE   97  146
        clus
vv       AMP PEAK 31(19Q12) MUTATED AMP PEAK 31(19Q12) WILD-TYPE
  FEMALE                         40                           97
  MALE                           63                          146
[1] 2 2
[1] FALSE
                              vv
clus                           STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 31(19Q12) MUTATED                                      15
  AMP PEAK 31(19Q12) WILD-TYPE                                    47
                              vv
clus                           STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 31(19Q12) MUTATED                                                       46
  AMP PEAK 31(19Q12) WILD-TYPE                                                    108
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 31(19Q12) MUTATED                                                                  15
  AMP PEAK 31(19Q12) WILD-TYPE                                                                39
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 31(19Q12) MUTATED                                                 14
  AMP PEAK 31(19Q12) WILD-TYPE                                               31
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK 31(19Q12) MUTATED                                                           1
  AMP PEAK 31(19Q12) WILD-TYPE                                                         0
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 31(19Q12) MUTATED                                                          6
  AMP PEAK 31(19Q12) WILD-TYPE                                                       13
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 31(19Q12) MUTATED                                                           3
  AMP PEAK 31(19Q12) WILD-TYPE                                                         2
                              vv
clus                           STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 31(19Q12) MUTATED                                          2
  AMP PEAK 31(19Q12) WILD-TYPE                                        2
D31V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 31(19Q12) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    46
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         15
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                          14
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                  1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                  3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   2
                                                                   clus
vv                                                                  AMP PEAK 31(19Q12) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     108
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            31
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V9, binary
                              cls
clus                             0   1
  AMP PEAK 31(19Q12) MUTATED     5  98
  AMP PEAK 31(19Q12) WILD-TYPE   2 241
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 31(19Q12) MUTATED      5   98
  AMP PEAK 31(19Q12) WILD-TYPE    2  241
     clus
vv    AMP PEAK 31(19Q12) MUTATED AMP PEAK 31(19Q12) WILD-TYPE
  NO                           5                            2
  YES                         98                          241
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 31(19Q12) MUTATED    77   5   6   6
  AMP PEAK 31(19Q12) WILD-TYPE 200   8   7  19
D31V10, multiclass
    clus
vv   AMP PEAK 31(19Q12) MUTATED AMP PEAK 31(19Q12) WILD-TYPE
  R0                         77                          200
  R1                          5                            8
  R2                          6                            7
  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"
D31V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 31(19Q12) MUTATED      29                         2
  AMP PEAK 31(19Q12) WILD-TYPE    55                         1
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 31(19Q12) MUTATED                                           1    58
  AMP PEAK 31(19Q12) WILD-TYPE                                         0   150
D31V12, multiclass
                                           clus
vv                                          AMP PEAK 31(19Q12) MUTATED
  ASIAN                                                             29
  BLACK OR AFRICAN AMERICAN                                          2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                             58
                                           clus
vv                                          AMP PEAK 31(19Q12) WILD-TYPE
  ASIAN                                                               55
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  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(32) Variable = AMP PEAK 32(20Q13.2) MUTATION ANALYSIS
D32V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 32(20Q13.2) MUTATED   147  64
  AMP PEAK 32(20Q13.2) WILD-TYPE  75  29
  AMP PEAK 32(20Q13.2) MUTATED AMP PEAK 32(20Q13.2) WILD-TYPE 
                           211                            104 
  AMP PEAK 32(20Q13.2) MUTATED AMP PEAK 32(20Q13.2) WILD-TYPE 
                            64                             29 
$`AMP PEAK 32(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         2.27         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         0.07         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        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 
       17.19        10.26        15.22        15.98        12.79        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8576 TCGA-D7-8578 
       12.33        24.72        16.80        19.50         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-A6RS 
        3.45         3.39        18.38         5.19         1.41         6.87 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-RD-A7BT 
        5.56         1.81         2.53         5.56        60.56         8.61 
TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-SW-A7EB 
       16.67        37.91       115.69        57.44         8.94         5.79 
TCGA-ZA-A8F6 
        4.21 

$`AMP PEAK 32(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         4.50        11.05         4.67       122.30        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 
      116.38        71.38 

  AMP PEAK 32(20Q13.2) MUTATED AMP PEAK 32(20Q13.2) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 32(20Q13.2) MUTATED AMP PEAK 32(20Q13.2) WILD-TYPE 
                        115.69                         122.30 
  AMP PEAK 32(20Q13.2) MUTATED AMP PEAK 32(20Q13.2) WILD-TYPE 
                        10.620                         11.425 
[1] "0.1 - 115.7 (10.6)" "0.1 - 122.3 (11.4)"
[1] "hr=" "1.2"
D32V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 32(20Q13.2) MUTATED         1       10       22       16        20
  AMP PEAK 32(20Q13.2) WILD-TYPE       1        2       16       11        12
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 32(20Q13.2) MUTATED          35         3         45         29
  AMP PEAK 32(20Q13.2) WILD-TYPE        12         0         16         16
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 32(20Q13.2) MUTATED           17       19
  AMP PEAK 32(20Q13.2) WILD-TYPE         15       12
D32V3, multiclass
            clus
vv           AMP PEAK 32(20Q13.2) MUTATED AMP PEAK 32(20Q13.2) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                             10                              2
  STAGE IB                             22                             16
  STAGE II                             16                             11
  STAGE IIA                            20                             12
  STAGE IIB                            35                             12
  STAGE III                             3                              0
  STAGE IIIA                           45                             16
  STAGE IIIB                           29                             16
  STAGE IIIC                           17                             15
  STAGE IV                             19                             12
[1] 11  2
[1] TRUE
[1] "dimension of 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(20Q13.2) MUTATED    12  59 101  49
  AMP PEAK 32(20Q13.2) WILD-TYPE   8  26  45  36
D32V4, multiclass
    clus
vv   AMP PEAK 32(20Q13.2) MUTATED AMP PEAK 32(20Q13.2) WILD-TYPE
  T1                           12                              8
  T2                           59                             26
  T3                          101                             45
  T4                           49                             36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 32(20Q13.2) MUTATED   67 68 46 38
  AMP PEAK 32(20Q13.2) WILD-TYPE 42 24 20 29
D32V5, multiclass
    clus
vv   AMP PEAK 32(20Q13.2) MUTATED AMP PEAK 32(20Q13.2) WILD-TYPE
  N0                           67                             42
  N1                           68                             24
  N2                           46                             20
  N3                           38                             29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  AMP PEAK 32(20Q13.2) MUTATED   201  12  14
  AMP PEAK 32(20Q13.2) WILD-TYPE 107   9   3
D32V6, multiclass
    clus
vv   AMP PEAK 32(20Q13.2) MUTATED AMP PEAK 32(20Q13.2) WILD-TYPE
  M0                          201                            107
  M1                           12                              9
  MX                           14                              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"
D32V7, binary
                                cls
clus                               0   1
  AMP PEAK 32(20Q13.2) MUTATED    77 150
  AMP PEAK 32(20Q13.2) WILD-TYPE  60  59
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 32(20Q13.2) MUTATED     77  150
  AMP PEAK 32(20Q13.2) WILD-TYPE   60   59
        clus
vv       AMP PEAK 32(20Q13.2) MUTATED AMP PEAK 32(20Q13.2) WILD-TYPE
  FEMALE                           77                             60
  MALE                            150                             59
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 32(20Q13.2) MUTATED                                      28
  AMP PEAK 32(20Q13.2) WILD-TYPE                                    34
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 32(20Q13.2) MUTATED                                                       96
  AMP PEAK 32(20Q13.2) WILD-TYPE                                                     58
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 32(20Q13.2) MUTATED                                                                  45
  AMP PEAK 32(20Q13.2) WILD-TYPE                                                                 9
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 32(20Q13.2) MUTATED                                                 36
  AMP PEAK 32(20Q13.2) WILD-TYPE                                                9
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK 32(20Q13.2) MUTATED                                                           1
  AMP PEAK 32(20Q13.2) WILD-TYPE                                                         0
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 32(20Q13.2) MUTATED                                                         12
  AMP PEAK 32(20Q13.2) WILD-TYPE                                                        7
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 32(20Q13.2) MUTATED                                                           4
  AMP PEAK 32(20Q13.2) WILD-TYPE                                                         1
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 32(20Q13.2) MUTATED                                          3
  AMP PEAK 32(20Q13.2) WILD-TYPE                                        1
D32V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 32(20Q13.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       28
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      96
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           45
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            36
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     3
                                                                   clus
vv                                                                  AMP PEAK 32(20Q13.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         34
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        58
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              9
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               9
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V9, binary
                                cls
clus                               0   1
  AMP PEAK 32(20Q13.2) MUTATED     5 222
  AMP PEAK 32(20Q13.2) WILD-TYPE   2 117
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 32(20Q13.2) MUTATED      5  222
  AMP PEAK 32(20Q13.2) WILD-TYPE    2  117
     clus
vv    AMP PEAK 32(20Q13.2) MUTATED AMP PEAK 32(20Q13.2) WILD-TYPE
  NO                             5                              2
  YES                          222                            117
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 32(20Q13.2) MUTATED   186   8   8  14
  AMP PEAK 32(20Q13.2) WILD-TYPE  91   5   5  11
D32V10, multiclass
    clus
vv   AMP PEAK 32(20Q13.2) MUTATED AMP PEAK 32(20Q13.2) WILD-TYPE
  R0                          186                             91
  R1                            8                              5
  R2                            8                              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"
D32V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 32(20Q13.2) MUTATED      57                         2
  AMP PEAK 32(20Q13.2) WILD-TYPE    27                         1
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 32(20Q13.2) MUTATED                                           1
  AMP PEAK 32(20Q13.2) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 32(20Q13.2) MUTATED     131
  AMP PEAK 32(20Q13.2) WILD-TYPE    77
D32V12, multiclass
                                           clus
vv                                          AMP PEAK 32(20Q13.2) MUTATED
  ASIAN                                                               57
  BLACK OR AFRICAN AMERICAN                                            2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              131
                                           clus
vv                                          AMP PEAK 32(20Q13.2) WILD-TYPE
  ASIAN                                                                 27
  BLACK OR AFRICAN AMERICAN                                              1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                 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"

Clustering(33) Variable = AMP PEAK 33(XQ27.3) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 33(XQ27.3) MUTATED    39  18
  AMP PEAK 33(XQ27.3) WILD-TYPE 183  75
  AMP PEAK 33(XQ27.3) MUTATED AMP PEAK 33(XQ27.3) WILD-TYPE 
                           57                           258 
  AMP PEAK 33(XQ27.3) MUTATED AMP PEAK 33(XQ27.3) WILD-TYPE 
                           18                            75 
$`AMP PEAK 33(XQ27.3) MUTATED`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-6458 TCGA-BR-6801 TCGA-BR-7717 
       11.70         6.61        18.35         7.00        21.11         0.69 
TCGA-BR-8059 TCGA-BR-8362 TCGA-BR-8370 TCGA-BR-8486 TCGA-BR-8677 TCGA-BR-8680 
        0.82         0.36         3.32        20.22         0.49        15.81 
TCGA-BR-8683 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J2 TCGA-BR-A4QI 
        0.59         1.15         2.27        12.89        14.17        13.64 
TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-A4MG TCGA-CG-4300 TCGA-CG-4437 TCGA-CG-4438 
        0.07         0.07         0.07        20.02         8.05        54.08 
TCGA-CG-4460 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5720 TCGA-CG-5727 TCGA-CG-5734 
       21.99         7.07        12.00         0.99        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-HU-8244 TCGA-HU-8604 TCGA-HU-A4G2 
        7.79        72.23         0.39        14.27        12.10        24.30 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4H5 TCGA-IN-7808 
       12.30        24.20        22.75        25.81        12.30         3.45 
TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RP 
        3.39         5.19         6.44 

$`AMP PEAK 33(XQ27.3) 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-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-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-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-7901 
       15.42        28.01         0.16        18.54        12.43         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 
        0.69        12.76        18.71        17.49         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-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-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.26        22.19         2.96         0.95        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-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-8678 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
        7.53        11.54        16.44        15.68         0.62        10.68 
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-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.79         0.72         0.53        12.82         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL 
       13.51         0.46        20.65        20.42         1.15        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.10         0.10         0.13         0.13         0.10         0.07 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        0.13         0.13         0.13         0.13         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-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-4465 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97        22.98        30.97         6.97         1.02 
TCGA-CG-5719 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         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 
       13.35        10.26        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-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-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
        5.92        12.59        14.17        11.41        10.62         0.76 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        5.59        11.84         3.25        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        19.36        17.69         9.67         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ 
        8.81        27.42        21.21        18.81        18.38         5.36 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 
       13.08         1.41         6.87         5.56         1.81         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BT 
        5.56        60.56         3.72         4.50        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-SW-A7EB TCGA-ZA-A8F6 
      116.38        71.38        57.44         8.94         5.79         4.21 

  AMP PEAK 33(XQ27.3) MUTATED AMP PEAK 33(XQ27.3) WILD-TYPE 
                         0.07                          0.07 
  AMP PEAK 33(XQ27.3) MUTATED AMP PEAK 33(XQ27.3) WILD-TYPE 
                        79.07                        122.30 
  AMP PEAK 33(XQ27.3) MUTATED AMP PEAK 33(XQ27.3) WILD-TYPE 
                       11.930                        10.585 
[1] "0.1 - 79.1 (11.9)"  "0.1 - 122.3 (10.6)"
[1] "hr=" "1"  
D33V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 33(XQ27.3) MUTATED         1        5        8        4         5
  AMP PEAK 33(XQ27.3) WILD-TYPE       1        7       30       23        27
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 33(XQ27.3) MUTATED          10         2          9          6
  AMP PEAK 33(XQ27.3) WILD-TYPE        37         1         52         39
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 33(XQ27.3) MUTATED            2        9
  AMP PEAK 33(XQ27.3) WILD-TYPE         30       22
D33V3, multiclass
            clus
vv           AMP PEAK 33(XQ27.3) MUTATED AMP PEAK 33(XQ27.3) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             5                             7
  STAGE IB                             8                            30
  STAGE II                             4                            23
  STAGE IIA                            5                            27
  STAGE IIB                           10                            37
  STAGE III                            2                             1
  STAGE IIIA                           9                            52
  STAGE IIIB                           6                            39
  STAGE IIIC                           2                            30
  STAGE IV                             9                            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 33(XQ27.3) MUTATED     6  18  25  13
  AMP PEAK 33(XQ27.3) WILD-TYPE  14  67 121  72
D33V4, multiclass
    clus
vv   AMP PEAK 33(XQ27.3) MUTATED AMP PEAK 33(XQ27.3) WILD-TYPE
  T1                           6                            14
  T2                          18                            67
  T3                          25                           121
  T4                          13                            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
  AMP PEAK 33(XQ27.3) MUTATED   23 18 13  9
  AMP PEAK 33(XQ27.3) WILD-TYPE 86 74 53 58
D33V5, multiclass
    clus
vv   AMP PEAK 33(XQ27.3) MUTATED AMP PEAK 33(XQ27.3) WILD-TYPE
  N0                          23                            86
  N1                          18                            74
  N2                          13                            53
  N3                           9                            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
  AMP PEAK 33(XQ27.3) MUTATED    58   4   2
  AMP PEAK 33(XQ27.3) WILD-TYPE 250  17  15
D33V6, multiclass
    clus
vv   AMP PEAK 33(XQ27.3) MUTATED AMP PEAK 33(XQ27.3) WILD-TYPE
  M0                          58                           250
  M1                           4                            17
  MX                           2                            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"
D33V7, binary
                               cls
clus                              0   1
  AMP PEAK 33(XQ27.3) MUTATED    24  40
  AMP PEAK 33(XQ27.3) WILD-TYPE 113 169
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 33(XQ27.3) MUTATED     24   40
  AMP PEAK 33(XQ27.3) WILD-TYPE  113  169
        clus
vv       AMP PEAK 33(XQ27.3) MUTATED AMP PEAK 33(XQ27.3) WILD-TYPE
  FEMALE                          24                           113
  MALE                            40                           169
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 33(XQ27.3) MUTATED                                       7
  AMP PEAK 33(XQ27.3) WILD-TYPE                                    55
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 33(XQ27.3) MUTATED                                                       27
  AMP PEAK 33(XQ27.3) WILD-TYPE                                                    127
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 33(XQ27.3) MUTATED                                                                  12
  AMP PEAK 33(XQ27.3) WILD-TYPE                                                                42
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 33(XQ27.3) MUTATED                                                 13
  AMP PEAK 33(XQ27.3) WILD-TYPE                                               32
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  AMP PEAK 33(XQ27.3) MUTATED                                                           0
  AMP PEAK 33(XQ27.3) WILD-TYPE                                                         1
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 33(XQ27.3) MUTATED                                                          2
  AMP PEAK 33(XQ27.3) WILD-TYPE                                                       17
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 33(XQ27.3) MUTATED                                                           2
  AMP PEAK 33(XQ27.3) WILD-TYPE                                                         3
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 33(XQ27.3) MUTATED                                          0
  AMP PEAK 33(XQ27.3) WILD-TYPE                                        4
D33V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 33(XQ27.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     27
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          12
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           13
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    0
                                                                   clus
vv                                                                  AMP PEAK 33(XQ27.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        55
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            42
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             32
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      4
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V9, binary
                               cls
clus                              0   1
  AMP PEAK 33(XQ27.3) MUTATED     1  63
  AMP PEAK 33(XQ27.3) WILD-TYPE   6 276
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 33(XQ27.3) MUTATED      1   63
  AMP PEAK 33(XQ27.3) WILD-TYPE    6  276
     clus
vv    AMP PEAK 33(XQ27.3) MUTATED AMP PEAK 33(XQ27.3) WILD-TYPE
  NO                            1                             6
  YES                          63                           276
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 33(XQ27.3) MUTATED    51   3   2   5
  AMP PEAK 33(XQ27.3) WILD-TYPE 226  10  11  20
D33V10, multiclass
    clus
vv   AMP PEAK 33(XQ27.3) MUTATED AMP PEAK 33(XQ27.3) WILD-TYPE
  R0                          51                           226
  R1                           3                            10
  R2                           2                            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"
D33V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 33(XQ27.3) MUTATED      16                         2
  AMP PEAK 33(XQ27.3) WILD-TYPE    68                         1
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 33(XQ27.3) MUTATED                                           0    35
  AMP PEAK 33(XQ27.3) WILD-TYPE                                         1   173
D33V12, multiclass
                                           clus
vv                                          AMP PEAK 33(XQ27.3) MUTATED
  ASIAN                                                              16
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              35
                                           clus
vv                                          AMP PEAK 33(XQ27.3) WILD-TYPE
  ASIAN                                                                68
  BLACK OR AFRICAN AMERICAN                                             1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               173
[1] 4 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 = DEL PEAK  1(1P36.11) MUTATION ANALYSIS
D34V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.11) MUTATED    63  23
  DEL PEAK  1(1P36.11) WILD-TYPE 159  70
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            86                            229 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            23                             70 
$`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         2.27        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         0.07         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 
       10.26        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-RD-A7BT 
       12.95        17.69        12.30        27.42        60.56         8.61 
TCGA-RD-A7C1 TCGA-RD-A8MV 
       16.67       122.30 

$`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        13.35        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-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-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 
        3.72         4.50        11.05         4.67        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-SW-A7EB 
      115.69       116.38        71.38        57.44         8.94         5.79 
TCGA-ZA-A8F6 
        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 
                          9.39                          11.44 
[1] "0.1 - 122.3 (9.4)"  "0.1 - 116.4 (11.4)"
[1] "hr=" "1"  
D34V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  1(1P36.11) MUTATED         0        1       12       10        11
  DEL PEAK  1(1P36.11) WILD-TYPE       2       11       26       17        21
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  1(1P36.11) MUTATED          11         0         20         12
  DEL PEAK  1(1P36.11) WILD-TYPE        36         3         41         33
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK  1(1P36.11) MUTATED            2       11
  DEL PEAK  1(1P36.11) WILD-TYPE         30       20
D34V3, multiclass
            clus
vv           DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              1                             11
  STAGE IB                             12                             26
  STAGE II                             10                             17
  STAGE IIA                            11                             21
  STAGE IIB                            11                             36
  STAGE III                             0                              3
  STAGE IIIA                           20                             41
  STAGE IIIB                           12                             33
  STAGE IIIC                            2                             30
  STAGE IV                             11                             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  1(1P36.11) MUTATED     2  27  45  18
  DEL PEAK  1(1P36.11) WILD-TYPE  18  58 101  67
D34V4, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  T1                            2                             18
  T2                           27                             58
  T3                           45                            101
  T4                           18                             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  1(1P36.11) MUTATED   31 27 19 14
  DEL PEAK  1(1P36.11) WILD-TYPE 78 65 47 53
D34V5, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  N0                           31                             78
  N1                           27                             65
  N2                           19                             47
  N3                           14                             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
  DEL PEAK  1(1P36.11) MUTATED    84   7   5
  DEL PEAK  1(1P36.11) WILD-TYPE 224  14  12
D34V6, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  M0                           84                            224
  M1                            7                             14
  MX                            5                             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"
D34V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED    35  61
  DEL PEAK  1(1P36.11) WILD-TYPE 102 148
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     35   61
  DEL PEAK  1(1P36.11) WILD-TYPE  102  148
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  FEMALE                           35                            102
  MALE                             61                            148
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK  1(1P36.11) MUTATED                                       9
  DEL PEAK  1(1P36.11) WILD-TYPE                                    53
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  1(1P36.11) MUTATED                                                       39
  DEL PEAK  1(1P36.11) WILD-TYPE                                                    115
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  1(1P36.11) MUTATED                                                                  20
  DEL PEAK  1(1P36.11) WILD-TYPE                                                                34
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  1(1P36.11) MUTATED                                                 19
  DEL PEAK  1(1P36.11) WILD-TYPE                                               26
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK  1(1P36.11) MUTATED                                                           1
  DEL PEAK  1(1P36.11) WILD-TYPE                                                         0
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK  1(1P36.11) MUTATED                                                          6
  DEL PEAK  1(1P36.11) WILD-TYPE                                                       13
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK  1(1P36.11) MUTATED                                                           1
  DEL PEAK  1(1P36.11) WILD-TYPE                                                         4
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK  1(1P36.11) MUTATED                                          1
  DEL PEAK  1(1P36.11) WILD-TYPE                                        3
D34V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  1(1P36.11) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      39
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           20
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            19
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     1
                                                                   clus
vv                                                                  DEL PEAK  1(1P36.11) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         53
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       115
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             34
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              26
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V9, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED     4  92
  DEL PEAK  1(1P36.11) WILD-TYPE   3 247
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      4   92
  DEL PEAK  1(1P36.11) WILD-TYPE    3  247
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  NO                             4                              3
  YES                           92                            247
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  1(1P36.11) MUTATED    69   6   5   9
  DEL PEAK  1(1P36.11) WILD-TYPE 208   7   8  16
D34V10, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  R0                           69                            208
  R1                            6                              7
  R2                            5                              8
  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"
D34V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  1(1P36.11) MUTATED      26                         0
  DEL PEAK  1(1P36.11) WILD-TYPE    58                         3
                                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      51
  DEL PEAK  1(1P36.11) WILD-TYPE   157
D34V12, multiclass
                                           clus
vv                                          DEL PEAK  1(1P36.11) MUTATED
  ASIAN                                                               26
  BLACK OR AFRICAN AMERICAN                                            0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               51
                                           clus
vv                                          DEL PEAK  1(1P36.11) WILD-TYPE
  ASIAN                                                                 58
  BLACK OR AFRICAN AMERICAN                                              3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                157
[1] 4 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 = DEL PEAK  2(1P13.2) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P13.2) MUTATED    48  13
  DEL PEAK  2(1P13.2) WILD-TYPE 174  80
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           61                           254 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           13                            80 
$`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 
        2.27        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 
        0.07         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        10.26        15.22        12.79 
TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 
       24.72        19.50        11.31        15.65         7.40         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-FP-7829 TCGA-FP-A4BF TCGA-HU-8238 TCGA-HU-8249 
        7.79        16.24        19.53         1.55         1.51        14.17 
TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4HD TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IP-7968 
       12.10        22.75        27.42         5.19         1.41         2.53 
TCGA-RD-A7BT 
        8.61 

$`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 
       13.35        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-A6EZ TCGA-D7-A6F0 TCGA-D7-A748 TCGA-D7-A74B 
       11.24        11.44         9.76         2.96         4.34         7.13 
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-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 
        0.56         0.23        18.08        26.47         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-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-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-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-7806 TCGA-IN-7808 
       12.30         9.67         8.88         8.81        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP 
       18.81         3.39        18.38         5.36        13.08         6.44 
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 
        4.50        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-SW-A7EB TCGA-ZA-A8F6 
        5.79         4.21 

  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 
                         9.21                         11.36 
[1] "0.1 - 54.1 (9.2)"   "0.1 - 122.3 (11.4)"
[1] "hr=" "1.3"
D35V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  2(1P13.2) MUTATED         0        2        6        7         8
  DEL PEAK  2(1P13.2) WILD-TYPE       2       10       32       20        24
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  2(1P13.2) MUTATED           9         0         14          8
  DEL PEAK  2(1P13.2) WILD-TYPE        38         3         47         37
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  2(1P13.2) MUTATED            2        7
  DEL PEAK  2(1P13.2) WILD-TYPE         30       24
D35V3, multiclass
            clus
vv           DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             2                            10
  STAGE IB                             6                            32
  STAGE II                             7                            20
  STAGE IIA                            8                            24
  STAGE IIB                            9                            38
  STAGE III                            0                             3
  STAGE IIIA                          14                            47
  STAGE IIIB                           8                            37
  STAGE IIIC                           2                            30
  STAGE IV                             7                            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  2(1P13.2) MUTATED     2  15  34  13
  DEL PEAK  2(1P13.2) WILD-TYPE  18  70 112  72
D35V4, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  T1                           2                            18
  T2                          15                            70
  T3                          34                           112
  T4                          13                            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  2(1P13.2) MUTATED   22 18 15  8
  DEL PEAK  2(1P13.2) WILD-TYPE 87 74 51 59
D35V5, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  N0                          22                            87
  N1                          18                            74
  N2                          15                            51
  N3                           8                            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  2(1P13.2) MUTATED    58   5   3
  DEL PEAK  2(1P13.2) WILD-TYPE 250  16  14
D35V6, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  M0                          58                           250
  M1                           5                            16
  MX                           3                            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"
D35V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED    24  42
  DEL PEAK  2(1P13.2) WILD-TYPE 113 167
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     24   42
  DEL PEAK  2(1P13.2) WILD-TYPE  113  167
        clus
vv       DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  FEMALE                          24                           113
  MALE                            42                           167
[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                                    56
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  2(1P13.2) MUTATED                                                       28
  DEL PEAK  2(1P13.2) WILD-TYPE                                                    126
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  2(1P13.2) MUTATED                                                                  12
  DEL PEAK  2(1P13.2) WILD-TYPE                                                                42
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  2(1P13.2) MUTATED                                                 14
  DEL PEAK  2(1P13.2) WILD-TYPE                                               31
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK  2(1P13.2) MUTATED                                                           1
  DEL PEAK  2(1P13.2) WILD-TYPE                                                         0
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK  2(1P13.2) MUTATED                                                          3
  DEL PEAK  2(1P13.2) WILD-TYPE                                                       16
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK  2(1P13.2) MUTATED                                                           0
  DEL PEAK  2(1P13.2) WILD-TYPE                                                         5
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK  2(1P13.2) MUTATED                                          1
  DEL PEAK  2(1P13.2) WILD-TYPE                                        3
D35V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  2(1P13.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     28
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          12
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           14
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    1
                                                                   clus
vv                                                                  DEL PEAK  2(1P13.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            42
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             31
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V9, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED     2  64
  DEL PEAK  2(1P13.2) WILD-TYPE   5 275
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      2   64
  DEL PEAK  2(1P13.2) WILD-TYPE    5  275
     clus
vv    DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  NO                            2                             5
  YES                          64                           275
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  2(1P13.2) MUTATED    49   3   5   3
  DEL PEAK  2(1P13.2) WILD-TYPE 228  10   8  22
D35V10, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  R0                          49                           228
  R1                           3                            10
  R2                           5                             8
  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"
D35V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  2(1P13.2) MUTATED      18                         0
  DEL PEAK  2(1P13.2) WILD-TYPE    66                         3
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  2(1P13.2) MUTATED                                           1    39
  DEL PEAK  2(1P13.2) WILD-TYPE                                         0   169
D35V12, multiclass
                                           clus
vv                                          DEL PEAK  2(1P13.2) MUTATED
  ASIAN                                                              18
  BLACK OR AFRICAN AMERICAN                                           0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              39
                                           clus
vv                                          DEL PEAK  2(1P13.2) WILD-TYPE
  ASIAN                                                                66
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               169
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = DEL PEAK  3(1Q25.1) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(1Q25.1) MUTATED    10   2
  DEL PEAK  3(1Q25.1) WILD-TYPE 212  91
  DEL PEAK  3(1Q25.1) MUTATED DEL PEAK  3(1Q25.1) WILD-TYPE 
                           12                           303 
  DEL PEAK  3(1Q25.1) MUTATED DEL PEAK  3(1Q25.1) WILD-TYPE 
                            2                            91 
$`DEL PEAK  3(1Q25.1) MUTATED`
TCGA-BR-7704 TCGA-BR-A4PD TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-8529 TCGA-CD-A48A 
       35.24        20.65         3.25         0.30         0.13         0.13 
TCGA-CG-4475 TCGA-CG-5724 TCGA-HU-8604 TCGA-HU-A4H5 TCGA-IN-8663 TCGA-IP-7968 
       22.98        12.03        12.10        12.30         3.39         2.53 

$`DEL PEAK  3(1Q25.1) 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-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-7715 TCGA-BR-7716 
       12.82         9.21        24.76        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.69         0.16        18.54        12.43         0.95         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       12.76        18.71        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-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-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         2.27         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-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.15        13.18         0.07         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-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C 
        0.13         0.10         0.07         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-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-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
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-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 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 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-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-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-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-7808 TCGA-IN-8462 
        8.88         8.81        27.42        21.21         3.45        18.81 
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-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-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        4.50        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-SW-A7EB TCGA-ZA-A8F6 
        8.94         5.79         4.21 

  DEL PEAK  3(1Q25.1) MUTATED DEL PEAK  3(1Q25.1) WILD-TYPE 
                         0.13                          0.07 
  DEL PEAK  3(1Q25.1) MUTATED DEL PEAK  3(1Q25.1) WILD-TYPE 
                        35.24                        122.30 
  DEL PEAK  3(1Q25.1) MUTATED DEL PEAK  3(1Q25.1) WILD-TYPE 
                         7.71                         11.05 
[1] "0.1 - 35.2 (7.7)"   "0.1 - 122.3 (11.1)"
[1] "hr=" "1.5"
D36V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  3(1Q25.1) MUTATED         0        0        1        3         2
  DEL PEAK  3(1Q25.1) WILD-TYPE       2       12       37       24        30
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  3(1Q25.1) MUTATED           3         0          0          1
  DEL PEAK  3(1Q25.1) WILD-TYPE        44         3         61         44
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  3(1Q25.1) MUTATED            0        2
  DEL PEAK  3(1Q25.1) WILD-TYPE         32       29
D36V3, multiclass
            clus
vv           DEL PEAK  3(1Q25.1) MUTATED DEL PEAK  3(1Q25.1) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             0                            12
  STAGE IB                             1                            37
  STAGE II                             3                            24
  STAGE IIA                            2                            30
  STAGE IIB                            3                            44
  STAGE III                            0                             3
  STAGE IIIA                           0                            61
  STAGE IIIB                           1                            44
  STAGE IIIC                           0                            32
  STAGE IV                             2                            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  3(1Q25.1) MUTATED     0   3   7   2
  DEL PEAK  3(1Q25.1) WILD-TYPE  20  82 139  83
D36V4, multiclass
    clus
vv   DEL PEAK  3(1Q25.1) MUTATED DEL PEAK  3(1Q25.1) WILD-TYPE
  T1                           0                            20
  T2                           3                            82
  T3                           7                           139
  T4                           2                            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  3(1Q25.1) MUTATED     7   2   2   1
  DEL PEAK  3(1Q25.1) WILD-TYPE 102  90  64  66
D36V5, multiclass
    clus
vv   DEL PEAK  3(1Q25.1) MUTATED DEL PEAK  3(1Q25.1) WILD-TYPE
  N0                           7                           102
  N1                           2                            90
  N2                           2                            64
  N3                           1                            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  3(1Q25.1) MUTATED     9   2   1
  DEL PEAK  3(1Q25.1) WILD-TYPE 299  19  16
D36V6, multiclass
    clus
vv   DEL PEAK  3(1Q25.1) MUTATED DEL PEAK  3(1Q25.1) WILD-TYPE
  M0                           9                           299
  M1                           2                            19
  MX                           1                            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
  DEL PEAK  3(1Q25.1) MUTATED     3   9
  DEL PEAK  3(1Q25.1) WILD-TYPE 134 200
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1Q25.1) MUTATED      3    9
  DEL PEAK  3(1Q25.1) WILD-TYPE  134  200
        clus
vv       DEL PEAK  3(1Q25.1) MUTATED DEL PEAK  3(1Q25.1) WILD-TYPE
  FEMALE                           3                           134
  MALE                             9                           200
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK  3(1Q25.1) MUTATED                                       1
  DEL PEAK  3(1Q25.1) WILD-TYPE                                    61
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  3(1Q25.1) MUTATED                                                        5
  DEL PEAK  3(1Q25.1) WILD-TYPE                                                    149
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  3(1Q25.1) MUTATED                                                                   2
  DEL PEAK  3(1Q25.1) WILD-TYPE                                                                52
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  3(1Q25.1) MUTATED                                                  1
  DEL PEAK  3(1Q25.1) WILD-TYPE                                               44
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK  3(1Q25.1) MUTATED                                                           0
  DEL PEAK  3(1Q25.1) WILD-TYPE                                                         1
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK  3(1Q25.1) MUTATED                                                          1
  DEL PEAK  3(1Q25.1) WILD-TYPE                                                       18
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK  3(1Q25.1) MUTATED                                                           1
  DEL PEAK  3(1Q25.1) WILD-TYPE                                                         4
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK  3(1Q25.1) MUTATED                                          0
  DEL PEAK  3(1Q25.1) WILD-TYPE                                        4
D36V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  3(1Q25.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            1
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    0
                                                                   clus
vv                                                                  DEL PEAK  3(1Q25.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        61
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      149
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            52
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             44
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      4
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V9, binary
                               cls
clus                              0   1
  DEL PEAK  3(1Q25.1) MUTATED     0  12
  DEL PEAK  3(1Q25.1) WILD-TYPE   7 327
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1Q25.1) MUTATED      0   12
  DEL PEAK  3(1Q25.1) WILD-TYPE    7  327
     clus
vv    DEL PEAK  3(1Q25.1) MUTATED DEL PEAK  3(1Q25.1) WILD-TYPE
  NO                            0                             7
  YES                          12                           327
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  3(1Q25.1) MUTATED     8   0   1   0
  DEL PEAK  3(1Q25.1) WILD-TYPE 269  13  12  25
D36V10, multiclass
    clus
vv   DEL PEAK  3(1Q25.1) MUTATED DEL PEAK  3(1Q25.1) WILD-TYPE
  R0                           8                           269
  R1                           0                            13
  R2                           1                            12
  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"
D36V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  3(1Q25.1) MUTATED       6                         0
  DEL PEAK  3(1Q25.1) WILD-TYPE    78                         3
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  3(1Q25.1) MUTATED                                           0     4
  DEL PEAK  3(1Q25.1) WILD-TYPE                                         1   204
D36V12, multiclass
                                           clus
vv                                          DEL PEAK  3(1Q25.1) MUTATED
  ASIAN                                                               6
  BLACK OR AFRICAN AMERICAN                                           0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                               4
                                           clus
vv                                          DEL PEAK  3(1Q25.1) WILD-TYPE
  ASIAN                                                                78
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               204
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = DEL PEAK  4(1Q44) MUTATION ANALYSIS
D37V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  4(1Q44) MUTATED    13   7
  DEL PEAK  4(1Q44) WILD-TYPE 209  86
  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE 
                         20                         295 
  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE 
                          7                          86 
$`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         0.07         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 
       18.38         2.53 

$`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         2.27 
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        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19         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-A6RS TCGA-IN-A7NT 
        5.19        13.08         1.41         6.44         6.87         5.56 
TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS 
        1.81         5.56        60.56         3.72         4.50        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-SW-A7EB 
      115.69       116.38        71.38        57.44         8.94         5.79 
TCGA-ZA-A8F6 
        4.21 

  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE 
                       0.07                        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 
                      9.555                      11.240 
[1] "0.1 - 35.2 (9.6)"   "0.1 - 122.3 (11.2)"
[1] "hr=" "1.4"
D37V2, 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       12       36       26        28
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  4(1Q44) MUTATED           4         0          1          5
  DEL PEAK  4(1Q44) WILD-TYPE        43         3         60         40
                             vv
clus                          STAGE IIIC STAGE IV
  DEL PEAK  4(1Q44) MUTATED            3        1
  DEL PEAK  4(1Q44) WILD-TYPE         29       30
D37V3, multiclass
            clus
vv           DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  STAGE I                            0                           2
  STAGE IA                           0                          12
  STAGE IB                           2                          36
  STAGE II                           1                          26
  STAGE IIA                          4                          28
  STAGE IIB                          4                          43
  STAGE III                          0                           3
  STAGE IIIA                         1                          60
  STAGE IIIB                         5                          40
  STAGE IIIC                         3                          29
  STAGE IV                           1                          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  4(1Q44) MUTATED     1   5  10   5
  DEL PEAK  4(1Q44) WILD-TYPE  19  80 136  80
D37V4, multiclass
    clus
vv   DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  T1                         1                          19
  T2                         5                          80
  T3                        10                         136
  T4                         5                          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  4(1Q44) MUTATED     7   5   3   6
  DEL PEAK  4(1Q44) WILD-TYPE 102  87  63  61
D37V5, multiclass
    clus
vv   DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  N0                         7                         102
  N1                         5                          87
  N2                         3                          63
  N3                         6                          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  4(1Q44) MUTATED    19   1   1
  DEL PEAK  4(1Q44) WILD-TYPE 289  20  16
D37V6, multiclass
    clus
vv   DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  M0                        19                         289
  M1                         1                          20
  MX                         1                          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"
D37V7, binary
                             cls
clus                            0   1
  DEL PEAK  4(1Q44) MUTATED    11  10
  DEL PEAK  4(1Q44) WILD-TYPE 126 199
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(1Q44) MUTATED     11   10
  DEL PEAK  4(1Q44) WILD-TYPE  126  199
        clus
vv       DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  FEMALE                        11                         126
  MALE                          10                         199
[1] 2 2
[1] FALSE
                             vv
clus                          STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK  4(1Q44) MUTATED                                       4
  DEL PEAK  4(1Q44) WILD-TYPE                                    58
                             vv
clus                          STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  4(1Q44) MUTATED                                                       11
  DEL PEAK  4(1Q44) WILD-TYPE                                                    143
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  4(1Q44) MUTATED                                                                   3
  DEL PEAK  4(1Q44) WILD-TYPE                                                                51
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  4(1Q44) MUTATED                                                  3
  DEL PEAK  4(1Q44) WILD-TYPE                                               42
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK  4(1Q44) MUTATED                                                           0
  DEL PEAK  4(1Q44) WILD-TYPE                                                         1
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK  4(1Q44) MUTATED                                                          0
  DEL PEAK  4(1Q44) WILD-TYPE                                                       19
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK  4(1Q44) MUTATED                                                           0
  DEL PEAK  4(1Q44) WILD-TYPE                                                         5
                             vv
clus                          STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK  4(1Q44) MUTATED                                          0
  DEL PEAK  4(1Q44) WILD-TYPE                                        4
D37V8, 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                                          3
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                 0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                  0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                 0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                  0
                                                                   clus
vv                                                                  DEL PEAK  4(1Q44) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      58
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    143
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          51
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           42
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    4
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V9, binary
                             cls
clus                            0   1
  DEL PEAK  4(1Q44) MUTATED     0  21
  DEL PEAK  4(1Q44) WILD-TYPE   7 318
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(1Q44) MUTATED      0   21
  DEL PEAK  4(1Q44) WILD-TYPE    7  318
     clus
vv    DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  NO                          0                           7
  YES                        21                         318
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  4(1Q44) MUTATED    18   0   1   0
  DEL PEAK  4(1Q44) WILD-TYPE 259  13  12  25
D37V10, multiclass
    clus
vv   DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  R0                        18                         259
  R1                         0                          13
  R2                         1                          12
  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"
D37V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  4(1Q44) MUTATED       5                         0
  DEL PEAK  4(1Q44) WILD-TYPE    79                         3
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  4(1Q44) MUTATED                                           0    14
  DEL PEAK  4(1Q44) WILD-TYPE                                         1   194
D37V12, multiclass
                                           clus
vv                                          DEL PEAK  4(1Q44) MUTATED
  ASIAN                                                             5
  BLACK OR AFRICAN AMERICAN                                         0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         0
  WHITE                                                            14
                                           clus
vv                                          DEL PEAK  4(1Q44) WILD-TYPE
  ASIAN                                                              79
  BLACK OR AFRICAN AMERICAN                                           3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             194
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(38) Variable = DEL PEAK  5(2Q32.1) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(2Q32.1) MUTATED    25  16
  DEL PEAK  5(2Q32.1) WILD-TYPE 197  77
  DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE 
                           41                           274 
  DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE 
                           16                            77 
$`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         0.07        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-RD-A7C1 TCGA-ZA-A8F6 
        6.25        27.42        18.38        16.67         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         2.27         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        13.35        10.26 
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-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-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BT 
        5.56        60.56         3.72         4.50        11.05         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-SW-A7EB 
       71.38        57.44         8.94         5.79 

  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 
                        7.530                        11.275 
[1] "0.1 - 47.0 (7.5)"   "0.1 - 122.3 (11.3)"
[1] "hr=" "1.6"
D38V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  5(2Q32.1) MUTATED         0        0        8        3         1
  DEL PEAK  5(2Q32.1) WILD-TYPE       2       12       30       24        31
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  5(2Q32.1) MUTATED          10         0          5          9
  DEL PEAK  5(2Q32.1) WILD-TYPE        37         3         56         36
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  5(2Q32.1) MUTATED            4        4
  DEL PEAK  5(2Q32.1) WILD-TYPE         28       27
D38V3, multiclass
            clus
vv           DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             0                            12
  STAGE IB                             8                            30
  STAGE II                             3                            24
  STAGE IIA                            1                            31
  STAGE IIB                           10                            37
  STAGE III                            0                             3
  STAGE IIIA                           5                            56
  STAGE IIIB                           9                            36
  STAGE IIIC                           4                            28
  STAGE IV                             4                            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  5(2Q32.1) MUTATED     1  10  24  10
  DEL PEAK  5(2Q32.1) WILD-TYPE  19  75 122  75
D38V4, multiclass
    clus
vv   DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE
  T1                           1                            19
  T2                          10                            75
  T3                          24                           122
  T4                          10                            75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK  5(2Q32.1) MUTATED   15  9 10 11
  DEL PEAK  5(2Q32.1) WILD-TYPE 94 83 56 56
D38V5, multiclass
    clus
vv   DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE
  N0                          15                            94
  N1                           9                            83
  N2                          10                            56
  N3                          11                            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  5(2Q32.1) MUTATED    42   2   3
  DEL PEAK  5(2Q32.1) WILD-TYPE 266  19  14
D38V6, multiclass
    clus
vv   DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE
  M0                          42                           266
  M1                           2                            19
  MX                           3                            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"
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q32.1) MUTATED    17  30
  DEL PEAK  5(2Q32.1) WILD-TYPE 120 179
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q32.1) MUTATED     17   30
  DEL PEAK  5(2Q32.1) WILD-TYPE  120  179
        clus
vv       DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE
  FEMALE                          17                           120
  MALE                            30                           179
[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                                    54
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  5(2Q32.1) MUTATED                                                       20
  DEL PEAK  5(2Q32.1) WILD-TYPE                                                    134
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  5(2Q32.1) MUTATED                                                                   4
  DEL PEAK  5(2Q32.1) WILD-TYPE                                                                50
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  5(2Q32.1) MUTATED                                                  8
  DEL PEAK  5(2Q32.1) WILD-TYPE                                               37
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK  5(2Q32.1) MUTATED                                                           0
  DEL PEAK  5(2Q32.1) WILD-TYPE                                                         1
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK  5(2Q32.1) MUTATED                                                          5
  DEL PEAK  5(2Q32.1) WILD-TYPE                                                       14
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK  5(2Q32.1) MUTATED                                                           0
  DEL PEAK  5(2Q32.1) WILD-TYPE                                                         5
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK  5(2Q32.1) MUTATED                                          1
  DEL PEAK  5(2Q32.1) WILD-TYPE                                        3
D38V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  5(2Q32.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     20
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            8
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    1
                                                                   clus
vv                                                                  DEL PEAK  5(2Q32.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        54
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            50
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             37
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V9, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q32.1) MUTATED     1  46
  DEL PEAK  5(2Q32.1) WILD-TYPE   6 293
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q32.1) MUTATED      1   46
  DEL PEAK  5(2Q32.1) WILD-TYPE    6  293
     clus
vv    DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE
  NO                            1                             6
  YES                          46                           293
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  5(2Q32.1) MUTATED    38   3   2   3
  DEL PEAK  5(2Q32.1) WILD-TYPE 239  10  11  22
D38V10, multiclass
    clus
vv   DEL PEAK  5(2Q32.1) MUTATED DEL PEAK  5(2Q32.1) WILD-TYPE
  R0                          38                           239
  R1                           3                            10
  R2                           2                            11
  RX                           3                            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  5(2Q32.1) MUTATED      11                         0
  DEL PEAK  5(2Q32.1) WILD-TYPE    73                         3
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  5(2Q32.1) MUTATED                                           0    27
  DEL PEAK  5(2Q32.1) WILD-TYPE                                         1   181
D38V12, multiclass
                                           clus
vv                                          DEL PEAK  5(2Q32.1) MUTATED
  ASIAN                                                              11
  BLACK OR AFRICAN AMERICAN                                           0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              27
                                           clus
vv                                          DEL PEAK  5(2Q32.1) WILD-TYPE
  ASIAN                                                                73
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               181
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(39) Variable = DEL PEAK  6(2Q37.2) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(2Q37.2) MUTATED    34  13
  DEL PEAK  6(2Q37.2) WILD-TYPE 188  80
  DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE 
                           47                           268 
  DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE 
                           13                            80 
$`DEL PEAK  6(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-8381 TCGA-BR-8484 
        1.32         0.49        12.95        19.50         0.26         0.72 
TCGA-BR-8485 TCGA-BR-8677 TCGA-BR-8687 TCGA-BR-A4PD TCGA-CD-5800 TCGA-CD-8525 
        9.21         0.49         0.62        20.65        13.15         0.07 
TCGA-CD-8526 TCGA-CD-8529 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 
        0.07         0.13         0.13         0.13         0.07         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-D7-6822 TCGA-D7-8576 TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-HJ-7597 TCGA-HU-8243 
       12.33         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 
       22.75         8.98        12.95        27.42         1.41 

$`DEL PEAK  6(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-8373 TCGA-BR-8380 TCGA-BR-8382 
        3.32         0.36        19.17        14.79         0.69        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-8678 TCGA-BR-8680 
        2.14        13.45         0.20         7.53        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         2.27         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-5801 
       13.64        11.57         5.13         2.83         3.25        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 
        0.30         0.07         0.07         0.07         0.10         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        13.35 
TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 
       10.26        12.79        10.55        11.31        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-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        3.72         4.50        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-SW-A7EB TCGA-ZA-A8F6 
       57.44         8.94         5.79         4.21 

  DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE 
                        35.24                        122.30 
  DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE 
                         8.98                         11.31 
[1] "0.1 - 35.2 (9.0)"   "0.1 - 122.3 (11.3)"
[1] "hr=" "1.2"
D39V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  6(2Q37.2) MUTATED         1        1        6        7         3
  DEL PEAK  6(2Q37.2) WILD-TYPE       1       11       32       20        29
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  6(2Q37.2) MUTATED           8         1          7          8
  DEL PEAK  6(2Q37.2) WILD-TYPE        39         2         54         37
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  6(2Q37.2) MUTATED            6        3
  DEL PEAK  6(2Q37.2) WILD-TYPE         26       28
D39V3, multiclass
            clus
vv           DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             1                            11
  STAGE IB                             6                            32
  STAGE II                             7                            20
  STAGE IIA                            3                            29
  STAGE IIB                            8                            39
  STAGE III                            1                             2
  STAGE IIIA                           7                            54
  STAGE IIIB                           8                            37
  STAGE IIIC                           6                            26
  STAGE IV                             3                            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  6(2Q37.2) MUTATED     2  14  21  14
  DEL PEAK  6(2Q37.2) WILD-TYPE  18  71 125  71
D39V4, multiclass
    clus
vv   DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE
  T1                           2                            18
  T2                          14                            71
  T3                          21                           125
  T4                          14                            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  6(2Q37.2) MUTATED   19 13 11  8
  DEL PEAK  6(2Q37.2) WILD-TYPE 90 79 55 59
D39V5, multiclass
    clus
vv   DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE
  N0                          19                            90
  N1                          13                            79
  N2                          11                            55
  N3                           8                            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  6(2Q37.2) MUTATED    47   2   2
  DEL PEAK  6(2Q37.2) WILD-TYPE 261  19  15
D39V6, multiclass
    clus
vv   DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE
  M0                          47                           261
  M1                           2                            19
  MX                           2                            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"
D39V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q37.2) MUTATED    27  24
  DEL PEAK  6(2Q37.2) WILD-TYPE 110 185
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q37.2) MUTATED     27   24
  DEL PEAK  6(2Q37.2) WILD-TYPE  110  185
        clus
vv       DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE
  FEMALE                          27                           110
  MALE                            24                           185
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK  6(2Q37.2) MUTATED                                       5
  DEL PEAK  6(2Q37.2) WILD-TYPE                                    57
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  6(2Q37.2) MUTATED                                                       20
  DEL PEAK  6(2Q37.2) WILD-TYPE                                                    134
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  6(2Q37.2) MUTATED                                                                   9
  DEL PEAK  6(2Q37.2) WILD-TYPE                                                                45
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  6(2Q37.2) MUTATED                                                 10
  DEL PEAK  6(2Q37.2) WILD-TYPE                                               35
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK  6(2Q37.2) MUTATED                                                           0
  DEL PEAK  6(2Q37.2) WILD-TYPE                                                         1
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK  6(2Q37.2) MUTATED                                                          4
  DEL PEAK  6(2Q37.2) WILD-TYPE                                                       15
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK  6(2Q37.2) MUTATED                                                           1
  DEL PEAK  6(2Q37.2) WILD-TYPE                                                         4
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK  6(2Q37.2) MUTATED                                          1
  DEL PEAK  6(2Q37.2) WILD-TYPE                                        3
D39V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  6(2Q37.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     20
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           9
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           10
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    1
                                                                   clus
vv                                                                  DEL PEAK  6(2Q37.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        57
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            45
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             35
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V9, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q37.2) MUTATED     1  50
  DEL PEAK  6(2Q37.2) WILD-TYPE   6 289
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q37.2) MUTATED      1   50
  DEL PEAK  6(2Q37.2) WILD-TYPE    6  289
     clus
vv    DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE
  NO                            1                             6
  YES                          50                           289
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  6(2Q37.2) MUTATED    47   2   0   0
  DEL PEAK  6(2Q37.2) WILD-TYPE 230  11  13  25
D39V10, multiclass
    clus
vv   DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE
  R0                          47                           230
  R1                           2                            11
  R2                           0                            13
  RX                           0                            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  6(2Q37.2) MUTATED      15                         0
  DEL PEAK  6(2Q37.2) WILD-TYPE    69                         3
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  6(2Q37.2) MUTATED                                           0    26
  DEL PEAK  6(2Q37.2) WILD-TYPE                                         1   182
D39V12, multiclass
                                           clus
vv                                          DEL PEAK  6(2Q37.2) MUTATED
  ASIAN                                                              15
  BLACK OR AFRICAN AMERICAN                                           0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              26
                                           clus
vv                                          DEL PEAK  6(2Q37.2) WILD-TYPE
  ASIAN                                                                69
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               182
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(40) Variable = DEL PEAK  7(3P26.1) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(3P26.1) MUTATED    70  26
  DEL PEAK  7(3P26.1) WILD-TYPE 152  67
  DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE 
                           96                           219 
  DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE 
                           26                            67 
$`DEL PEAK  7(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         2.27         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        13.35        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-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB 
        8.61        16.67        37.91       115.69         8.94         5.79 

$`DEL PEAK  7(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         0.07         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        10.26        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-A7NU TCGA-IP-7968 TCGA-MX-A5UG 
        5.36         5.19        13.08         1.81         2.53         3.72 
TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 
        4.50        11.05         4.67       122.30        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-ZA-A8F6 
       71.38        57.44         4.21 

  DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE 
                       115.69                        122.30 
  DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE 
                       11.425                        10.620 
[1] "0.1 - 115.7 (11.4)" "0.1 - 122.3 (10.6)"
[1] "hr=" "1.2"
D40V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  7(3P26.1) MUTATED         0        4       14        8         5
  DEL PEAK  7(3P26.1) WILD-TYPE       2        8       24       19        27
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  7(3P26.1) MUTATED          14         0         24         13
  DEL PEAK  7(3P26.1) WILD-TYPE        33         3         37         32
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  7(3P26.1) MUTATED            9        9
  DEL PEAK  7(3P26.1) WILD-TYPE         23       22
D40V3, multiclass
            clus
vv           DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             4                             8
  STAGE IB                            14                            24
  STAGE II                             8                            19
  STAGE IIA                            5                            27
  STAGE IIB                           14                            33
  STAGE III                            0                             3
  STAGE IIIA                          24                            37
  STAGE IIIB                          13                            32
  STAGE IIIC                           9                            23
  STAGE IV                             9                            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  7(3P26.1) MUTATED     7  26  41  27
  DEL PEAK  7(3P26.1) WILD-TYPE  13  59 105  58
D40V4, multiclass
    clus
vv   DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE
  T1                           7                            13
  T2                          26                            59
  T3                          41                           105
  T4                          27                            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
  DEL PEAK  7(3P26.1) MUTATED   27 31 26 17
  DEL PEAK  7(3P26.1) WILD-TYPE 82 61 40 50
D40V5, multiclass
    clus
vv   DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE
  N0                          27                            82
  N1                          31                            61
  N2                          26                            40
  N3                          17                            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
  DEL PEAK  7(3P26.1) MUTATED    91   7   6
  DEL PEAK  7(3P26.1) WILD-TYPE 217  14  11
D40V6, multiclass
    clus
vv   DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE
  M0                          91                           217
  M1                           7                            14
  MX                           6                            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"
D40V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P26.1) MUTATED    37  67
  DEL PEAK  7(3P26.1) WILD-TYPE 100 142
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P26.1) MUTATED     37   67
  DEL PEAK  7(3P26.1) WILD-TYPE  100  142
        clus
vv       DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE
  FEMALE                          37                           100
  MALE                            67                           142
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK  7(3P26.1) MUTATED                                      15
  DEL PEAK  7(3P26.1) WILD-TYPE                                    47
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  7(3P26.1) MUTATED                                                       45
  DEL PEAK  7(3P26.1) WILD-TYPE                                                    109
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  7(3P26.1) MUTATED                                                                  25
  DEL PEAK  7(3P26.1) WILD-TYPE                                                                29
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  7(3P26.1) MUTATED                                                 11
  DEL PEAK  7(3P26.1) WILD-TYPE                                               34
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK  7(3P26.1) MUTATED                                                           0
  DEL PEAK  7(3P26.1) WILD-TYPE                                                         1
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK  7(3P26.1) MUTATED                                                          4
  DEL PEAK  7(3P26.1) WILD-TYPE                                                       15
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK  7(3P26.1) MUTATED                                                           3
  DEL PEAK  7(3P26.1) WILD-TYPE                                                         2
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK  7(3P26.1) MUTATED                                          1
  DEL PEAK  7(3P26.1) WILD-TYPE                                        3
D40V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  7(3P26.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     45
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          25
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           11
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    1
                                                                   clus
vv                                                                  DEL PEAK  7(3P26.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      109
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            29
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             34
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V9, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P26.1) MUTATED     2 102
  DEL PEAK  7(3P26.1) WILD-TYPE   5 237
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P26.1) MUTATED      2  102
  DEL PEAK  7(3P26.1) WILD-TYPE    5  237
     clus
vv    DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE
  NO                            2                             5
  YES                         102                           237
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  7(3P26.1) MUTATED    87   3   5   5
  DEL PEAK  7(3P26.1) WILD-TYPE 190  10   8  20
D40V10, multiclass
    clus
vv   DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE
  R0                          87                           190
  R1                           3                            10
  R2                           5                             8
  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"
D40V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  7(3P26.1) MUTATED      24                         0
  DEL PEAK  7(3P26.1) WILD-TYPE    60                         3
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  7(3P26.1) MUTATED                                           1    61
  DEL PEAK  7(3P26.1) WILD-TYPE                                         0   147
D40V12, multiclass
                                           clus
vv                                          DEL PEAK  7(3P26.1) MUTATED
  ASIAN                                                              24
  BLACK OR AFRICAN AMERICAN                                           0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              61
                                           clus
vv                                          DEL PEAK  7(3P26.1) WILD-TYPE
  ASIAN                                                                60
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               147
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = DEL PEAK  8(3P14.2) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(3P14.2) MUTATED    78  36
  DEL PEAK  8(3P14.2) WILD-TYPE 144  57
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                          114                           201 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                           36                            57 
$`DEL PEAK  8(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         2.27         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        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-A4YT 
       17.19        10.26        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-A6RS TCGA-IN-A7NT 
       18.38         5.19         1.41         6.44         6.87         5.56 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB 
        5.56        60.56        16.67        37.91         8.94         5.79 

$`DEL PEAK  8(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         0.07 
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         4.50        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-ZA-A8F6 
       71.38        57.44         4.21 

  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                        60.56                        122.30 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                        9.945                        11.310 
[1] "0.1 - 60.6 (9.9)"   "0.1 - 122.3 (11.3)"
[1] "hr=" "1.3"
D41V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  8(3P14.2) MUTATED         0        5       12       11         9
  DEL PEAK  8(3P14.2) WILD-TYPE       2        7       26       16        23
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  8(3P14.2) MUTATED          17         0         32         15
  DEL PEAK  8(3P14.2) WILD-TYPE        30         3         29         30
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  8(3P14.2) MUTATED            9        9
  DEL PEAK  8(3P14.2) WILD-TYPE         23       22
D41V3, multiclass
            clus
vv           DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             5                             7
  STAGE IB                            12                            26
  STAGE II                            11                            16
  STAGE IIA                            9                            23
  STAGE IIB                           17                            30
  STAGE III                            0                             3
  STAGE IIIA                          32                            29
  STAGE IIIB                          15                            30
  STAGE IIIC                           9                            23
  STAGE IV                             9                            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  8(3P14.2) MUTATED    9 31 50 29
  DEL PEAK  8(3P14.2) WILD-TYPE 11 54 96 56
D41V4, multiclass
    clus
vv   DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  T1                           9                            11
  T2                          31                            54
  T3                          50                            96
  T4                          29                            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                            N0 N1 N2 N3
  DEL PEAK  8(3P14.2) MUTATED   33 39 27 20
  DEL PEAK  8(3P14.2) WILD-TYPE 76 53 39 47
D41V5, multiclass
    clus
vv   DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  N0                          33                            76
  N1                          39                            53
  N2                          27                            39
  N3                          20                            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  8(3P14.2) MUTATED   106   8   6
  DEL PEAK  8(3P14.2) WILD-TYPE 202  13  11
D41V6, multiclass
    clus
vv   DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  M0                         106                           202
  M1                           8                            13
  MX                           6                            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"
D41V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P14.2) MUTATED    49  71
  DEL PEAK  8(3P14.2) WILD-TYPE  88 138
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.2) MUTATED     49   71
  DEL PEAK  8(3P14.2) WILD-TYPE   88  138
        clus
vv       DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  FEMALE                          49                            88
  MALE                            71                           138
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK  8(3P14.2) MUTATED                                      17
  DEL PEAK  8(3P14.2) WILD-TYPE                                    45
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  8(3P14.2) MUTATED                                                       48
  DEL PEAK  8(3P14.2) WILD-TYPE                                                    106
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  8(3P14.2) MUTATED                                                                  25
  DEL PEAK  8(3P14.2) WILD-TYPE                                                                29
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  8(3P14.2) MUTATED                                                 20
  DEL PEAK  8(3P14.2) WILD-TYPE                                               25
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK  8(3P14.2) MUTATED                                                           1
  DEL PEAK  8(3P14.2) WILD-TYPE                                                         0
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK  8(3P14.2) MUTATED                                                          4
  DEL PEAK  8(3P14.2) WILD-TYPE                                                       15
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK  8(3P14.2) MUTATED                                                           3
  DEL PEAK  8(3P14.2) WILD-TYPE                                                         2
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK  8(3P14.2) MUTATED                                          2
  DEL PEAK  8(3P14.2) WILD-TYPE                                        2
D41V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  8(3P14.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      17
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     48
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          25
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           20
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    2
                                                                   clus
vv                                                                  DEL PEAK  8(3P14.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        45
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      106
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            29
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             25
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V9, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P14.2) MUTATED     3 117
  DEL PEAK  8(3P14.2) WILD-TYPE   4 222
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.2) MUTATED      3  117
  DEL PEAK  8(3P14.2) WILD-TYPE    4  222
     clus
vv    DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  NO                            3                             4
  YES                         117                           222
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  8(3P14.2) MUTATED   106   2   5   3
  DEL PEAK  8(3P14.2) WILD-TYPE 171  11   8  22
D41V10, multiclass
    clus
vv   DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  R0                         106                           171
  R1                           2                            11
  R2                           5                             8
  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  8(3P14.2) MUTATED      33                         0
  DEL PEAK  8(3P14.2) WILD-TYPE    51                         3
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  8(3P14.2) MUTATED                                           0    67
  DEL PEAK  8(3P14.2) WILD-TYPE                                         1   141
D41V12, multiclass
                                           clus
vv                                          DEL PEAK  8(3P14.2) MUTATED
  ASIAN                                                              33
  BLACK OR AFRICAN AMERICAN                                           0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              67
                                           clus
vv                                          DEL PEAK  8(3P14.2) WILD-TYPE
  ASIAN                                                                51
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               141
[1] 4 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  9(3Q26.31) MUTATION ANALYSIS
D42V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  9(3Q26.31) MUTATED    28   9
  DEL PEAK  9(3Q26.31) WILD-TYPE 194  84
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                            37                            278 
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                             9                             84 
$`DEL PEAK  9(3Q26.31) MUTATED`
TCGA-BR-4188 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7959 
        7.43         7.00         0.62        35.24        15.42        18.71 
TCGA-BR-8077 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4IY 
        0.69         9.21        20.22        10.68         1.15        12.89 
TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-CD-8533 TCGA-CD-A487 TCGA-CG-4438 
        0.72        13.51         1.15         0.13         0.13        54.08 
TCGA-CG-4441 TCGA-CG-4466 TCGA-D7-5578 TCGA-D7-6526 TCGA-D7-8573 TCGA-D7-A6EV 
       14.01        18.97        12.66        17.19        19.50        11.24 
TCGA-D7-A6EX TCGA-EQ-8122 TCGA-FP-A4BF TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-A4G3 
       11.31         7.79         1.55         1.51        14.17         5.59 
TCGA-HU-A4GF TCGA-HU-A4GU TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-A6RI TCGA-KB-A6F5 
       25.81         6.25         9.67        21.21        18.38         5.56 
TCGA-RD-A8N6 
        8.94 

$`DEL PEAK  9(3Q26.31) 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-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-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       23.93        28.01         0.69         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-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-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-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-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-A44T TCGA-BR-A452 TCGA-BR-A453 
        0.59        15.68         0.62        12.56         0.66         3.02 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 
        2.27         0.92        13.41        13.51         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-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 
       13.15        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A 
        0.10         0.13         0.10         0.07         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-4440 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
        4.01        29.98        47.05        19.07        12.03        21.99 
TCGA-CG-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-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-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-D7-5579 TCGA-D7-6518 
       55.04        21.07         7.99        12.36        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       12.33        24.72        16.80        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-A6F0 
       13.78        14.76        13.71        11.44         9.76         2.96 
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-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-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56         0.23        18.08        26.47         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       14.27        12.59        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-A4GD 
       24.30        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        17.69 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 
       12.30         8.88         8.81        27.42         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
        3.39         5.36         5.19        13.08         1.41         6.44 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F7 TCGA-MX-A5UG 
        6.87         5.56         1.81         2.53        60.56         3.72 
TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        4.50        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-SW-A7EB TCGA-ZA-A8F6 
        5.79         4.21 

  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                          0.13                           0.07 
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                         54.08                         122.30 
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                         10.68                          11.18 
[1] "0.1 - 54.1 (10.7)"  "0.1 - 122.3 (11.2)"
[1] "hr=" "1.2"
D42V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  9(3Q26.31) MUTATED         0        1        3        2         3
  DEL PEAK  9(3Q26.31) WILD-TYPE       2       11       35       25        29
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  9(3Q26.31) MUTATED          10         0         10          6
  DEL PEAK  9(3Q26.31) WILD-TYPE        37         3         51         39
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK  9(3Q26.31) MUTATED            2        1
  DEL PEAK  9(3Q26.31) WILD-TYPE         30       30
D42V3, multiclass
            clus
vv           DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              1                             11
  STAGE IB                              3                             35
  STAGE II                              2                             25
  STAGE IIA                             3                             29
  STAGE IIB                            10                             37
  STAGE III                             0                              3
  STAGE IIIA                           10                             51
  STAGE IIIB                            6                             39
  STAGE IIIC                            2                             30
  STAGE IV                              1                             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  9(3Q26.31) MUTATED     2   6  22   9
  DEL PEAK  9(3Q26.31) WILD-TYPE  18  79 124  76
D42V4, multiclass
    clus
vv   DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  T1                            2                             18
  T2                            6                             79
  T3                           22                            124
  T4                            9                             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  9(3Q26.31) MUTATED   11  9 14  5
  DEL PEAK  9(3Q26.31) WILD-TYPE 98 83 52 62
D42V5, multiclass
    clus
vv   DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  N0                           11                             98
  N1                            9                             83
  N2                           14                             52
  N3                            5                             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  9(3Q26.31) MUTATED    38   0   3
  DEL PEAK  9(3Q26.31) WILD-TYPE 270  21  14
D42V6, multiclass
    clus
vv   DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  M0                           38                            270
  M1                            0                             21
  MX                            3                             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"
D42V7, binary
                                cls
clus                               0   1
  DEL PEAK  9(3Q26.31) MUTATED    17  24
  DEL PEAK  9(3Q26.31) WILD-TYPE 120 185
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(3Q26.31) MUTATED     17   24
  DEL PEAK  9(3Q26.31) WILD-TYPE  120  185
        clus
vv       DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  FEMALE                           17                            120
  MALE                             24                            185
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK  9(3Q26.31) MUTATED                                       3
  DEL PEAK  9(3Q26.31) WILD-TYPE                                    59
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  9(3Q26.31) MUTATED                                                       20
  DEL PEAK  9(3Q26.31) WILD-TYPE                                                    134
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  9(3Q26.31) MUTATED                                                                   8
  DEL PEAK  9(3Q26.31) WILD-TYPE                                                                46
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  9(3Q26.31) MUTATED                                                  8
  DEL PEAK  9(3Q26.31) WILD-TYPE                                               37
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK  9(3Q26.31) MUTATED                                                           0
  DEL PEAK  9(3Q26.31) WILD-TYPE                                                         1
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK  9(3Q26.31) MUTATED                                                          1
  DEL PEAK  9(3Q26.31) WILD-TYPE                                                       18
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK  9(3Q26.31) MUTATED                                                           0
  DEL PEAK  9(3Q26.31) WILD-TYPE                                                         5
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK  9(3Q26.31) MUTATED                                          1
  DEL PEAK  9(3Q26.31) WILD-TYPE                                        3
D42V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  9(3Q26.31) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      20
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            8
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             8
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     1
                                                                   clus
vv                                                                  DEL PEAK  9(3Q26.31) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             46
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              37
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V9, binary
                                cls
clus                               0   1
  DEL PEAK  9(3Q26.31) MUTATED     1  40
  DEL PEAK  9(3Q26.31) WILD-TYPE   6 299
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(3Q26.31) MUTATED      1   40
  DEL PEAK  9(3Q26.31) WILD-TYPE    6  299
     clus
vv    DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  NO                             1                              6
  YES                           40                            299
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  9(3Q26.31) MUTATED    35   1   0   3
  DEL PEAK  9(3Q26.31) WILD-TYPE 242  12  13  22
D42V10, multiclass
    clus
vv   DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  R0                           35                            242
  R1                            1                             12
  R2                            0                             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"
D42V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  9(3Q26.31) MUTATED      10                         0
  DEL PEAK  9(3Q26.31) WILD-TYPE    74                         3
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK  9(3Q26.31) MUTATED                                           0
  DEL PEAK  9(3Q26.31) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK  9(3Q26.31) MUTATED      26
  DEL PEAK  9(3Q26.31) WILD-TYPE   182
D42V12, multiclass
                                           clus
vv                                          DEL PEAK  9(3Q26.31) MUTATED
  ASIAN                                                               10
  BLACK OR AFRICAN AMERICAN                                            0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               26
                                           clus
vv                                          DEL PEAK  9(3Q26.31) WILD-TYPE
  ASIAN                                                                 74
  BLACK OR AFRICAN AMERICAN                                              3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                182
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(43) Variable = DEL PEAK 10(4P16.3) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(4P16.3) MUTATED    84  36
  DEL PEAK 10(4P16.3) WILD-TYPE 138  57
  DEL PEAK 10(4P16.3) MUTATED DEL PEAK 10(4P16.3) WILD-TYPE 
                          120                           195 
  DEL PEAK 10(4P16.3) MUTATED DEL PEAK 10(4P16.3) WILD-TYPE 
                           36                            57 
$`DEL PEAK 10(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         2.27         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        10.26 
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-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB 
       11.05        16.67        37.91       115.69         8.94         5.79 

$`DEL PEAK 10(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         0.07         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        13.35        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-A6RS TCGA-IN-A7NT TCGA-IN-A7NU 
       18.38         5.19        13.08         6.87         5.56         1.81 
TCGA-MX-A5UJ TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 
        4.50         8.61         4.67       122.30        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-ZA-A8F6 
       71.38        57.44         4.21 

  DEL PEAK 10(4P16.3) MUTATED DEL PEAK 10(4P16.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 10(4P16.3) MUTATED DEL PEAK 10(4P16.3) WILD-TYPE 
                       115.69                        122.30 
  DEL PEAK 10(4P16.3) MUTATED DEL PEAK 10(4P16.3) WILD-TYPE 
                         9.21                         11.77 
[1] "0.1 - 115.7 (9.2)"  "0.1 - 122.3 (11.8)"
[1] "hr=" "1.1"
D43V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 10(4P16.3) MUTATED         0        4       11       11        15
  DEL PEAK 10(4P16.3) WILD-TYPE       2        8       27       16        17
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 10(4P16.3) MUTATED          15         0         28         17
  DEL PEAK 10(4P16.3) WILD-TYPE        32         3         33         28
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 10(4P16.3) MUTATED           14        9
  DEL PEAK 10(4P16.3) WILD-TYPE         18       22
D43V3, multiclass
            clus
vv           DEL PEAK 10(4P16.3) MUTATED DEL PEAK 10(4P16.3) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             4                             8
  STAGE IB                            11                            27
  STAGE II                            11                            16
  STAGE IIA                           15                            17
  STAGE IIB                           15                            32
  STAGE III                            0                             3
  STAGE IIIA                          28                            33
  STAGE IIIB                          17                            28
  STAGE IIIC                          14                            18
  STAGE IV                             9                            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 10(4P16.3) MUTATED    6 25 67 28
  DEL PEAK 10(4P16.3) WILD-TYPE 14 60 79 57
D43V4, multiclass
    clus
vv   DEL PEAK 10(4P16.3) MUTATED DEL PEAK 10(4P16.3) WILD-TYPE
  T1                           6                            14
  T2                          25                            60
  T3                          67                            79
  T4                          28                            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
  DEL PEAK 10(4P16.3) MUTATED   38 38 26 25
  DEL PEAK 10(4P16.3) WILD-TYPE 71 54 40 42
D43V5, multiclass
    clus
vv   DEL PEAK 10(4P16.3) MUTATED DEL PEAK 10(4P16.3) WILD-TYPE
  N0                          38                            71
  N1                          38                            54
  N2                          26                            40
  N3                          25                            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 10(4P16.3) MUTATED   121   4   6
  DEL PEAK 10(4P16.3) WILD-TYPE 187  17  11
D43V6, multiclass
    clus
vv   DEL PEAK 10(4P16.3) MUTATED DEL PEAK 10(4P16.3) WILD-TYPE
  M0                         121                           187
  M1                           4                            17
  MX                           6                            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"
D43V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(4P16.3) MUTATED    49  82
  DEL PEAK 10(4P16.3) WILD-TYPE  88 127
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4P16.3) MUTATED     49   82
  DEL PEAK 10(4P16.3) WILD-TYPE   88  127
        clus
vv       DEL PEAK 10(4P16.3) MUTATED DEL PEAK 10(4P16.3) WILD-TYPE
  FEMALE                          49                            88
  MALE                            82                           127
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 10(4P16.3) MUTATED                                      21
  DEL PEAK 10(4P16.3) WILD-TYPE                                    41
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 10(4P16.3) MUTATED                                                       54
  DEL PEAK 10(4P16.3) WILD-TYPE                                                    100
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 10(4P16.3) MUTATED                                                                  19
  DEL PEAK 10(4P16.3) WILD-TYPE                                                                35
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 10(4P16.3) MUTATED                                                 23
  DEL PEAK 10(4P16.3) WILD-TYPE                                               22
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 10(4P16.3) MUTATED                                                           1
  DEL PEAK 10(4P16.3) WILD-TYPE                                                         0
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 10(4P16.3) MUTATED                                                          9
  DEL PEAK 10(4P16.3) WILD-TYPE                                                       10
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 10(4P16.3) MUTATED                                                           2
  DEL PEAK 10(4P16.3) WILD-TYPE                                                         3
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 10(4P16.3) MUTATED                                          2
  DEL PEAK 10(4P16.3) WILD-TYPE                                        2
D43V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 10(4P16.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      21
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     54
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          19
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           23
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    2
                                                                   clus
vv                                                                  DEL PEAK 10(4P16.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        41
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      100
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             22
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V9, binary
                               cls
clus                              0   1
  DEL PEAK 10(4P16.3) MUTATED     3 128
  DEL PEAK 10(4P16.3) WILD-TYPE   4 211
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4P16.3) MUTATED      3  128
  DEL PEAK 10(4P16.3) WILD-TYPE    4  211
     clus
vv    DEL PEAK 10(4P16.3) MUTATED DEL PEAK 10(4P16.3) WILD-TYPE
  NO                            3                             4
  YES                         128                           211
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 10(4P16.3) MUTATED   106   7   1   9
  DEL PEAK 10(4P16.3) WILD-TYPE 171   6  12  16
D43V10, multiclass
    clus
vv   DEL PEAK 10(4P16.3) MUTATED DEL PEAK 10(4P16.3) WILD-TYPE
  R0                         106                           171
  R1                           7                             6
  R2                           1                            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"
D43V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 10(4P16.3) MUTATED      36                         1
  DEL PEAK 10(4P16.3) WILD-TYPE    48                         2
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 10(4P16.3) MUTATED                                           0    77
  DEL PEAK 10(4P16.3) WILD-TYPE                                         1   131
D43V12, multiclass
                                           clus
vv                                          DEL PEAK 10(4P16.3) MUTATED
  ASIAN                                                              36
  BLACK OR AFRICAN AMERICAN                                           1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              77
                                           clus
vv                                          DEL PEAK 10(4P16.3) WILD-TYPE
  ASIAN                                                                48
  BLACK OR AFRICAN AMERICAN                                             2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               131
[1] 4 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 11(4Q22.1) MUTATION ANALYSIS
D44V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(4Q22.1) MUTATED    97  39
  DEL PEAK 11(4Q22.1) WILD-TYPE 125  54
  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                          136                           179 
  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                           39                            54 
$`DEL PEAK 11(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         2.27 
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 
       10.26        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-A7NT TCGA-IP-7968 TCGA-RD-A7BS TCGA-RD-A7BT 
        1.41         6.44         5.56         2.53        11.05         8.61 
TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 
       16.67        37.91       115.69         8.94 

$`DEL PEAK 11(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 
        0.07         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        13.35        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-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 
       60.56         3.72         4.50         4.67       122.30        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-SW-A7EB TCGA-ZA-A8F6 
      116.38        71.38        57.44         5.79         4.21 

  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                       115.69                        122.30 
  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                        8.365                        12.300 
[1] "0.1 - 115.7 (8.4)"  "0.1 - 122.3 (12.3)"
[1] "hr=" "1.1"
D44V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 11(4Q22.1) MUTATED         0        4       12       15        15
  DEL PEAK 11(4Q22.1) WILD-TYPE       2        8       26       12        17
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 11(4Q22.1) MUTATED          21         1         30         16
  DEL PEAK 11(4Q22.1) WILD-TYPE        26         2         31         29
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 11(4Q22.1) MUTATED           14       15
  DEL PEAK 11(4Q22.1) WILD-TYPE         18       16
D44V3, multiclass
            clus
vv           DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             4                             8
  STAGE IB                            12                            26
  STAGE II                            15                            12
  STAGE IIA                           15                            17
  STAGE IIB                           21                            26
  STAGE III                            1                             2
  STAGE IIIA                          30                            31
  STAGE IIIB                          16                            29
  STAGE IIIC                          14                            18
  STAGE IV                            15                            16
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK 11(4Q22.1) MUTATED    5 35 70 34
  DEL PEAK 11(4Q22.1) WILD-TYPE 15 50 76 51
D44V4, multiclass
    clus
vv   DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  T1                           5                            15
  T2                          35                            50
  T3                          70                            76
  T4                          34                            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                            N0 N1 N2 N3
  DEL PEAK 11(4Q22.1) MUTATED   42 45 31 27
  DEL PEAK 11(4Q22.1) WILD-TYPE 67 47 35 40
D44V5, multiclass
    clus
vv   DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  N0                          42                            67
  N1                          45                            47
  N2                          31                            35
  N3                          27                            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 11(4Q22.1) MUTATED   134   7   8
  DEL PEAK 11(4Q22.1) WILD-TYPE 174  14   9
D44V6, multiclass
    clus
vv   DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  M0                         134                           174
  M1                           7                            14
  MX                           8                             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"
D44V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q22.1) MUTATED    59  90
  DEL PEAK 11(4Q22.1) WILD-TYPE  78 119
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q22.1) MUTATED     59   90
  DEL PEAK 11(4Q22.1) WILD-TYPE   78  119
        clus
vv       DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  FEMALE                          59                            78
  MALE                            90                           119
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 11(4Q22.1) MUTATED                                      22
  DEL PEAK 11(4Q22.1) WILD-TYPE                                    40
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 11(4Q22.1) MUTATED                                                       63
  DEL PEAK 11(4Q22.1) WILD-TYPE                                                     91
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 11(4Q22.1) MUTATED                                                                  25
  DEL PEAK 11(4Q22.1) WILD-TYPE                                                                29
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 11(4Q22.1) MUTATED                                                 24
  DEL PEAK 11(4Q22.1) WILD-TYPE                                               21
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 11(4Q22.1) MUTATED                                                           1
  DEL PEAK 11(4Q22.1) WILD-TYPE                                                         0
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 11(4Q22.1) MUTATED                                                          8
  DEL PEAK 11(4Q22.1) WILD-TYPE                                                       11
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 11(4Q22.1) MUTATED                                                           3
  DEL PEAK 11(4Q22.1) WILD-TYPE                                                         2
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 11(4Q22.1) MUTATED                                          2
  DEL PEAK 11(4Q22.1) WILD-TYPE                                        2
D44V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 11(4Q22.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      22
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     63
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          25
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           24
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    2
                                                                   clus
vv                                                                  DEL PEAK 11(4Q22.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        40
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       91
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            29
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             21
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V9, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q22.1) MUTATED     5 144
  DEL PEAK 11(4Q22.1) WILD-TYPE   2 195
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q22.1) MUTATED      5  144
  DEL PEAK 11(4Q22.1) WILD-TYPE    2  195
     clus
vv    DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  NO                            5                             2
  YES                         144                           195
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 11(4Q22.1) MUTATED   117   8   6   8
  DEL PEAK 11(4Q22.1) WILD-TYPE 160   5   7  17
D44V10, multiclass
    clus
vv   DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  R0                         117                           160
  R1                           8                             5
  R2                           6                             7
  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"
D44V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 11(4Q22.1) MUTATED      41                         2
  DEL PEAK 11(4Q22.1) WILD-TYPE    43                         1
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 11(4Q22.1) MUTATED                                           1    83
  DEL PEAK 11(4Q22.1) WILD-TYPE                                         0   125
D44V12, multiclass
                                           clus
vv                                          DEL PEAK 11(4Q22.1) MUTATED
  ASIAN                                                              41
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              83
                                           clus
vv                                          DEL PEAK 11(4Q22.1) WILD-TYPE
  ASIAN                                                                43
  BLACK OR AFRICAN AMERICAN                                             1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               125
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(45) Variable = DEL PEAK 12(4Q34.3) MUTATION ANALYSIS
D45V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(4Q34.3) MUTATED   100  38
  DEL PEAK 12(4Q34.3) WILD-TYPE 122  55
  DEL PEAK 12(4Q34.3) MUTATED DEL PEAK 12(4Q34.3) WILD-TYPE 
                          138                           177 
  DEL PEAK 12(4Q34.3) MUTATED DEL PEAK 12(4Q34.3) WILD-TYPE 
                           38                            55 
$`DEL PEAK 12(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         2.27         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        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.22        15.98        12.79        11.31        12.33 
TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6EX 
       19.50         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-A7NT TCGA-IN-A7NU TCGA-IP-7968 
       13.08         1.41         6.44         5.56         1.81         2.53 
TCGA-KB-A6F7 TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N6 
       60.56        11.05        16.67       122.30        37.91         8.94 

$`DEL PEAK 12(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         0.07         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-MX-A5UG TCGA-MX-A5UJ 
        3.39        18.38         6.87         5.56         3.72         4.50 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
        8.61         4.67        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-SW-A7EB TCGA-ZA-A8F6 
       57.44         5.79         4.21 

  DEL PEAK 12(4Q34.3) MUTATED DEL PEAK 12(4Q34.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 12(4Q34.3) MUTATED DEL PEAK 12(4Q34.3) WILD-TYPE 
                       122.30                        116.38 
  DEL PEAK 12(4Q34.3) MUTATED DEL PEAK 12(4Q34.3) WILD-TYPE 
                        8.995                        12.000 
[1] "0.1 - 122.3 (9.0)"  "0.1 - 116.4 (12.0)"
[1] "hr=" "1.1"
D45V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 12(4Q34.3) MUTATED         0        3       14       18        14
  DEL PEAK 12(4Q34.3) WILD-TYPE       2        9       24        9        18
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 12(4Q34.3) MUTATED          18         1         29         19
  DEL PEAK 12(4Q34.3) WILD-TYPE        29         2         32         26
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 12(4Q34.3) MUTATED           17       10
  DEL PEAK 12(4Q34.3) WILD-TYPE         15       21
D45V3, multiclass
            clus
vv           DEL PEAK 12(4Q34.3) MUTATED DEL PEAK 12(4Q34.3) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             3                             9
  STAGE IB                            14                            24
  STAGE II                            18                             9
  STAGE IIA                           14                            18
  STAGE IIB                           18                            29
  STAGE III                            1                             2
  STAGE IIIA                          29                            32
  STAGE IIIB                          19                            26
  STAGE IIIC                          17                            15
  STAGE IV                            10                            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 12(4Q34.3) MUTATED    7 33 66 38
  DEL PEAK 12(4Q34.3) WILD-TYPE 13 52 80 47
D45V4, multiclass
    clus
vv   DEL PEAK 12(4Q34.3) MUTATED DEL PEAK 12(4Q34.3) WILD-TYPE
  T1                           7                            13
  T2                          33                            52
  T3                          66                            80
  T4                          38                            47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 12(4Q34.3) MUTATED   46 40 28 31
  DEL PEAK 12(4Q34.3) WILD-TYPE 63 52 38 36
D45V5, multiclass
    clus
vv   DEL PEAK 12(4Q34.3) MUTATED DEL PEAK 12(4Q34.3) WILD-TYPE
  N0                          46                            63
  N1                          40                            52
  N2                          28                            38
  N3                          31                            36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK 12(4Q34.3) MUTATED   135   6   8
  DEL PEAK 12(4Q34.3) WILD-TYPE 173  15   9
D45V6, multiclass
    clus
vv   DEL PEAK 12(4Q34.3) MUTATED DEL PEAK 12(4Q34.3) WILD-TYPE
  M0                         135                           173
  M1                           6                            15
  MX                           8                             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"
D45V7, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q34.3) MUTATED    63  86
  DEL PEAK 12(4Q34.3) WILD-TYPE  74 123
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q34.3) MUTATED     63   86
  DEL PEAK 12(4Q34.3) WILD-TYPE   74  123
        clus
vv       DEL PEAK 12(4Q34.3) MUTATED DEL PEAK 12(4Q34.3) WILD-TYPE
  FEMALE                          63                            74
  MALE                            86                           123
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 12(4Q34.3) MUTATED                                      19
  DEL PEAK 12(4Q34.3) WILD-TYPE                                    43
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 12(4Q34.3) MUTATED                                                       63
  DEL PEAK 12(4Q34.3) WILD-TYPE                                                     91
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 12(4Q34.3) MUTATED                                                                  28
  DEL PEAK 12(4Q34.3) WILD-TYPE                                                                26
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 12(4Q34.3) MUTATED                                                 25
  DEL PEAK 12(4Q34.3) WILD-TYPE                                               20
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 12(4Q34.3) MUTATED                                                           1
  DEL PEAK 12(4Q34.3) WILD-TYPE                                                         0
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 12(4Q34.3) MUTATED                                                          7
  DEL PEAK 12(4Q34.3) WILD-TYPE                                                       12
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 12(4Q34.3) MUTATED                                                           3
  DEL PEAK 12(4Q34.3) WILD-TYPE                                                         2
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 12(4Q34.3) MUTATED                                          2
  DEL PEAK 12(4Q34.3) WILD-TYPE                                        2
D45V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 12(4Q34.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      19
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     63
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          28
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           25
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    2
                                                                   clus
vv                                                                  DEL PEAK 12(4Q34.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        43
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       91
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            26
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             20
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V9, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q34.3) MUTATED     5 144
  DEL PEAK 12(4Q34.3) WILD-TYPE   2 195
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q34.3) MUTATED      5  144
  DEL PEAK 12(4Q34.3) WILD-TYPE    2  195
     clus
vv    DEL PEAK 12(4Q34.3) MUTATED DEL PEAK 12(4Q34.3) WILD-TYPE
  NO                            5                             2
  YES                         144                           195
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 12(4Q34.3) MUTATED   125   6   3   6
  DEL PEAK 12(4Q34.3) WILD-TYPE 152   7  10  19
D45V10, multiclass
    clus
vv   DEL PEAK 12(4Q34.3) MUTATED DEL PEAK 12(4Q34.3) WILD-TYPE
  R0                         125                           152
  R1                           6                             7
  R2                           3                            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"
D45V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 12(4Q34.3) MUTATED      39                         0
  DEL PEAK 12(4Q34.3) WILD-TYPE    45                         3
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 12(4Q34.3) MUTATED                                           0    88
  DEL PEAK 12(4Q34.3) WILD-TYPE                                         1   120
D45V12, multiclass
                                           clus
vv                                          DEL PEAK 12(4Q34.3) MUTATED
  ASIAN                                                              39
  BLACK OR AFRICAN AMERICAN                                           0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              88
                                           clus
vv                                          DEL PEAK 12(4Q34.3) WILD-TYPE
  ASIAN                                                                45
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               120
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(46) Variable = DEL PEAK 13(5Q11.2) MUTATION ANALYSIS
D46V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(5Q11.2) MUTATED    83  30
  DEL PEAK 13(5Q11.2) WILD-TYPE 139  63
  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                          113                           202 
  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                           30                            63 
$`DEL PEAK 13(5Q11.2) 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         2.27         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-A489 TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4304 TCGA-CG-4436 
        0.07         0.13         0.13         0.10        27.02         7.99 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 
        4.01        14.01        47.05        19.07        12.03        18.97 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-5579 
       22.98        30.97         1.02        15.02        55.04        11.93 
TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.84        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-A6EV TCGA-D7-A6EX 
       12.79        11.31        12.33        24.72        11.24        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-7829 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8238 
       19.53        17.06        13.58         0.56         1.55         1.51 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4GC 
        5.92        12.59        14.17         0.76         5.59         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 
       22.75        25.81        11.77         6.25         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 
       17.69         9.67        27.42        21.21        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IP-7968 
       18.38         5.19        13.08         6.44         5.56         2.53 
TCGA-KB-A6F7 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB 
       60.56        37.91       115.69         8.94         5.79 

$`DEL PEAK 13(5Q11.2) 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-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-A487 TCGA-CD-A48A 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-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 
       20.02         3.02        15.95         1.02         8.05        54.08 
TCGA-CG-4443 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 
       29.98        21.99         9.01         7.07        12.00         6.97 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07        65.10         4.01        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 
       12.36        12.66        19.13        20.55        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6818 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       17.85        10.55        16.80        19.50        17.19         0.23 
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-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-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
        8.12         0.39         3.02        22.29        59.54         5.03 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 
        0.23        18.08        26.47        14.27        11.41        12.10 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ 
       10.62        24.30        12.30        11.84        24.20        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        10.19         0.26 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-A6RJ 
       19.36        12.30         8.88         8.81         3.45         5.36 
TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-MX-A5UG TCGA-MX-A5UJ 
        1.41         6.87         1.81         5.56         3.72         4.50 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 
       11.05         8.61         4.67        16.67       122.30        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-ZA-A8F6 
      116.38        71.38        57.44         4.21 

  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                       115.69                        122.30 
  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                        10.68                         11.23 
[1] "0.1 - 115.7 (10.7)" "0.1 - 122.3 (11.2)"
[1] "hr=" "1.1"
D46V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 13(5Q11.2) MUTATED         0        4       13       11         9
  DEL PEAK 13(5Q11.2) WILD-TYPE       2        8       25       16        23
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 13(5Q11.2) MUTATED          21         0         31         15
  DEL PEAK 13(5Q11.2) WILD-TYPE        26         3         30         30
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 13(5Q11.2) MUTATED            8        6
  DEL PEAK 13(5Q11.2) WILD-TYPE         24       25
D46V3, multiclass
            clus
vv           DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             4                             8
  STAGE IB                            13                            25
  STAGE II                            11                            16
  STAGE IIA                            9                            23
  STAGE IIB                           21                            26
  STAGE III                            0                             3
  STAGE IIIA                          31                            30
  STAGE IIIB                          15                            30
  STAGE IIIC                           8                            24
  STAGE IV                             6                            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 13(5Q11.2) MUTATED    8 34 55 22
  DEL PEAK 13(5Q11.2) WILD-TYPE 12 51 91 63
D46V4, multiclass
    clus
vv   DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE
  T1                           8                            12
  T2                          34                            51
  T3                          55                            91
  T4                          22                            63
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 13(5Q11.2) MUTATED   36 34 30 19
  DEL PEAK 13(5Q11.2) WILD-TYPE 73 58 36 48
D46V5, multiclass
    clus
vv   DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE
  N0                          36                            73
  N1                          34                            58
  N2                          30                            36
  N3                          19                            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 13(5Q11.2) MUTATED   113   4   5
  DEL PEAK 13(5Q11.2) WILD-TYPE 195  17  12
D46V6, multiclass
    clus
vv   DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE
  M0                         113                           195
  M1                           4                            17
  MX                           5                            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"
D46V7, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q11.2) MUTATED    48  74
  DEL PEAK 13(5Q11.2) WILD-TYPE  89 135
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q11.2) MUTATED     48   74
  DEL PEAK 13(5Q11.2) WILD-TYPE   89  135
        clus
vv       DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE
  FEMALE                          48                            89
  MALE                            74                           135
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 13(5Q11.2) MUTATED                                       9
  DEL PEAK 13(5Q11.2) WILD-TYPE                                    53
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 13(5Q11.2) MUTATED                                                       54
  DEL PEAK 13(5Q11.2) WILD-TYPE                                                    100
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 13(5Q11.2) MUTATED                                                                  21
  DEL PEAK 13(5Q11.2) WILD-TYPE                                                                33
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 13(5Q11.2) MUTATED                                                 24
  DEL PEAK 13(5Q11.2) WILD-TYPE                                               21
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 13(5Q11.2) MUTATED                                                           1
  DEL PEAK 13(5Q11.2) WILD-TYPE                                                         0
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 13(5Q11.2) MUTATED                                                          9
  DEL PEAK 13(5Q11.2) WILD-TYPE                                                       10
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 13(5Q11.2) MUTATED                                                           2
  DEL PEAK 13(5Q11.2) WILD-TYPE                                                         3
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 13(5Q11.2) MUTATED                                          1
  DEL PEAK 13(5Q11.2) WILD-TYPE                                        3
D46V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 13(5Q11.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     54
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          21
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           24
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    1
                                                                   clus
vv                                                                  DEL PEAK 13(5Q11.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        53
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      100
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            33
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             21
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V9, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q11.2) MUTATED     4 118
  DEL PEAK 13(5Q11.2) WILD-TYPE   3 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q11.2) MUTATED      4  118
  DEL PEAK 13(5Q11.2) WILD-TYPE    3  221
     clus
vv    DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE
  NO                            4                             3
  YES                         118                           221
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 13(5Q11.2) MUTATED   101   8   2   5
  DEL PEAK 13(5Q11.2) WILD-TYPE 176   5  11  20
D46V10, multiclass
    clus
vv   DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE
  R0                         101                           176
  R1                           8                             5
  R2                           2                            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"
D46V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 13(5Q11.2) MUTATED      34                         1
  DEL PEAK 13(5Q11.2) WILD-TYPE    50                         2
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 13(5Q11.2) MUTATED                                           0    71
  DEL PEAK 13(5Q11.2) WILD-TYPE                                         1   137
D46V12, multiclass
                                           clus
vv                                          DEL PEAK 13(5Q11.2) MUTATED
  ASIAN                                                              34
  BLACK OR AFRICAN AMERICAN                                           1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              71
                                           clus
vv                                          DEL PEAK 13(5Q11.2) WILD-TYPE
  ASIAN                                                                50
  BLACK OR AFRICAN AMERICAN                                             2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               137
[1] 4 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 14(5Q23.2) MUTATION ANALYSIS
D47V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(5Q23.2) MUTATED    79  25
  DEL PEAK 14(5Q23.2) WILD-TYPE 143  68
  DEL PEAK 14(5Q23.2) MUTATED DEL PEAK 14(5Q23.2) WILD-TYPE 
                          104                           211 
  DEL PEAK 14(5Q23.2) MUTATED DEL PEAK 14(5Q23.2) WILD-TYPE 
                           25                            68 
$`DEL PEAK 14(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-8286 
       15.42        28.01         0.95        12.76        18.71        12.95 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8483 
        0.26         1.55         4.31        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-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.66         2.27         0.92         0.72        20.65        20.42 
TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 
       13.64        13.15        13.18         0.30         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A4MH 
        0.07         0.10         0.13         0.13         0.13         0.10 
TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4444 
       27.02         7.99        54.08         4.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5725 TCGA-D7-5579 
       19.07        18.97        30.97         1.02        15.02        11.93 
TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6822 
       18.84        17.19        10.26        15.98        12.79        12.33 
TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-A4YT TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 
       24.72        19.50        14.27        11.24        11.31         2.96 
TCGA-D7-A6F2 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-8211 
       15.65         7.79        16.24        72.23        19.53        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8610 
        0.56         1.55         1.51         5.92        12.59         0.76 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU 
        3.25        22.75        25.81        11.77         8.98         6.25 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 
        2.10        12.95        17.69         9.67        27.42        21.21 
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-A7NT TCGA-IP-7968 TCGA-KB-A6F7 TCGA-RD-A7BT TCGA-RD-A8MW TCGA-RD-A8N1 
        5.56         2.53        60.56         8.61        37.91       115.69 
TCGA-RD-A8N6 TCGA-SW-A7EB 
        8.94         5.79 

$`DEL PEAK 14(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-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-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        0.26        16.31         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-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-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
       15.68        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-A4J6 
       12.89         0.79        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM 
       19.36        13.51         0.46         1.15        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5803 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 
        2.83         3.25         0.07         0.07         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         0.07         0.13         0.13 
TCGA-CD-A48C 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-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4460 
       15.95         1.02         8.05        14.01        12.03        21.99 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5719 
        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-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        55.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 
       12.36        12.66        19.13        20.55        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8572 
       17.85        13.35        15.22        10.55        11.31        16.80 
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-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY 
        5.92        15.16        13.78        14.76        13.71        11.44 
TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6177 
        9.76         4.34         7.40         7.13         0.62         6.58 
TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
       14.47        21.27         8.12         0.39         3.02        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 
       17.06        59.54         5.03         0.23        18.08        26.47 
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-A4GJ TCGA-HU-A4GN 
        5.59        12.30        11.84        24.20        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H5 
        0.10         6.51        10.19         0.26        19.36        12.30 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RS 
        8.88         8.81         3.45         3.39         5.36         6.87 
TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW 
        1.81         5.56         3.72         4.50        11.05         4.67 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       16.67       122.30        40.64       116.38        71.38        57.44 
TCGA-ZA-A8F6 
        4.21 

  DEL PEAK 14(5Q23.2) MUTATED DEL PEAK 14(5Q23.2) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 14(5Q23.2) MUTATED DEL PEAK 14(5Q23.2) WILD-TYPE 
                       115.69                        122.30 
  DEL PEAK 14(5Q23.2) MUTATED DEL PEAK 14(5Q23.2) WILD-TYPE 
                       11.275                        10.620 
[1] "0.1 - 115.7 (11.3)" "0.1 - 122.3 (10.6)"
[1] "hr=" "1.4"
D47V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 14(5Q23.2) MUTATED         0        6       14       10         9
  DEL PEAK 14(5Q23.2) WILD-TYPE       2        6       24       17        23
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 14(5Q23.2) MUTATED          16         0         28         12
  DEL PEAK 14(5Q23.2) WILD-TYPE        31         3         33         33
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 14(5Q23.2) MUTATED            8        4
  DEL PEAK 14(5Q23.2) WILD-TYPE         24       27
D47V3, multiclass
            clus
vv           DEL PEAK 14(5Q23.2) MUTATED DEL PEAK 14(5Q23.2) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             6                             6
  STAGE IB                            14                            24
  STAGE II                            10                            17
  STAGE IIA                            9                            23
  STAGE IIB                           16                            31
  STAGE III                            0                             3
  STAGE IIIA                          28                            33
  STAGE IIIB                          12                            33
  STAGE IIIC                           8                            24
  STAGE IV                             4                            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 14(5Q23.2) MUTATED    9 27 50 21
  DEL PEAK 14(5Q23.2) WILD-TYPE 11 58 96 64
D47V4, multiclass
    clus
vv   DEL PEAK 14(5Q23.2) MUTATED DEL PEAK 14(5Q23.2) WILD-TYPE
  T1                           9                            11
  T2                          27                            58
  T3                          50                            96
  T4                          21                            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 14(5Q23.2) MUTATED   39 30 23 16
  DEL PEAK 14(5Q23.2) WILD-TYPE 70 62 43 51
D47V5, multiclass
    clus
vv   DEL PEAK 14(5Q23.2) MUTATED DEL PEAK 14(5Q23.2) WILD-TYPE
  N0                          39                            70
  N1                          30                            62
  N2                          23                            43
  N3                          16                            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 14(5Q23.2) MUTATED   102   2   5
  DEL PEAK 14(5Q23.2) WILD-TYPE 206  19  12
D47V6, multiclass
    clus
vv   DEL PEAK 14(5Q23.2) MUTATED DEL PEAK 14(5Q23.2) WILD-TYPE
  M0                         102                           206
  M1                           2                            19
  MX                           5                            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 14(5Q23.2) MUTATED    41  68
  DEL PEAK 14(5Q23.2) WILD-TYPE  96 141
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q23.2) MUTATED     41   68
  DEL PEAK 14(5Q23.2) WILD-TYPE   96  141
        clus
vv       DEL PEAK 14(5Q23.2) MUTATED DEL PEAK 14(5Q23.2) WILD-TYPE
  FEMALE                          41                            96
  MALE                            68                           141
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 14(5Q23.2) MUTATED                                       8
  DEL PEAK 14(5Q23.2) WILD-TYPE                                    54
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 14(5Q23.2) MUTATED                                                       50
  DEL PEAK 14(5Q23.2) WILD-TYPE                                                    104
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 14(5Q23.2) MUTATED                                                                  20
  DEL PEAK 14(5Q23.2) WILD-TYPE                                                                34
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 14(5Q23.2) MUTATED                                                 21
  DEL PEAK 14(5Q23.2) WILD-TYPE                                               24
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 14(5Q23.2) MUTATED                                                           1
  DEL PEAK 14(5Q23.2) WILD-TYPE                                                         0
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 14(5Q23.2) MUTATED                                                          6
  DEL PEAK 14(5Q23.2) WILD-TYPE                                                       13
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 14(5Q23.2) MUTATED                                                           2
  DEL PEAK 14(5Q23.2) WILD-TYPE                                                         3
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 14(5Q23.2) MUTATED                                          1
  DEL PEAK 14(5Q23.2) WILD-TYPE                                        3
D47V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 14(5Q23.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     50
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          20
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           21
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    1
                                                                   clus
vv                                                                  DEL PEAK 14(5Q23.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        54
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      104
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            34
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             24
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V9, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q23.2) MUTATED     3 106
  DEL PEAK 14(5Q23.2) WILD-TYPE   4 233
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q23.2) MUTATED      3  106
  DEL PEAK 14(5Q23.2) WILD-TYPE    4  233
     clus
vv    DEL PEAK 14(5Q23.2) MUTATED DEL PEAK 14(5Q23.2) WILD-TYPE
  NO                            3                             4
  YES                         106                           233
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 14(5Q23.2) MUTATED    93   6   2   4
  DEL PEAK 14(5Q23.2) WILD-TYPE 184   7  11  21
D47V10, multiclass
    clus
vv   DEL PEAK 14(5Q23.2) MUTATED DEL PEAK 14(5Q23.2) WILD-TYPE
  R0                          93                           184
  R1                           6                             7
  R2                           2                            11
  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"
D47V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 14(5Q23.2) MUTATED      30                         1
  DEL PEAK 14(5Q23.2) WILD-TYPE    54                         2
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 14(5Q23.2) MUTATED                                           1    64
  DEL PEAK 14(5Q23.2) WILD-TYPE                                         0   144
D47V12, multiclass
                                           clus
vv                                          DEL PEAK 14(5Q23.2) MUTATED
  ASIAN                                                              30
  BLACK OR AFRICAN AMERICAN                                           1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              64
                                           clus
vv                                          DEL PEAK 14(5Q23.2) WILD-TYPE
  ASIAN                                                                54
  BLACK OR AFRICAN AMERICAN                                             2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               144
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = DEL PEAK 15(6P25.3) MUTATION ANALYSIS
D48V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(6P25.3) MUTATED    59  20
  DEL PEAK 15(6P25.3) WILD-TYPE 163  73
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           79                           236 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           20                            73 
$`DEL PEAK 15(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         2.27         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        13.35        15.22        15.98        12.33 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-A4SO TCGA-F1-6875 
       11.31        11.44        15.65         7.40        16.24        72.23 
TCGA-F1-A72C TCGA-FP-8099 TCGA-FP-8211 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 
        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-A7NU TCGA-KB-A6F5 TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N5 
        1.81         5.56        16.67       122.30       115.69        57.44 
TCGA-RD-A8N6 
        8.94 

$`DEL PEAK 15(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         0.07         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        10.26        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-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS 
        5.56         2.53        60.56         3.72         4.50        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
        8.61         4.67        37.91        40.64       116.38        71.38 
TCGA-SW-A7EB TCGA-ZA-A8F6 
        5.79         4.21 

  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                       122.30                        116.38 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                        11.44                         10.65 
[1] "0.1 - 122.3 (11.4)" "0.1 - 116.4 (10.6)"
[1] "hr=" "1.4"
D48V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 15(6P25.3) MUTATED         0        4        9        6         8
  DEL PEAK 15(6P25.3) WILD-TYPE       2        8       29       21        24
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 15(6P25.3) MUTATED          12         0         18         11
  DEL PEAK 15(6P25.3) WILD-TYPE        35         3         43         34
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 15(6P25.3) MUTATED            7        5
  DEL PEAK 15(6P25.3) WILD-TYPE         25       26
D48V3, multiclass
            clus
vv           DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             4                             8
  STAGE IB                             9                            29
  STAGE II                             6                            21
  STAGE IIA                            8                            24
  STAGE IIB                           12                            35
  STAGE III                            0                             3
  STAGE IIIA                          18                            43
  STAGE IIIB                          11                            34
  STAGE IIIC                           7                            25
  STAGE IV                             5                            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 15(6P25.3) MUTATED     4  24  39  16
  DEL PEAK 15(6P25.3) WILD-TYPE  16  61 107  69
D48V4, multiclass
    clus
vv   DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  T1                           4                            16
  T2                          24                            61
  T3                          39                           107
  T4                          16                            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 15(6P25.3) MUTATED   28 21 18 13
  DEL PEAK 15(6P25.3) WILD-TYPE 81 71 48 54
D48V5, multiclass
    clus
vv   DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  N0                          28                            81
  N1                          21                            71
  N2                          18                            48
  N3                          13                            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
  DEL PEAK 15(6P25.3) MUTATED    76   2   7
  DEL PEAK 15(6P25.3) WILD-TYPE 232  19  10
D48V6, multiclass
    clus
vv   DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  M0                          76                           232
  M1                           2                            19
  MX                           7                            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 15(6P25.3) MUTATED    34  51
  DEL PEAK 15(6P25.3) WILD-TYPE 103 158
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED     34   51
  DEL PEAK 15(6P25.3) WILD-TYPE  103  158
        clus
vv       DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  FEMALE                          34                           103
  MALE                            51                           158
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 15(6P25.3) MUTATED                                      13
  DEL PEAK 15(6P25.3) WILD-TYPE                                    49
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 15(6P25.3) MUTATED                                                       35
  DEL PEAK 15(6P25.3) WILD-TYPE                                                    119
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 15(6P25.3) MUTATED                                                                  13
  DEL PEAK 15(6P25.3) WILD-TYPE                                                                41
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 15(6P25.3) MUTATED                                                 18
  DEL PEAK 15(6P25.3) WILD-TYPE                                               27
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 15(6P25.3) MUTATED                                                           0
  DEL PEAK 15(6P25.3) WILD-TYPE                                                         1
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 15(6P25.3) MUTATED                                                          4
  DEL PEAK 15(6P25.3) WILD-TYPE                                                       15
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 15(6P25.3) MUTATED                                                           1
  DEL PEAK 15(6P25.3) WILD-TYPE                                                         4
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 15(6P25.3) MUTATED                                          1
  DEL PEAK 15(6P25.3) WILD-TYPE                                        3
D48V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 15(6P25.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      13
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     35
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           18
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    1
                                                                   clus
vv                                                                  DEL PEAK 15(6P25.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      119
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            41
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             27
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V9, binary
                               cls
clus                              0   1
  DEL PEAK 15(6P25.3) MUTATED     1  84
  DEL PEAK 15(6P25.3) WILD-TYPE   6 255
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED      1   84
  DEL PEAK 15(6P25.3) WILD-TYPE    6  255
     clus
vv    DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  NO                            1                             6
  YES                          84                           255
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 15(6P25.3) MUTATED    67   7   1   6
  DEL PEAK 15(6P25.3) WILD-TYPE 210   6  12  19
D48V10, multiclass
    clus
vv   DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  R0                          67                           210
  R1                           7                             6
  R2                           1                            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"
D48V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 15(6P25.3) MUTATED      24                         1
  DEL PEAK 15(6P25.3) WILD-TYPE    60                         2
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 15(6P25.3) MUTATED                                           0    50
  DEL PEAK 15(6P25.3) WILD-TYPE                                         1   158
D48V12, multiclass
                                           clus
vv                                          DEL PEAK 15(6P25.3) MUTATED
  ASIAN                                                              24
  BLACK OR AFRICAN AMERICAN                                           1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              50
                                           clus
vv                                          DEL PEAK 15(6P25.3) WILD-TYPE
  ASIAN                                                                60
  BLACK OR AFRICAN AMERICAN                                             2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               158
[1] 4 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 16(6Q14.1) MUTATION ANALYSIS
D49V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 16(6Q14.1) MUTATED    45  16
  DEL PEAK 16(6Q14.1) WILD-TYPE 177  77
  DEL PEAK 16(6Q14.1) MUTATED DEL PEAK 16(6Q14.1) WILD-TYPE 
                           61                           254 
  DEL PEAK 16(6Q14.1) MUTATED DEL PEAK 16(6Q14.1) WILD-TYPE 
                           16                            77 
$`DEL PEAK 16(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         2.27         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         0.07 
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        13.35        10.26        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-ZA-A8F6 
        4.21 

$`DEL PEAK 16(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-IP-7968 
        3.45        18.81         3.39        18.38         5.36         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BT 
        5.56        60.56         3.72         4.50        11.05         8.61 
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-A8N6 TCGA-SW-A7EB 
        8.94         5.79 

  DEL PEAK 16(6Q14.1) MUTATED DEL PEAK 16(6Q14.1) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 16(6Q14.1) MUTATED DEL PEAK 16(6Q14.1) WILD-TYPE 
                       122.30                        116.38 
  DEL PEAK 16(6Q14.1) MUTATED DEL PEAK 16(6Q14.1) WILD-TYPE 
                       10.260                        11.145 
[1] "0.1 - 122.3 (10.3)" "0.1 - 116.4 (11.1)"
[1] "hr=" "1.1"
D49V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 16(6Q14.1) MUTATED         0        5        7        7         5
  DEL PEAK 16(6Q14.1) WILD-TYPE       2        7       31       20        27
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 16(6Q14.1) MUTATED           9         0         14          8
  DEL PEAK 16(6Q14.1) WILD-TYPE        38         3         47         37
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 16(6Q14.1) MUTATED            5        3
  DEL PEAK 16(6Q14.1) WILD-TYPE         27       28
D49V3, multiclass
            clus
vv           DEL PEAK 16(6Q14.1) MUTATED DEL PEAK 16(6Q14.1) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             5                             7
  STAGE IB                             7                            31
  STAGE II                             7                            20
  STAGE IIA                            5                            27
  STAGE IIB                            9                            38
  STAGE III                            0                             3
  STAGE IIIA                          14                            47
  STAGE IIIB                           8                            37
  STAGE IIIC                           5                            27
  STAGE IV                             3                            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(6Q14.1) MUTATED     7  18  30  10
  DEL PEAK 16(6Q14.1) WILD-TYPE  13  67 116  75
D49V4, multiclass
    clus
vv   DEL PEAK 16(6Q14.1) MUTATED DEL PEAK 16(6Q14.1) WILD-TYPE
  T1                           7                            13
  T2                          18                            67
  T3                          30                           116
  T4                          10                            75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 16(6Q14.1) MUTATED   22 21 12 10
  DEL PEAK 16(6Q14.1) WILD-TYPE 87 71 54 57
D49V5, multiclass
    clus
vv   DEL PEAK 16(6Q14.1) MUTATED DEL PEAK 16(6Q14.1) WILD-TYPE
  N0                          22                            87
  N1                          21                            71
  N2                          12                            54
  N3                          10                            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 16(6Q14.1) MUTATED    56   3   8
  DEL PEAK 16(6Q14.1) WILD-TYPE 252  18   9
D49V6, multiclass
    clus
vv   DEL PEAK 16(6Q14.1) MUTATED DEL PEAK 16(6Q14.1) WILD-TYPE
  M0                          56                           252
  M1                           3                            18
  MX                           8                             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 16(6Q14.1) MUTATED    18  49
  DEL PEAK 16(6Q14.1) WILD-TYPE 119 160
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6Q14.1) MUTATED     18   49
  DEL PEAK 16(6Q14.1) WILD-TYPE  119  160
        clus
vv       DEL PEAK 16(6Q14.1) MUTATED DEL PEAK 16(6Q14.1) WILD-TYPE
  FEMALE                          18                           119
  MALE                            49                           160
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 16(6Q14.1) MUTATED                                       9
  DEL PEAK 16(6Q14.1) WILD-TYPE                                    53
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 16(6Q14.1) MUTATED                                                       35
  DEL PEAK 16(6Q14.1) WILD-TYPE                                                    119
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 16(6Q14.1) MUTATED                                                                   8
  DEL PEAK 16(6Q14.1) WILD-TYPE                                                                46
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 16(6Q14.1) MUTATED                                                  9
  DEL PEAK 16(6Q14.1) WILD-TYPE                                               36
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 16(6Q14.1) MUTATED                                                           1
  DEL PEAK 16(6Q14.1) WILD-TYPE                                                         0
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 16(6Q14.1) MUTATED                                                          3
  DEL PEAK 16(6Q14.1) WILD-TYPE                                                       16
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 16(6Q14.1) MUTATED                                                           1
  DEL PEAK 16(6Q14.1) WILD-TYPE                                                         4
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 16(6Q14.1) MUTATED                                          1
  DEL PEAK 16(6Q14.1) WILD-TYPE                                        3
D49V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 16(6Q14.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     35
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           8
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            9
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    1
                                                                   clus
vv                                                                  DEL PEAK 16(6Q14.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        53
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      119
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            46
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             36
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V9, binary
                               cls
clus                              0   1
  DEL PEAK 16(6Q14.1) MUTATED     2  65
  DEL PEAK 16(6Q14.1) WILD-TYPE   5 274
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6Q14.1) MUTATED      2   65
  DEL PEAK 16(6Q14.1) WILD-TYPE    5  274
     clus
vv    DEL PEAK 16(6Q14.1) MUTATED DEL PEAK 16(6Q14.1) WILD-TYPE
  NO                            2                             5
  YES                          65                           274
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 16(6Q14.1) MUTATED    56   1   2   5
  DEL PEAK 16(6Q14.1) WILD-TYPE 221  12  11  20
D49V10, multiclass
    clus
vv   DEL PEAK 16(6Q14.1) MUTATED DEL PEAK 16(6Q14.1) WILD-TYPE
  R0                          56                           221
  R1                           1                            12
  R2                           2                            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"
D49V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 16(6Q14.1) MUTATED      15                         0
  DEL PEAK 16(6Q14.1) WILD-TYPE    69                         3
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 16(6Q14.1) MUTATED                                           0    41
  DEL PEAK 16(6Q14.1) WILD-TYPE                                         1   167
D49V12, multiclass
                                           clus
vv                                          DEL PEAK 16(6Q14.1) MUTATED
  ASIAN                                                              15
  BLACK OR AFRICAN AMERICAN                                           0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              41
                                           clus
vv                                          DEL PEAK 16(6Q14.1) WILD-TYPE
  ASIAN                                                                69
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(50) Variable = DEL PEAK 17(6Q26) MUTATION ANALYSIS
D50V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 17(6Q26) MUTATED    47  23
  DEL PEAK 17(6Q26) WILD-TYPE 175  70
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         70                         245 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         23                          70 
$`DEL PEAK 17(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         0.07 
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        13.35 
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-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N5 TCGA-RD-A8N6 
       16.67       122.30        57.44         8.94 

$`DEL PEAK 17(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         2.27 
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        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8574 
       12.79        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-A6RS TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG 
        1.41         6.87         2.53         5.56        60.56         3.72 
TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 
        4.50        11.05         8.61         4.67        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-SW-A7EB TCGA-ZA-A8F6 
      115.69       116.38        71.38         5.79         4.21 

  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                       0.07                        0.07 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                     122.30                      116.38 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                      8.085                      11.310 
[1] "0.1 - 122.3 (8.1)"  "0.1 - 116.4 (11.3)"
[1] "hr=" "1.3"
D50V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 17(6Q26) MUTATED         0        1        5        9         4
  DEL PEAK 17(6Q26) WILD-TYPE       2       11       33       18        28
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 17(6Q26) MUTATED          11         0         16         12
  DEL PEAK 17(6Q26) WILD-TYPE        36         3         45         33
                             vv
clus                          STAGE IIIC STAGE IV
  DEL PEAK 17(6Q26) MUTATED            5       11
  DEL PEAK 17(6Q26) WILD-TYPE         27       20
D50V3, multiclass
            clus
vv           DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  STAGE I                            0                           2
  STAGE IA                           1                          11
  STAGE IB                           5                          33
  STAGE II                           9                          18
  STAGE IIA                          4                          28
  STAGE IIB                         11                          36
  STAGE III                          0                           3
  STAGE IIIA                        16                          45
  STAGE IIIB                        12                          33
  STAGE IIIC                         5                          27
  STAGE IV                          11                          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 17(6Q26) MUTATED     2  19  40  14
  DEL PEAK 17(6Q26) WILD-TYPE  18  66 106  71
D50V4, multiclass
    clus
vv   DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  T1                         2                          18
  T2                        19                          66
  T3                        40                         106
  T4                        14                          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 17(6Q26) MUTATED   20 23 16 16
  DEL PEAK 17(6Q26) WILD-TYPE 89 69 50 51
D50V5, multiclass
    clus
vv   DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  N0                        20                          89
  N1                        23                          69
  N2                        16                          50
  N3                        16                          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 17(6Q26) MUTATED    65   6   5
  DEL PEAK 17(6Q26) WILD-TYPE 243  15  12
D50V6, multiclass
    clus
vv   DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  M0                        65                         243
  M1                         6                          15
  MX                         5                          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 17(6Q26) MUTATED    24  52
  DEL PEAK 17(6Q26) WILD-TYPE 113 157
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED     24   52
  DEL PEAK 17(6Q26) WILD-TYPE  113  157
        clus
vv       DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  FEMALE                        24                         113
  MALE                          52                         157
[1] 2 2
[1] FALSE
                             vv
clus                          STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 17(6Q26) MUTATED                                       9
  DEL PEAK 17(6Q26) WILD-TYPE                                    53
                             vv
clus                          STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 17(6Q26) MUTATED                                                       32
  DEL PEAK 17(6Q26) WILD-TYPE                                                    122
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 17(6Q26) MUTATED                                                                  11
  DEL PEAK 17(6Q26) WILD-TYPE                                                                43
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 17(6Q26) MUTATED                                                 14
  DEL PEAK 17(6Q26) WILD-TYPE                                               31
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 17(6Q26) MUTATED                                                           0
  DEL PEAK 17(6Q26) WILD-TYPE                                                         1
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 17(6Q26) MUTATED                                                          5
  DEL PEAK 17(6Q26) WILD-TYPE                                                       14
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 17(6Q26) MUTATED                                                           1
  DEL PEAK 17(6Q26) WILD-TYPE                                                         4
                             vv
clus                          STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 17(6Q26) MUTATED                                          3
  DEL PEAK 17(6Q26) WILD-TYPE                                        1
D50V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 17(6Q26) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                   32
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                         14
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                 0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                  5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                 1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                  3
                                                                   clus
vv                                                                  DEL PEAK 17(6Q26) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      53
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    122
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          43
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           31
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V9, binary
                             cls
clus                            0   1
  DEL PEAK 17(6Q26) MUTATED     2  74
  DEL PEAK 17(6Q26) WILD-TYPE   5 265
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED      2   74
  DEL PEAK 17(6Q26) WILD-TYPE    5  265
     clus
vv    DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  NO                          2                           5
  YES                        74                         265
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 17(6Q26) MUTATED    61   6   3   3
  DEL PEAK 17(6Q26) WILD-TYPE 216   7  10  22
D50V10, multiclass
    clus
vv   DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  R0                        61                         216
  R1                         6                           7
  R2                         3                          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"
D50V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 17(6Q26) MUTATED      17                         0
  DEL PEAK 17(6Q26) WILD-TYPE    67                         3
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 17(6Q26) MUTATED                                           0    43
  DEL PEAK 17(6Q26) WILD-TYPE                                         1   165
D50V12, multiclass
                                           clus
vv                                          DEL PEAK 17(6Q26) MUTATED
  ASIAN                                                            17
  BLACK OR AFRICAN AMERICAN                                         0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         0
  WHITE                                                            43
                                           clus
vv                                          DEL PEAK 17(6Q26) WILD-TYPE
  ASIAN                                                              67
  BLACK OR AFRICAN AMERICAN                                           3
  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(51) Variable = DEL PEAK 18(7Q31.1) MUTATION ANALYSIS
D51V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 18(7Q31.1) MUTATED    36  11
  DEL PEAK 18(7Q31.1) WILD-TYPE 186  82
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                           47                           268 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                           11                            82 
$`DEL PEAK 18(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         0.07         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-RD-A7BT TCGA-RD-A8MW TCGA-RD-A8N6 
       13.08         2.53         8.61        37.91         8.94 

$`DEL PEAK 18(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         2.27        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        13.35        17.19        10.26 
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-A6RS TCGA-IN-A7NT 
        5.36         5.19         1.41         6.44         6.87         5.56 
TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS 
        1.81         5.56        60.56         3.72         4.50        11.05 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        4.67        16.67       122.30        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-SW-A7EB TCGA-ZA-A8F6 
       71.38        57.44         5.79         4.21 

  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                        72.23                        122.30 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                       11.540                        10.585 
[1] "0.1 - 72.2 (11.5)"  "0.1 - 122.3 (10.6)"
[1] "hr=" "1.3"
D51V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 18(7Q31.1) MUTATED         0        2        3        6         5
  DEL PEAK 18(7Q31.1) WILD-TYPE       2       10       35       21        27
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 18(7Q31.1) MUTATED          10         0         12          6
  DEL PEAK 18(7Q31.1) WILD-TYPE        37         3         49         39
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 18(7Q31.1) MUTATED            3        4
  DEL PEAK 18(7Q31.1) WILD-TYPE         29       27
D51V3, multiclass
            clus
vv           DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             2                            10
  STAGE IB                             3                            35
  STAGE II                             6                            21
  STAGE IIA                            5                            27
  STAGE IIB                           10                            37
  STAGE III                            0                             3
  STAGE IIIA                          12                            49
  STAGE IIIB                           6                            39
  STAGE IIIC                           3                            29
  STAGE IV                             4                            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 18(7Q31.1) MUTATED     4  12  28   7
  DEL PEAK 18(7Q31.1) WILD-TYPE  16  73 118  78
D51V4, multiclass
    clus
vv   DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  T1                           4                            16
  T2                          12                            73
  T3                          28                           118
  T4                           7                            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 18(7Q31.1) MUTATED   11 19 15  6
  DEL PEAK 18(7Q31.1) WILD-TYPE 98 73 51 61
D51V5, multiclass
    clus
vv   DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  N0                          11                            98
  N1                          19                            73
  N2                          15                            51
  N3                           6                            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 18(7Q31.1) MUTATED    49   1   2
  DEL PEAK 18(7Q31.1) WILD-TYPE 259  20  15
D51V6, multiclass
    clus
vv   DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  M0                          49                           259
  M1                           1                            20
  MX                           2                            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"
D51V7, binary
                               cls
clus                              0   1
  DEL PEAK 18(7Q31.1) MUTATED    15  37
  DEL PEAK 18(7Q31.1) WILD-TYPE 122 172
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(7Q31.1) MUTATED     15   37
  DEL PEAK 18(7Q31.1) WILD-TYPE  122  172
        clus
vv       DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  FEMALE                          15                           122
  MALE                            37                           172
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 18(7Q31.1) MUTATED                                       5
  DEL PEAK 18(7Q31.1) WILD-TYPE                                    57
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 18(7Q31.1) MUTATED                                                       22
  DEL PEAK 18(7Q31.1) WILD-TYPE                                                    132
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 18(7Q31.1) MUTATED                                                                   9
  DEL PEAK 18(7Q31.1) WILD-TYPE                                                                45
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 18(7Q31.1) MUTATED                                                 11
  DEL PEAK 18(7Q31.1) WILD-TYPE                                               34
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 18(7Q31.1) MUTATED                                                           0
  DEL PEAK 18(7Q31.1) WILD-TYPE                                                         1
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 18(7Q31.1) MUTATED                                                          3
  DEL PEAK 18(7Q31.1) WILD-TYPE                                                       16
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 18(7Q31.1) MUTATED                                                           0
  DEL PEAK 18(7Q31.1) WILD-TYPE                                                         5
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 18(7Q31.1) MUTATED                                          0
  DEL PEAK 18(7Q31.1) WILD-TYPE                                        4
D51V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 18(7Q31.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     22
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           9
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           11
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    0
                                                                   clus
vv                                                                  DEL PEAK 18(7Q31.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        57
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            45
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             34
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      4
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V9, binary
                               cls
clus                              0   1
  DEL PEAK 18(7Q31.1) MUTATED     1  51
  DEL PEAK 18(7Q31.1) WILD-TYPE   6 288
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(7Q31.1) MUTATED      1   51
  DEL PEAK 18(7Q31.1) WILD-TYPE    6  288
     clus
vv    DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  NO                            1                             6
  YES                          51                           288
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 18(7Q31.1) MUTATED    44   1   2   2
  DEL PEAK 18(7Q31.1) WILD-TYPE 233  12  11  23
D51V10, multiclass
    clus
vv   DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  R0                          44                           233
  R1                           1                            12
  R2                           2                            11
  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"
D51V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 18(7Q31.1) MUTATED      15                         1
  DEL PEAK 18(7Q31.1) WILD-TYPE    69                         2
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 18(7Q31.1) MUTATED                                           1    27
  DEL PEAK 18(7Q31.1) WILD-TYPE                                         0   181
D51V12, multiclass
                                           clus
vv                                          DEL PEAK 18(7Q31.1) MUTATED
  ASIAN                                                              15
  BLACK OR AFRICAN AMERICAN                                           1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              27
                                           clus
vv                                          DEL PEAK 18(7Q31.1) WILD-TYPE
  ASIAN                                                                69
  BLACK OR AFRICAN AMERICAN                                             2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               181
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = DEL PEAK 19(7Q36.3) MUTATION ANALYSIS
D52V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 19(7Q36.3) MUTATED    49  15
  DEL PEAK 19(7Q36.3) WILD-TYPE 173  78
  DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE 
                           64                           251 
  DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE 
                           15                            78 
$`DEL PEAK 19(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         0.07         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        13.35        17.19        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8575 TCGA-D7-A6EV TCGA-D7-A6EX 
       12.79        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-A7NT TCGA-RD-A8MW 
       13.08         6.44         5.56        37.91 

$`DEL PEAK 19(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         2.27 
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        10.26 
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-RD-A7BS TCGA-RD-A7BT 
        5.56        60.56         3.72         4.50        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        4.67        16.67       122.30        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-ZA-A8F6 
       71.38        57.44         8.94         5.79         4.21 

  DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE 
                        54.08                        122.30 
  DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE 
                         9.44                         11.57 
[1] "0.1 - 54.1 (9.4)"   "0.1 - 122.3 (11.6)"
[1] "hr=" "1.1"
D52V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 19(7Q36.3) MUTATED         0        1        4        7         3
  DEL PEAK 19(7Q36.3) WILD-TYPE       2       11       34       20        29
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 19(7Q36.3) MUTATED          15         1         16          9
  DEL PEAK 19(7Q36.3) WILD-TYPE        32         2         45         36
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 19(7Q36.3) MUTATED            6        6
  DEL PEAK 19(7Q36.3) WILD-TYPE         26       25
D52V3, multiclass
            clus
vv           DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             1                            11
  STAGE IB                             4                            34
  STAGE II                             7                            20
  STAGE IIA                            3                            29
  STAGE IIB                           15                            32
  STAGE III                            1                             2
  STAGE IIIA                          16                            45
  STAGE IIIB                           9                            36
  STAGE IIIC                           6                            26
  STAGE IV                             6                            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 19(7Q36.3) MUTATED     5  16  35  12
  DEL PEAK 19(7Q36.3) WILD-TYPE  15  69 111  73
D52V4, multiclass
    clus
vv   DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE
  T1                           5                            15
  T2                          16                            69
  T3                          35                           111
  T4                          12                            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 19(7Q36.3) MUTATED   14 24 18 12
  DEL PEAK 19(7Q36.3) WILD-TYPE 95 68 48 55
D52V5, multiclass
    clus
vv   DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE
  N0                          14                            95
  N1                          24                            68
  N2                          18                            48
  N3                          12                            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                             M0  M1  MX
  DEL PEAK 19(7Q36.3) MUTATED    64   4   2
  DEL PEAK 19(7Q36.3) WILD-TYPE 244  17  15
D52V6, multiclass
    clus
vv   DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE
  M0                          64                           244
  M1                           4                            17
  MX                           2                            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"
D52V7, binary
                               cls
clus                              0   1
  DEL PEAK 19(7Q36.3) MUTATED    27  43
  DEL PEAK 19(7Q36.3) WILD-TYPE 110 166
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(7Q36.3) MUTATED     27   43
  DEL PEAK 19(7Q36.3) WILD-TYPE  110  166
        clus
vv       DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE
  FEMALE                          27                           110
  MALE                            43                           166
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 19(7Q36.3) MUTATED                                      10
  DEL PEAK 19(7Q36.3) WILD-TYPE                                    52
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 19(7Q36.3) MUTATED                                                       31
  DEL PEAK 19(7Q36.3) WILD-TYPE                                                    123
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 19(7Q36.3) MUTATED                                                                   9
  DEL PEAK 19(7Q36.3) WILD-TYPE                                                                45
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 19(7Q36.3) MUTATED                                                 13
  DEL PEAK 19(7Q36.3) WILD-TYPE                                               32
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 19(7Q36.3) MUTATED                                                           0
  DEL PEAK 19(7Q36.3) WILD-TYPE                                                         1
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 19(7Q36.3) MUTATED                                                          5
  DEL PEAK 19(7Q36.3) WILD-TYPE                                                       14
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 19(7Q36.3) MUTATED                                                           0
  DEL PEAK 19(7Q36.3) WILD-TYPE                                                         5
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 19(7Q36.3) MUTATED                                          0
  DEL PEAK 19(7Q36.3) WILD-TYPE                                        4
D52V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 19(7Q36.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      10
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     31
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           9
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           13
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    0
                                                                   clus
vv                                                                  DEL PEAK 19(7Q36.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        52
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      123
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            45
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             32
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      4
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V9, binary
                               cls
clus                              0   1
  DEL PEAK 19(7Q36.3) MUTATED     3  67
  DEL PEAK 19(7Q36.3) WILD-TYPE   4 272
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(7Q36.3) MUTATED      3   67
  DEL PEAK 19(7Q36.3) WILD-TYPE    4  272
     clus
vv    DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE
  NO                            3                             4
  YES                          67                           272
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 19(7Q36.3) MUTATED    58   1   2   3
  DEL PEAK 19(7Q36.3) WILD-TYPE 219  12  11  22
D52V10, multiclass
    clus
vv   DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE
  R0                          58                           219
  R1                           1                            12
  R2                           2                            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"
D52V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 19(7Q36.3) MUTATED      19                         0
  DEL PEAK 19(7Q36.3) WILD-TYPE    65                         3
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 19(7Q36.3) MUTATED                                           0    42
  DEL PEAK 19(7Q36.3) WILD-TYPE                                         1   166
D52V12, multiclass
                                           clus
vv                                          DEL PEAK 19(7Q36.3) MUTATED
  ASIAN                                                              19
  BLACK OR AFRICAN AMERICAN                                           0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              42
                                           clus
vv                                          DEL PEAK 19(7Q36.3) WILD-TYPE
  ASIAN                                                                65
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(53) Variable = DEL PEAK 20(8P23.3) MUTATION ANALYSIS
D53V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 20(8P23.3) MUTATED    58  29
  DEL PEAK 20(8P23.3) WILD-TYPE 164  64
  DEL PEAK 20(8P23.3) MUTATED DEL PEAK 20(8P23.3) WILD-TYPE 
                           87                           228 
  DEL PEAK 20(8P23.3) MUTATED DEL PEAK 20(8P23.3) WILD-TYPE 
                           29                            64 
$`DEL PEAK 20(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         0.07         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-IP-7968 TCGA-KB-A6F5 TCGA-RD-A7BT TCGA-RD-A8MV 
        1.41         6.44         2.53         5.56         8.61       122.30 
TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB 
       37.91         8.94         5.79 

$`DEL PEAK 20(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         2.27        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        13.35        10.26        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-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
       60.56         3.72         4.50        11.05         4.67        16.67 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-ZA-A8F6 
       40.64       115.69       116.38        71.38        57.44         4.21 

  DEL PEAK 20(8P23.3) MUTATED DEL PEAK 20(8P23.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 20(8P23.3) MUTATED DEL PEAK 20(8P23.3) WILD-TYPE 
                       122.30                        116.38 
  DEL PEAK 20(8P23.3) MUTATED DEL PEAK 20(8P23.3) WILD-TYPE 
                       10.130                        11.275 
[1] "0.1 - 122.3 (10.1)" "0.1 - 116.4 (11.3)"
[1] "hr=" "1.2"
D53V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 20(8P23.3) MUTATED         1        4        5        8         8
  DEL PEAK 20(8P23.3) WILD-TYPE       1        8       33       19        24
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 20(8P23.3) MUTATED          13         0         13         16
  DEL PEAK 20(8P23.3) WILD-TYPE        34         3         48         29
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 20(8P23.3) MUTATED           11       12
  DEL PEAK 20(8P23.3) WILD-TYPE         21       19
D53V3, multiclass
            clus
vv           DEL PEAK 20(8P23.3) MUTATED DEL PEAK 20(8P23.3) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                             4                             8
  STAGE IB                             5                            33
  STAGE II                             8                            19
  STAGE IIA                            8                            24
  STAGE IIB                           13                            34
  STAGE III                            0                             3
  STAGE IIIA                          13                            48
  STAGE IIIB                          16                            29
  STAGE IIIC                          11                            21
  STAGE IV                            12                            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
  DEL PEAK 20(8P23.3) MUTATED     5  19  43  25
  DEL PEAK 20(8P23.3) WILD-TYPE  15  66 103  60
D53V4, multiclass
    clus
vv   DEL PEAK 20(8P23.3) MUTATED DEL PEAK 20(8P23.3) WILD-TYPE
  T1                           5                            15
  T2                          19                            66
  T3                          43                           103
  T4                          25                            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 20(8P23.3) MUTATED   27 20 21 24
  DEL PEAK 20(8P23.3) WILD-TYPE 82 72 45 43
D53V5, multiclass
    clus
vv   DEL PEAK 20(8P23.3) MUTATED DEL PEAK 20(8P23.3) WILD-TYPE
  N0                          27                            82
  N1                          20                            72
  N2                          21                            45
  N3                          24                            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 20(8P23.3) MUTATED    84   7   3
  DEL PEAK 20(8P23.3) WILD-TYPE 224  14  14
D53V6, multiclass
    clus
vv   DEL PEAK 20(8P23.3) MUTATED DEL PEAK 20(8P23.3) WILD-TYPE
  M0                          84                           224
  M1                           7                            14
  MX                           3                            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"
D53V7, binary
                               cls
clus                              0   1
  DEL PEAK 20(8P23.3) MUTATED    30  64
  DEL PEAK 20(8P23.3) WILD-TYPE 107 145
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(8P23.3) MUTATED     30   64
  DEL PEAK 20(8P23.3) WILD-TYPE  107  145
        clus
vv       DEL PEAK 20(8P23.3) MUTATED DEL PEAK 20(8P23.3) WILD-TYPE
  FEMALE                          30                           107
  MALE                            64                           145
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 20(8P23.3) MUTATED                                       6
  DEL PEAK 20(8P23.3) WILD-TYPE                                    56
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 20(8P23.3) MUTATED                                                       46
  DEL PEAK 20(8P23.3) WILD-TYPE                                                    108
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 20(8P23.3) MUTATED                                                                  17
  DEL PEAK 20(8P23.3) WILD-TYPE                                                                37
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 20(8P23.3) MUTATED                                                 17
  DEL PEAK 20(8P23.3) WILD-TYPE                                               28
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 20(8P23.3) MUTATED                                                           0
  DEL PEAK 20(8P23.3) WILD-TYPE                                                         1
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 20(8P23.3) MUTATED                                                          5
  DEL PEAK 20(8P23.3) WILD-TYPE                                                       14
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 20(8P23.3) MUTATED                                                           2
  DEL PEAK 20(8P23.3) WILD-TYPE                                                         3
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 20(8P23.3) MUTATED                                          0
  DEL PEAK 20(8P23.3) WILD-TYPE                                        4
D53V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 20(8P23.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     46
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           17
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    0
                                                                   clus
vv                                                                  DEL PEAK 20(8P23.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      108
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             28
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      4
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V9, binary
                               cls
clus                              0   1
  DEL PEAK 20(8P23.3) MUTATED     2  92
  DEL PEAK 20(8P23.3) WILD-TYPE   5 247
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(8P23.3) MUTATED      2   92
  DEL PEAK 20(8P23.3) WILD-TYPE    5  247
     clus
vv    DEL PEAK 20(8P23.3) MUTATED DEL PEAK 20(8P23.3) WILD-TYPE
  NO                            2                             5
  YES                          92                           247
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 20(8P23.3) MUTATED    75   5   6   3
  DEL PEAK 20(8P23.3) WILD-TYPE 202   8   7  22
D53V10, multiclass
    clus
vv   DEL PEAK 20(8P23.3) MUTATED DEL PEAK 20(8P23.3) WILD-TYPE
  R0                          75                           202
  R1                           5                             8
  R2                           6                             7
  RX                           3                            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 20(8P23.3) MUTATED      24                         2
  DEL PEAK 20(8P23.3) WILD-TYPE    60                         1
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 20(8P23.3) MUTATED                                           1    49
  DEL PEAK 20(8P23.3) WILD-TYPE                                         0   159
D53V12, multiclass
                                           clus
vv                                          DEL PEAK 20(8P23.3) MUTATED
  ASIAN                                                              24
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              49
                                           clus
vv                                          DEL PEAK 20(8P23.3) WILD-TYPE
  ASIAN                                                                60
  BLACK OR AFRICAN AMERICAN                                             1
  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(54) Variable = DEL PEAK 21(9P23) MUTATION ANALYSIS
D54V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 21(9P23) MUTATED    93  37
  DEL PEAK 21(9P23) WILD-TYPE 129  56
  DEL PEAK 21(9P23) MUTATED DEL PEAK 21(9P23) WILD-TYPE 
                        130                         185 
  DEL PEAK 21(9P23) MUTATED DEL PEAK 21(9P23) WILD-TYPE 
                         37                          56 
$`DEL PEAK 21(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         2.27         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 
        0.07         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        13.35        17.19        10.26        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-A6RS 
       18.38         5.36         5.19         1.41         6.44         6.87 
TCGA-IN-A7NT TCGA-KB-A6F5 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        5.56         5.56         8.61         4.67        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB 
       37.91       115.69         8.94         5.79 

$`DEL PEAK 21(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-RD-A7BS 
        1.81         2.53        60.56         3.72         4.50        11.05 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-ZA-A8F6 
       40.64       116.38        71.38        57.44         4.21 

  DEL PEAK 21(9P23) MUTATED DEL PEAK 21(9P23) WILD-TYPE 
                       0.07                        0.07 
  DEL PEAK 21(9P23) MUTATED DEL PEAK 21(9P23) WILD-TYPE 
                     122.30                      116.38 
  DEL PEAK 21(9P23) MUTATED DEL PEAK 21(9P23) WILD-TYPE 
                       9.44                       11.54 
[1] "0.1 - 122.3 (9.4)"  "0.1 - 116.4 (11.5)"
[1] "hr=" "1"  
D54V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 21(9P23) MUTATED         0        5       10       16        15
  DEL PEAK 21(9P23) WILD-TYPE       2        7       28       11        17
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 21(9P23) MUTATED          19         0         32         18
  DEL PEAK 21(9P23) WILD-TYPE        28         3         29         27
                             vv
clus                          STAGE IIIC STAGE IV
  DEL PEAK 21(9P23) MUTATED           10       13
  DEL PEAK 21(9P23) WILD-TYPE         22       18
D54V3, multiclass
            clus
vv           DEL PEAK 21(9P23) MUTATED DEL PEAK 21(9P23) WILD-TYPE
  STAGE I                            0                           2
  STAGE IA                           5                           7
  STAGE IB                          10                          28
  STAGE II                          16                          11
  STAGE IIA                         15                          17
  STAGE IIB                         19                          28
  STAGE III                          0                           3
  STAGE IIIA                        32                          29
  STAGE IIIB                        18                          27
  STAGE IIIC                        10                          22
  STAGE IV                          13                          18
[1] 11  2
[1] TRUE
[1] "dimension of 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(9P23) MUTATED    8 35 69 27
  DEL PEAK 21(9P23) WILD-TYPE 12 50 77 58
D54V4, multiclass
    clus
vv   DEL PEAK 21(9P23) MUTATED DEL PEAK 21(9P23) WILD-TYPE
  T1                         8                          12
  T2                        35                          50
  T3                        69                          77
  T4                        27                          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
  DEL PEAK 21(9P23) MUTATED   42 42 31 25
  DEL PEAK 21(9P23) WILD-TYPE 67 50 35 42
D54V5, multiclass
    clus
vv   DEL PEAK 21(9P23) MUTATED DEL PEAK 21(9P23) WILD-TYPE
  N0                        42                          67
  N1                        42                          50
  N2                        31                          35
  N3                        25                          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 21(9P23) MUTATED   133   6   5
  DEL PEAK 21(9P23) WILD-TYPE 175  15  12
D54V6, multiclass
    clus
vv   DEL PEAK 21(9P23) MUTATED DEL PEAK 21(9P23) WILD-TYPE
  M0                       133                         175
  M1                         6                          15
  MX                         5                          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"
D54V7, binary
                             cls
clus                            0   1
  DEL PEAK 21(9P23) MUTATED    56  88
  DEL PEAK 21(9P23) WILD-TYPE  81 121
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 21(9P23) MUTATED     56   88
  DEL PEAK 21(9P23) WILD-TYPE   81  121
        clus
vv       DEL PEAK 21(9P23) MUTATED DEL PEAK 21(9P23) WILD-TYPE
  FEMALE                        56                          81
  MALE                          88                         121
[1] 2 2
[1] FALSE
                             vv
clus                          STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 21(9P23) MUTATED                                      20
  DEL PEAK 21(9P23) WILD-TYPE                                    42
                             vv
clus                          STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 21(9P23) MUTATED                                                       62
  DEL PEAK 21(9P23) WILD-TYPE                                                     92
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 21(9P23) MUTATED                                                                  27
  DEL PEAK 21(9P23) WILD-TYPE                                                                27
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 21(9P23) MUTATED                                                 21
  DEL PEAK 21(9P23) WILD-TYPE                                               24
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 21(9P23) MUTATED                                                           1
  DEL PEAK 21(9P23) WILD-TYPE                                                         0
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 21(9P23) MUTATED                                                          9
  DEL PEAK 21(9P23) WILD-TYPE                                                       10
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 21(9P23) MUTATED                                                           2
  DEL PEAK 21(9P23) WILD-TYPE                                                         3
                             vv
clus                          STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 21(9P23) MUTATED                                          1
  DEL PEAK 21(9P23) WILD-TYPE                                        3
D54V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 21(9P23) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                    20
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                   62
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        27
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                         21
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                  9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                 2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                  1
                                                                   clus
vv                                                                  DEL PEAK 21(9P23) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      42
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     92
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          27
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           24
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V9, binary
                             cls
clus                            0   1
  DEL PEAK 21(9P23) MUTATED     4 140
  DEL PEAK 21(9P23) WILD-TYPE   3 199
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 21(9P23) MUTATED      4  140
  DEL PEAK 21(9P23) WILD-TYPE    3  199
     clus
vv    DEL PEAK 21(9P23) MUTATED DEL PEAK 21(9P23) WILD-TYPE
  NO                          4                           3
  YES                       140                         199
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 21(9P23) MUTATED   116   7   5   9
  DEL PEAK 21(9P23) WILD-TYPE 161   6   8  16
D54V10, multiclass
    clus
vv   DEL PEAK 21(9P23) MUTATED DEL PEAK 21(9P23) WILD-TYPE
  R0                       116                         161
  R1                         7                           6
  R2                         5                           8
  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"
D54V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 21(9P23) MUTATED      30                         0
  DEL PEAK 21(9P23) WILD-TYPE    54                         3
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 21(9P23) MUTATED                                           1    93
  DEL PEAK 21(9P23) WILD-TYPE                                         0   115
D54V12, multiclass
                                           clus
vv                                          DEL PEAK 21(9P23) MUTATED
  ASIAN                                                            30
  BLACK OR AFRICAN AMERICAN                                         0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         1
  WHITE                                                            93
                                           clus
vv                                          DEL PEAK 21(9P23) WILD-TYPE
  ASIAN                                                              54
  BLACK OR AFRICAN AMERICAN                                           3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             115
[1] 4 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 22(9P21.3) MUTATION ANALYSIS
D55V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 22(9P21.3) MUTATED    93  37
  DEL PEAK 22(9P21.3) WILD-TYPE 129  56
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                          130                           185 
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                           37                            56 
$`DEL PEAK 22(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         2.27         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 
        0.07         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        13.35        17.19        10.26 
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-A6RS TCGA-IN-A7NT TCGA-IP-7968 
        5.36         5.19         1.41         6.87         5.56         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW 
        5.56        60.56         8.61         4.67        16.67        37.91 
TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-ZA-A8F6 
      115.69         8.94         5.79         4.21 

$`DEL PEAK 22(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-RD-A7BS 
       13.08         6.44         1.81         3.72         4.50        11.05 
TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
      122.30        40.64       116.38        71.38        57.44 

  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                       115.69                        122.30 
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                         9.44                         11.54 
[1] "0.1 - 115.7 (9.4)"  "0.1 - 122.3 (11.5)"
[1] "hr=" "1"  
D55V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 22(9P21.3) MUTATED         0        7       16       16        12
  DEL PEAK 22(9P21.3) WILD-TYPE       2        5       22       11        20
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 22(9P21.3) MUTATED          20         1         29         18
  DEL PEAK 22(9P21.3) WILD-TYPE        27         2         32         27
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 22(9P21.3) MUTATED            6       11
  DEL PEAK 22(9P21.3) WILD-TYPE         26       20
D55V3, multiclass
            clus
vv           DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             7                             5
  STAGE IB                            16                            22
  STAGE II                            16                            11
  STAGE IIA                           12                            20
  STAGE IIB                           20                            27
  STAGE III                            1                             2
  STAGE IIIA                          29                            32
  STAGE IIIB                          18                            27
  STAGE IIIC                           6                            26
  STAGE IV                            11                            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 22(9P21.3) MUTATED    8 40 65 23
  DEL PEAK 22(9P21.3) WILD-TYPE 12 45 81 62
D55V4, multiclass
    clus
vv   DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  T1                           8                            12
  T2                          40                            45
  T3                          65                            81
  T4                          23                            62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 22(9P21.3) MUTATED   47 40 32 19
  DEL PEAK 22(9P21.3) WILD-TYPE 62 52 34 48
D55V5, multiclass
    clus
vv   DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  N0                          47                            62
  N1                          40                            52
  N2                          32                            34
  N3                          19                            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 22(9P21.3) MUTATED   128   5   7
  DEL PEAK 22(9P21.3) WILD-TYPE 180  16  10
D55V6, multiclass
    clus
vv   DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  M0                         128                           180
  M1                           5                            16
  MX                           7                            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"
D55V7, binary
                               cls
clus                              0   1
  DEL PEAK 22(9P21.3) MUTATED    57  83
  DEL PEAK 22(9P21.3) WILD-TYPE  80 126
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9P21.3) MUTATED     57   83
  DEL PEAK 22(9P21.3) WILD-TYPE   80  126
        clus
vv       DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  FEMALE                          57                            80
  MALE                            83                           126
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 22(9P21.3) MUTATED                                      16
  DEL PEAK 22(9P21.3) WILD-TYPE                                    46
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 22(9P21.3) MUTATED                                                       62
  DEL PEAK 22(9P21.3) WILD-TYPE                                                     92
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 22(9P21.3) MUTATED                                                                  28
  DEL PEAK 22(9P21.3) WILD-TYPE                                                                26
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 22(9P21.3) MUTATED                                                 20
  DEL PEAK 22(9P21.3) WILD-TYPE                                               25
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 22(9P21.3) MUTATED                                                           1
  DEL PEAK 22(9P21.3) WILD-TYPE                                                         0
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 22(9P21.3) MUTATED                                                          9
  DEL PEAK 22(9P21.3) WILD-TYPE                                                       10
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 22(9P21.3) MUTATED                                                           3
  DEL PEAK 22(9P21.3) WILD-TYPE                                                         2
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 22(9P21.3) MUTATED                                          0
  DEL PEAK 22(9P21.3) WILD-TYPE                                        4
D55V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 22(9P21.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      16
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     62
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          28
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           20
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    0
                                                                   clus
vv                                                                  DEL PEAK 22(9P21.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       92
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            26
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             25
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      4
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V9, binary
                               cls
clus                              0   1
  DEL PEAK 22(9P21.3) MUTATED     4 136
  DEL PEAK 22(9P21.3) WILD-TYPE   3 203
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9P21.3) MUTATED      4  136
  DEL PEAK 22(9P21.3) WILD-TYPE    3  203
     clus
vv    DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  NO                            4                             3
  YES                         136                           203
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 22(9P21.3) MUTATED   116   6   5   6
  DEL PEAK 22(9P21.3) WILD-TYPE 161   7   8  19
D55V10, multiclass
    clus
vv   DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  R0                         116                           161
  R1                           6                             7
  R2                           5                             8
  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"
D55V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 22(9P21.3) MUTATED      31                         1
  DEL PEAK 22(9P21.3) WILD-TYPE    53                         2
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 22(9P21.3) MUTATED                                           1    83
  DEL PEAK 22(9P21.3) WILD-TYPE                                         0   125
D55V12, multiclass
                                           clus
vv                                          DEL PEAK 22(9P21.3) MUTATED
  ASIAN                                                              31
  BLACK OR AFRICAN AMERICAN                                           1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              83
                                           clus
vv                                          DEL PEAK 22(9P21.3) WILD-TYPE
  ASIAN                                                                53
  BLACK OR AFRICAN AMERICAN                                             2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               125
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(56) Variable = DEL PEAK 23(9Q21.11) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(9Q21.11) MUTATED    55  21
  DEL PEAK 23(9Q21.11) WILD-TYPE 167  72
  DEL PEAK 23(9Q21.11) MUTATED DEL PEAK 23(9Q21.11) WILD-TYPE 
                            76                            239 
  DEL PEAK 23(9Q21.11) MUTATED DEL PEAK 23(9Q21.11) WILD-TYPE 
                            21                             72 
$`DEL PEAK 23(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         2.27         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         0.07 
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        13.35        10.26 
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-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB 
       16.67        37.91         8.94         5.79 

$`DEL PEAK 23(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-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 
        4.50        11.05         8.61         4.67       122.30        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-ZA-A8F6 
      115.69       116.38        71.38        57.44         4.21 

  DEL PEAK 23(9Q21.11) MUTATED DEL PEAK 23(9Q21.11) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 23(9Q21.11) MUTATED DEL PEAK 23(9Q21.11) WILD-TYPE 
                         72.23                         122.30 
  DEL PEAK 23(9Q21.11) MUTATED DEL PEAK 23(9Q21.11) WILD-TYPE 
                          9.44                          11.31 
[1] "0.1 - 72.2 (9.4)"   "0.1 - 122.3 (11.3)"
[1] "hr=" "1"  
D56V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 23(9Q21.11) MUTATED         0        2        7       10        13
  DEL PEAK 23(9Q21.11) WILD-TYPE       2       10       31       17        19
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 23(9Q21.11) MUTATED          10         0         18          9
  DEL PEAK 23(9Q21.11) WILD-TYPE        37         3         43         36
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 23(9Q21.11) MUTATED            8        4
  DEL PEAK 23(9Q21.11) WILD-TYPE         24       27
D56V3, multiclass
            clus
vv           DEL PEAK 23(9Q21.11) MUTATED DEL PEAK 23(9Q21.11) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              2                             10
  STAGE IB                              7                             31
  STAGE II                             10                             17
  STAGE IIA                            13                             19
  STAGE IIB                            10                             37
  STAGE III                             0                              3
  STAGE IIIA                           18                             43
  STAGE IIIB                            9                             36
  STAGE IIIC                            8                             24
  STAGE IV                              4                             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 23(9Q21.11) MUTATED     4  17  44  16
  DEL PEAK 23(9Q21.11) WILD-TYPE  16  68 102  69
D56V4, multiclass
    clus
vv   DEL PEAK 23(9Q21.11) MUTATED DEL PEAK 23(9Q21.11) WILD-TYPE
  T1                            4                             16
  T2                           17                             68
  T3                           44                            102
  T4                           16                             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(9Q21.11) MUTATED   29 23 18 12
  DEL PEAK 23(9Q21.11) WILD-TYPE 80 69 48 55
D56V5, multiclass
    clus
vv   DEL PEAK 23(9Q21.11) MUTATED DEL PEAK 23(9Q21.11) WILD-TYPE
  N0                           29                             80
  N1                           23                             69
  N2                           18                             48
  N3                           12                             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                              M0  M1  MX
  DEL PEAK 23(9Q21.11) MUTATED    79   1   4
  DEL PEAK 23(9Q21.11) WILD-TYPE 229  20  13
D56V6, multiclass
    clus
vv   DEL PEAK 23(9Q21.11) MUTATED DEL PEAK 23(9Q21.11) WILD-TYPE
  M0                           79                            229
  M1                            1                             20
  MX                            4                             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"
D56V7, binary
                                cls
clus                               0   1
  DEL PEAK 23(9Q21.11) MUTATED    30  54
  DEL PEAK 23(9Q21.11) WILD-TYPE 107 155
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(9Q21.11) MUTATED     30   54
  DEL PEAK 23(9Q21.11) WILD-TYPE  107  155
        clus
vv       DEL PEAK 23(9Q21.11) MUTATED DEL PEAK 23(9Q21.11) WILD-TYPE
  FEMALE                           30                            107
  MALE                             54                            155
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 23(9Q21.11) MUTATED                                      12
  DEL PEAK 23(9Q21.11) WILD-TYPE                                    50
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 23(9Q21.11) MUTATED                                                       42
  DEL PEAK 23(9Q21.11) WILD-TYPE                                                    112
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 23(9Q21.11) MUTATED                                                                  10
  DEL PEAK 23(9Q21.11) WILD-TYPE                                                                44
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 23(9Q21.11) MUTATED                                                 12
  DEL PEAK 23(9Q21.11) WILD-TYPE                                               33
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 23(9Q21.11) MUTATED                                                           1
  DEL PEAK 23(9Q21.11) WILD-TYPE                                                         0
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 23(9Q21.11) MUTATED                                                          5
  DEL PEAK 23(9Q21.11) WILD-TYPE                                                       14
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 23(9Q21.11) MUTATED                                                           2
  DEL PEAK 23(9Q21.11) WILD-TYPE                                                         3
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 23(9Q21.11) MUTATED                                          0
  DEL PEAK 23(9Q21.11) WILD-TYPE                                        4
D56V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 23(9Q21.11) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      42
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           10
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            12
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     0
                                                                   clus
vv                                                                  DEL PEAK 23(9Q21.11) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       112
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             44
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              33
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       4
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V9, binary
                                cls
clus                               0   1
  DEL PEAK 23(9Q21.11) MUTATED     2  82
  DEL PEAK 23(9Q21.11) WILD-TYPE   5 257
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(9Q21.11) MUTATED      2   82
  DEL PEAK 23(9Q21.11) WILD-TYPE    5  257
     clus
vv    DEL PEAK 23(9Q21.11) MUTATED DEL PEAK 23(9Q21.11) WILD-TYPE
  NO                             2                              5
  YES                           82                            257
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 23(9Q21.11) MUTATED    67   3   1   5
  DEL PEAK 23(9Q21.11) WILD-TYPE 210  10  12  20
D56V10, multiclass
    clus
vv   DEL PEAK 23(9Q21.11) MUTATED DEL PEAK 23(9Q21.11) WILD-TYPE
  R0                           67                            210
  R1                            3                             10
  R2                            1                             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"
D56V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 23(9Q21.11) MUTATED      24                         1
  DEL PEAK 23(9Q21.11) WILD-TYPE    60                         2
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 23(9Q21.11) MUTATED                                           0
  DEL PEAK 23(9Q21.11) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 23(9Q21.11) MUTATED      53
  DEL PEAK 23(9Q21.11) WILD-TYPE   155
D56V12, multiclass
                                           clus
vv                                          DEL PEAK 23(9Q21.11) MUTATED
  ASIAN                                                               24
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               53
                                           clus
vv                                          DEL PEAK 23(9Q21.11) WILD-TYPE
  ASIAN                                                                 60
  BLACK OR AFRICAN AMERICAN                                              2
  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(57) Variable = DEL PEAK 24(10P15.3) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 24(10P15.3) MUTATED    30  18
  DEL PEAK 24(10P15.3) WILD-TYPE 192  75
  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                            48                            267 
  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                            18                             75 
$`DEL PEAK 24(10P15.3) MUTATED`
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-7901 TCGA-BR-8059 
       18.35         6.18         7.00         0.82         0.95         0.82 
TCGA-BR-8060 TCGA-BR-8291 TCGA-BR-8365 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8683 
        1.32        16.31         2.96        20.22        11.54         0.59 
TCGA-BR-A452 TCGA-BR-A4IY TCGA-BR-A4J7 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 
        0.66        12.89        19.36         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8533 TCGA-CD-A487 TCGA-CG-4301 TCGA-CG-4441 TCGA-CG-4455 
        0.13         0.13         0.13         3.02        14.01        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-A4YT TCGA-D7-A6EV TCGA-EQ-8122 TCGA-FP-7829 
       24.72         0.23        14.27        11.24         7.79        19.53 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-A4GU 
        0.56         1.55         0.23         5.92        14.17         6.25 
TCGA-IN-8462 TCGA-IN-A6RO TCGA-IN-A6RP TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB 
       18.81         1.41         6.44       115.69         8.94         5.79 

$`DEL PEAK 24(10P15.3) 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-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-6565 TCGA-BR-6566 TCGA-BR-6705 
       10.13        13.68        39.12         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-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-8077 
       12.43         0.69        12.76        18.71        17.49         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-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        0.26         1.55         1.48         7.40         6.18        19.50 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.36         0.26        22.19         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-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-8686 TCGA-BR-8687 
        7.53         0.49        15.81        16.44        15.68         0.62 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       10.68        12.56         1.15         3.02         2.27         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-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
       12.82         0.66        13.51         0.46        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 
       13.15        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         0.07 
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-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-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-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        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8572 
       17.19        10.26        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-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-A6EX 
        5.92        15.16        13.78        14.76        13.71        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-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        7.13         0.62        16.24         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-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-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-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-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       27.42        21.21         3.45         3.39        18.38         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 
        5.19        13.08         6.87         5.56         1.81         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BT 
        5.56        60.56         3.72         4.50        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-ZA-A8F6 
       71.38        57.44         4.21 

  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                        115.69                         122.30 
  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                          6.72                          11.44 
[1] "0.1 - 115.7 (6.7)"  "0.1 - 122.3 (11.4)"
[1] "hr=" "1.6"
D57V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 24(10P15.3) MUTATED         0        2        3        3         1
  DEL PEAK 24(10P15.3) WILD-TYPE       2       10       35       24        31
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 24(10P15.3) MUTATED          14         1         15          3
  DEL PEAK 24(10P15.3) WILD-TYPE        33         2         46         42
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 24(10P15.3) MUTATED            4        4
  DEL PEAK 24(10P15.3) WILD-TYPE         28       27
D57V3, multiclass
            clus
vv           DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              2                             10
  STAGE IB                              3                             35
  STAGE II                              3                             24
  STAGE IIA                             1                             31
  STAGE IIB                            14                             33
  STAGE III                             1                              2
  STAGE IIIA                           15                             46
  STAGE IIIB                            3                             42
  STAGE IIIC                            4                             28
  STAGE IV                              4                             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 24(10P15.3) MUTATED     3  16  20  11
  DEL PEAK 24(10P15.3) WILD-TYPE  17  69 126  74
D57V4, multiclass
    clus
vv   DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  T1                            3                             17
  T2                           16                             69
  T3                           20                            126
  T4                           11                             74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 24(10P15.3) MUTATED   10 18 14  8
  DEL PEAK 24(10P15.3) WILD-TYPE 99 74 52 59
D57V5, multiclass
    clus
vv   DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  N0                           10                             99
  N1                           18                             74
  N2                           14                             52
  N3                            8                             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 24(10P15.3) MUTATED    49   2   3
  DEL PEAK 24(10P15.3) WILD-TYPE 259  19  14
D57V6, multiclass
    clus
vv   DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  M0                           49                            259
  M1                            2                             19
  MX                            3                             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"
D57V7, binary
                                cls
clus                               0   1
  DEL PEAK 24(10P15.3) MUTATED    19  35
  DEL PEAK 24(10P15.3) WILD-TYPE 118 174
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10P15.3) MUTATED     19   35
  DEL PEAK 24(10P15.3) WILD-TYPE  118  174
        clus
vv       DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  FEMALE                           19                            118
  MALE                             35                            174
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 24(10P15.3) MUTATED                                       6
  DEL PEAK 24(10P15.3) WILD-TYPE                                    56
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 24(10P15.3) MUTATED                                                       21
  DEL PEAK 24(10P15.3) WILD-TYPE                                                    133
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 24(10P15.3) MUTATED                                                                   7
  DEL PEAK 24(10P15.3) WILD-TYPE                                                                47
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 24(10P15.3) MUTATED                                                 10
  DEL PEAK 24(10P15.3) WILD-TYPE                                               35
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 24(10P15.3) MUTATED                                                           0
  DEL PEAK 24(10P15.3) WILD-TYPE                                                         1
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 24(10P15.3) MUTATED                                                          7
  DEL PEAK 24(10P15.3) WILD-TYPE                                                       12
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 24(10P15.3) MUTATED                                                           0
  DEL PEAK 24(10P15.3) WILD-TYPE                                                         5
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 24(10P15.3) MUTATED                                          2
  DEL PEAK 24(10P15.3) WILD-TYPE                                        2
D57V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 24(10P15.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      21
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            10
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
                                                                   clus
vv                                                                  DEL PEAK 24(10P15.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             47
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              35
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V9, binary
                                cls
clus                               0   1
  DEL PEAK 24(10P15.3) MUTATED     1  53
  DEL PEAK 24(10P15.3) WILD-TYPE   6 286
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10P15.3) MUTATED      1   53
  DEL PEAK 24(10P15.3) WILD-TYPE    6  286
     clus
vv    DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  NO                             1                              6
  YES                           53                            286
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 24(10P15.3) MUTATED    42   3   1   6
  DEL PEAK 24(10P15.3) WILD-TYPE 235  10  12  19
D57V10, multiclass
    clus
vv   DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  R0                           42                            235
  R1                            3                             10
  R2                            1                             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"
D57V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 24(10P15.3) MUTATED      14                         0
  DEL PEAK 24(10P15.3) WILD-TYPE    70                         3
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 24(10P15.3) MUTATED                                           0
  DEL PEAK 24(10P15.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 24(10P15.3) MUTATED      34
  DEL PEAK 24(10P15.3) WILD-TYPE   174
D57V12, multiclass
                                           clus
vv                                          DEL PEAK 24(10P15.3) MUTATED
  ASIAN                                                               14
  BLACK OR AFRICAN AMERICAN                                            0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               34
                                           clus
vv                                          DEL PEAK 24(10P15.3) WILD-TYPE
  ASIAN                                                                 70
  BLACK OR AFRICAN AMERICAN                                              3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                174
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(58) Variable = DEL PEAK 25(10Q22.3) MUTATION ANALYSIS
D58V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(10Q22.3) MUTATED    34  14
  DEL PEAK 25(10Q22.3) WILD-TYPE 188  79
  DEL PEAK 25(10Q22.3) MUTATED DEL PEAK 25(10Q22.3) WILD-TYPE 
                            48                            267 
  DEL PEAK 25(10Q22.3) MUTATED DEL PEAK 25(10Q22.3) WILD-TYPE 
                            14                             79 
$`DEL PEAK 25(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         2.27        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         0.07         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        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8578 TCGA-D7-A4YT TCGA-EQ-8122 
       15.22        15.98        12.79        21.14        14.27         7.79 
TCGA-FP-7829 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8604 
       19.53         1.55         0.23         5.92        14.17        12.10 
TCGA-HU-A4G6 TCGA-HU-A4GH TCGA-IN-8462 TCGA-IN-A6RO TCGA-RD-A8N6 TCGA-SW-A7EB 
       12.30        11.77        18.81         1.41         8.94         5.79 

$`DEL PEAK 25(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        13.35        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-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-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-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-8211 TCGA-FP-8631 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        5.03        13.58         0.56        18.08        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.27        12.59        11.41        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        11.84        24.20         3.25        22.75        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-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-HU-A4HD TCGA-IN-7806 
       12.30         9.67         8.88         8.81        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45         3.39        18.38         5.36         5.19        13.08 
TCGA-IN-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-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
       60.56         3.72         4.50        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-ZA-A8F6 
       71.38        57.44         4.21 

  DEL PEAK 25(10Q22.3) MUTATED DEL PEAK 25(10Q22.3) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 25(10Q22.3) MUTATED DEL PEAK 25(10Q22.3) WILD-TYPE 
                         28.01                         122.30 
  DEL PEAK 25(10Q22.3) MUTATED DEL PEAK 25(10Q22.3) WILD-TYPE 
                         8.465                         11.310 
[1] "0.1 - 28.0 (8.5)"   "0.1 - 122.3 (11.3)"
[1] "hr=" "1.2"
D58V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 25(10Q22.3) MUTATED         0        4        4        5         7
  DEL PEAK 25(10Q22.3) WILD-TYPE       2        8       34       22        25
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 25(10Q22.3) MUTATED           8         0         13          2
  DEL PEAK 25(10Q22.3) WILD-TYPE        39         3         48         43
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 25(10Q22.3) MUTATED            3        3
  DEL PEAK 25(10Q22.3) WILD-TYPE         29       28
D58V3, multiclass
            clus
vv           DEL PEAK 25(10Q22.3) MUTATED DEL PEAK 25(10Q22.3) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              4                              8
  STAGE IB                              4                             34
  STAGE II                              5                             22
  STAGE IIA                             7                             25
  STAGE IIB                             8                             39
  STAGE III                             0                              3
  STAGE IIIA                           13                             48
  STAGE IIIB                            2                             43
  STAGE IIIC                            3                             29
  STAGE IV                              3                             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 25(10Q22.3) MUTATED     4  18  22   5
  DEL PEAK 25(10Q22.3) WILD-TYPE  16  67 124  80
D58V4, multiclass
    clus
vv   DEL PEAK 25(10Q22.3) MUTATED DEL PEAK 25(10Q22.3) WILD-TYPE
  T1                            4                             16
  T2                           18                             67
  T3                           22                            124
  T4                            5                             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 25(10Q22.3) MUTATED   17 15  9  9
  DEL PEAK 25(10Q22.3) WILD-TYPE 92 77 57 58
D58V5, multiclass
    clus
vv   DEL PEAK 25(10Q22.3) MUTATED DEL PEAK 25(10Q22.3) WILD-TYPE
  N0                           17                             92
  N1                           15                             77
  N2                            9                             57
  N3                            9                             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 25(10Q22.3) MUTATED    49   2   2
  DEL PEAK 25(10Q22.3) WILD-TYPE 259  19  15
D58V6, multiclass
    clus
vv   DEL PEAK 25(10Q22.3) MUTATED DEL PEAK 25(10Q22.3) WILD-TYPE
  M0                           49                            259
  M1                            2                             19
  MX                            2                             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 25(10Q22.3) MUTATED    19  34
  DEL PEAK 25(10Q22.3) WILD-TYPE 118 175
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q22.3) MUTATED     19   34
  DEL PEAK 25(10Q22.3) WILD-TYPE  118  175
        clus
vv       DEL PEAK 25(10Q22.3) MUTATED DEL PEAK 25(10Q22.3) WILD-TYPE
  FEMALE                           19                            118
  MALE                             34                            175
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 25(10Q22.3) MUTATED                                       4
  DEL PEAK 25(10Q22.3) WILD-TYPE                                    58
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 25(10Q22.3) MUTATED                                                       22
  DEL PEAK 25(10Q22.3) WILD-TYPE                                                    132
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 25(10Q22.3) MUTATED                                                                  11
  DEL PEAK 25(10Q22.3) WILD-TYPE                                                                43
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 25(10Q22.3) MUTATED                                                  8
  DEL PEAK 25(10Q22.3) WILD-TYPE                                               37
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 25(10Q22.3) MUTATED                                                           1
  DEL PEAK 25(10Q22.3) WILD-TYPE                                                         0
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 25(10Q22.3) MUTATED                                                          3
  DEL PEAK 25(10Q22.3) WILD-TYPE                                                       16
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 25(10Q22.3) MUTATED                                                           1
  DEL PEAK 25(10Q22.3) WILD-TYPE                                                         4
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 25(10Q22.3) MUTATED                                          2
  DEL PEAK 25(10Q22.3) WILD-TYPE                                        2
D58V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 25(10Q22.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      22
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             8
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
                                                                   clus
vv                                                                  DEL PEAK 25(10Q22.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         58
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             43
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              37
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V9, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q22.3) MUTATED     2  51
  DEL PEAK 25(10Q22.3) WILD-TYPE   5 288
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q22.3) MUTATED      2   51
  DEL PEAK 25(10Q22.3) WILD-TYPE    5  288
     clus
vv    DEL PEAK 25(10Q22.3) MUTATED DEL PEAK 25(10Q22.3) WILD-TYPE
  NO                             2                              5
  YES                           51                            288
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 25(10Q22.3) MUTATED    38   2   2   4
  DEL PEAK 25(10Q22.3) WILD-TYPE 239  11  11  21
D58V10, multiclass
    clus
vv   DEL PEAK 25(10Q22.3) MUTATED DEL PEAK 25(10Q22.3) WILD-TYPE
  R0                           38                            239
  R1                            2                             11
  R2                            2                             11
  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"
D58V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 25(10Q22.3) MUTATED      14                         0
  DEL PEAK 25(10Q22.3) WILD-TYPE    70                         3
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 25(10Q22.3) MUTATED                                           0
  DEL PEAK 25(10Q22.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 25(10Q22.3) MUTATED      31
  DEL PEAK 25(10Q22.3) WILD-TYPE   177
D58V12, multiclass
                                           clus
vv                                          DEL PEAK 25(10Q22.3) MUTATED
  ASIAN                                                               14
  BLACK OR AFRICAN AMERICAN                                            0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               31
                                           clus
vv                                          DEL PEAK 25(10Q22.3) WILD-TYPE
  ASIAN                                                                 70
  BLACK OR AFRICAN AMERICAN                                              3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  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(59) Variable = DEL PEAK 26(10Q23.31) MUTATION ANALYSIS
D59V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 26(10Q23.31) MUTATED    54  22
  DEL PEAK 26(10Q23.31) WILD-TYPE 168  71
  DEL PEAK 26(10Q23.31) MUTATED DEL PEAK 26(10Q23.31) WILD-TYPE 
                             76                             239 
  DEL PEAK 26(10Q23.31) MUTATED DEL PEAK 26(10Q23.31) WILD-TYPE 
                             22                              71 
$`DEL PEAK 26(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         2.27        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         0.07         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        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A6F0 
       15.22        15.98        12.79        21.14        14.27         2.96 
TCGA-EQ-8122 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
        7.79         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-A7NU TCGA-RD-A8N6 TCGA-SW-A7EB 
        6.44         1.81         8.94         5.79 

$`DEL PEAK 26(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        13.35        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-RD-A7BS 
        2.53         5.56        60.56         3.72         4.50        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-ZA-A8F6 
      115.69       116.38        71.38        57.44         4.21 

  DEL PEAK 26(10Q23.31) MUTATED DEL PEAK 26(10Q23.31) WILD-TYPE 
                           0.07                            0.07 
  DEL PEAK 26(10Q23.31) MUTATED DEL PEAK 26(10Q23.31) WILD-TYPE 
                          55.04                          122.30 
  DEL PEAK 26(10Q23.31) MUTATED DEL PEAK 26(10Q23.31) WILD-TYPE 
                          9.735                          11.240 
[1] "0.1 - 55.0 (9.7)"   "0.1 - 122.3 (11.2)"
[1] "hr=" "1.1"
D59V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 26(10Q23.31) MUTATED         0        4       12        7         7
  DEL PEAK 26(10Q23.31) WILD-TYPE       2        8       26       20        25
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 26(10Q23.31) MUTATED          11         0         20          4
  DEL PEAK 26(10Q23.31) WILD-TYPE        36         3         41         41
                                 vv
clus                              STAGE IIIC STAGE IV
  DEL PEAK 26(10Q23.31) MUTATED            6        5
  DEL PEAK 26(10Q23.31) WILD-TYPE         26       26
D59V3, multiclass
            clus
vv           DEL PEAK 26(10Q23.31) MUTATED DEL PEAK 26(10Q23.31) WILD-TYPE
  STAGE I                                0                               2
  STAGE IA                               4                               8
  STAGE IB                              12                              26
  STAGE II                               7                              20
  STAGE IIA                              7                              25
  STAGE IIB                             11                              36
  STAGE III                              0                               3
  STAGE IIIA                            20                              41
  STAGE IIIB                             4                              41
  STAGE IIIC                             6                              26
  STAGE IV                               5                              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 26(10Q23.31) MUTATED     6  28  31  11
  DEL PEAK 26(10Q23.31) WILD-TYPE  14  57 115  74
D59V4, multiclass
    clus
vv   DEL PEAK 26(10Q23.31) MUTATED DEL PEAK 26(10Q23.31) WILD-TYPE
  T1                             6                              14
  T2                            28                              57
  T3                            31                             115
  T4                            11                              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2 N3
  DEL PEAK 26(10Q23.31) MUTATED   28 22 14 14
  DEL PEAK 26(10Q23.31) WILD-TYPE 81 70 52 53
D59V5, multiclass
    clus
vv   DEL PEAK 26(10Q23.31) MUTATED DEL PEAK 26(10Q23.31) WILD-TYPE
  N0                            28                              81
  N1                            22                              70
  N2                            14                              52
  N3                            14                              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
  DEL PEAK 26(10Q23.31) MUTATED    73   3   5
  DEL PEAK 26(10Q23.31) WILD-TYPE 235  18  12
D59V6, multiclass
    clus
vv   DEL PEAK 26(10Q23.31) MUTATED DEL PEAK 26(10Q23.31) WILD-TYPE
  M0                            73                             235
  M1                             3                              18
  MX                             5                              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 26(10Q23.31) MUTATED    32  49
  DEL PEAK 26(10Q23.31) WILD-TYPE 105 160
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(10Q23.31) MUTATED     32   49
  DEL PEAK 26(10Q23.31) WILD-TYPE  105  160
        clus
vv       DEL PEAK 26(10Q23.31) MUTATED DEL PEAK 26(10Q23.31) WILD-TYPE
  FEMALE                            32                             105
  MALE                              49                             160
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 26(10Q23.31) MUTATED                                       6
  DEL PEAK 26(10Q23.31) WILD-TYPE                                    56
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 26(10Q23.31) MUTATED                                                       37
  DEL PEAK 26(10Q23.31) WILD-TYPE                                                    117
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 26(10Q23.31) MUTATED                                                                  18
  DEL PEAK 26(10Q23.31) WILD-TYPE                                                                36
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 26(10Q23.31) MUTATED                                                 12
  DEL PEAK 26(10Q23.31) WILD-TYPE                                               33
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 26(10Q23.31) MUTATED                                                           1
  DEL PEAK 26(10Q23.31) WILD-TYPE                                                         0
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 26(10Q23.31) MUTATED                                                          4
  DEL PEAK 26(10Q23.31) WILD-TYPE                                                       15
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 26(10Q23.31) MUTATED                                                           1
  DEL PEAK 26(10Q23.31) WILD-TYPE                                                         4
                                 vv
clus                              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 26(10Q23.31) MUTATED                                          2
  DEL PEAK 26(10Q23.31) WILD-TYPE                                        2
D59V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 26(10Q23.31) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       37
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            18
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             12
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      2
                                                                   clus
vv                                                                  DEL PEAK 26(10Q23.31) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        117
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               33
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                        2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V9, binary
                                 cls
clus                                0   1
  DEL PEAK 26(10Q23.31) MUTATED     2  79
  DEL PEAK 26(10Q23.31) WILD-TYPE   5 260
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(10Q23.31) MUTATED      2   79
  DEL PEAK 26(10Q23.31) WILD-TYPE    5  260
     clus
vv    DEL PEAK 26(10Q23.31) MUTATED DEL PEAK 26(10Q23.31) WILD-TYPE
  NO                              2                               5
  YES                            79                             260
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 26(10Q23.31) MUTATED    63   3   3   6
  DEL PEAK 26(10Q23.31) WILD-TYPE 214  10  10  19
D59V10, multiclass
    clus
vv   DEL PEAK 26(10Q23.31) MUTATED DEL PEAK 26(10Q23.31) WILD-TYPE
  R0                            63                             214
  R1                             3                              10
  R2                             3                              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"
D59V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 26(10Q23.31) MUTATED      19                         1
  DEL PEAK 26(10Q23.31) WILD-TYPE    65                         2
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 26(10Q23.31) MUTATED                                           0
  DEL PEAK 26(10Q23.31) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 26(10Q23.31) MUTATED      48
  DEL PEAK 26(10Q23.31) WILD-TYPE   160
D59V12, multiclass
                                           clus
vv                                          DEL PEAK 26(10Q23.31) MUTATED
  ASIAN                                                                19
  BLACK OR AFRICAN AMERICAN                                             1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                48
                                           clus
vv                                          DEL PEAK 26(10Q23.31) WILD-TYPE
  ASIAN                                                                  65
  BLACK OR AFRICAN AMERICAN                                               2
  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(60) Variable = DEL PEAK 27(11P15.4) MUTATION ANALYSIS
D60V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(11P15.4) MUTATED    42  24
  DEL PEAK 27(11P15.4) WILD-TYPE 180  69
  DEL PEAK 27(11P15.4) MUTATED DEL PEAK 27(11P15.4) WILD-TYPE 
                            66                            249 
  DEL PEAK 27(11P15.4) MUTATED DEL PEAK 27(11P15.4) WILD-TYPE 
                            24                             69 
$`DEL PEAK 27(11P15.4) 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-A486 TCGA-CD-A48A 
        0.30         0.07         0.07         0.07         0.07         0.13 
TCGA-CG-4304 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 
       27.02        14.01        29.98        47.05        19.07        21.99 
TCGA-CG-4466 TCGA-CG-5717 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 
       18.97         6.97        12.03        15.02         4.01        55.04 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6527 
       12.66        11.93        20.55        18.84        18.54        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A74A TCGA-EQ-5647 
       15.22        15.98        21.14        14.27         7.40         0.62 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-8211 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
       72.23         8.12        13.58        26.47         5.92        12.59 
TCGA-HU-A4GD TCGA-HU-A4H0 TCGA-HU-A4H5 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       22.75         2.10        12.30        18.81         3.39        18.38 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N6 
        5.19        13.08         6.44        16.67        37.91         8.94 

$`DEL PEAK 27(11P15.4) 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         2.27        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-A487 TCGA-CD-A489 TCGA-CD-A48C 
        0.13         0.13         0.10         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-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-4455 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
       12.03         9.01         7.07        12.00        22.98        30.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        1.02         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        79.07        65.10        21.07         7.99        12.36 
TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6817 
       19.13        18.61        17.85        13.35        17.19        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV 
       17.19         0.23         6.97        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-A74B 
       11.44         9.76         2.96        15.65         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-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-HU-8238 TCGA-HU-8244 
        0.56         1.55         0.23        18.08         1.51        14.27 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
        5.59        12.30        11.84        24.20         3.25        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.25        10.19         0.26        12.95        19.36        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-A6RJ TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 
        5.36         1.41         6.87         5.56         1.81         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BT 
        5.56        60.56         3.72         4.50        11.05         8.61 
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-SW-A7EB TCGA-ZA-A8F6 
       57.44         5.79         4.21 

  DEL PEAK 27(11P15.4) MUTATED DEL PEAK 27(11P15.4) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 27(11P15.4) MUTATED DEL PEAK 27(11P15.4) WILD-TYPE 
                         72.23                         122.30 
  DEL PEAK 27(11P15.4) MUTATED DEL PEAK 27(11P15.4) WILD-TYPE 
                         12.87                          10.13 
[1] "0.1 - 72.2 (12.9)"  "0.1 - 122.3 (10.1)"
[1] "hr=" "1.2"
D60V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 27(11P15.4) MUTATED         0        3        9       10         5
  DEL PEAK 27(11P15.4) WILD-TYPE       2        9       29       17        27
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 27(11P15.4) MUTATED           7         0         16          5
  DEL PEAK 27(11P15.4) WILD-TYPE        40         3         45         40
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 27(11P15.4) MUTATED            7        6
  DEL PEAK 27(11P15.4) WILD-TYPE         25       25
D60V3, multiclass
            clus
vv           DEL PEAK 27(11P15.4) MUTATED DEL PEAK 27(11P15.4) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              3                              9
  STAGE IB                              9                             29
  STAGE II                             10                             17
  STAGE IIA                             5                             27
  STAGE IIB                             7                             40
  STAGE III                             0                              3
  STAGE IIIA                           16                             45
  STAGE IIIB                            5                             40
  STAGE IIIC                            7                             25
  STAGE IV                              6                             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 27(11P15.4) MUTATED     5  30  25   9
  DEL PEAK 27(11P15.4) WILD-TYPE  15  55 121  76
D60V4, multiclass
    clus
vv   DEL PEAK 27(11P15.4) MUTATED DEL PEAK 27(11P15.4) WILD-TYPE
  T1                            5                             15
  T2                           30                             55
  T3                           25                            121
  T4                            9                             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 27(11P15.4) MUTATED   21 22 13 14
  DEL PEAK 27(11P15.4) WILD-TYPE 88 70 53 53
D60V5, multiclass
    clus
vv   DEL PEAK 27(11P15.4) MUTATED DEL PEAK 27(11P15.4) WILD-TYPE
  N0                           21                             88
  N1                           22                             70
  N2                           13                             53
  N3                           14                             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
  DEL PEAK 27(11P15.4) MUTATED    65   4   3
  DEL PEAK 27(11P15.4) WILD-TYPE 243  17  14
D60V6, multiclass
    clus
vv   DEL PEAK 27(11P15.4) MUTATED DEL PEAK 27(11P15.4) WILD-TYPE
  M0                           65                            243
  M1                            4                             17
  MX                            3                             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"
D60V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(11P15.4) MUTATED    23  49
  DEL PEAK 27(11P15.4) WILD-TYPE 114 160
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(11P15.4) MUTATED     23   49
  DEL PEAK 27(11P15.4) WILD-TYPE  114  160
        clus
vv       DEL PEAK 27(11P15.4) MUTATED DEL PEAK 27(11P15.4) WILD-TYPE
  FEMALE                           23                            114
  MALE                             49                            160
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 27(11P15.4) MUTATED                                       8
  DEL PEAK 27(11P15.4) WILD-TYPE                                    54
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 27(11P15.4) MUTATED                                                       31
  DEL PEAK 27(11P15.4) WILD-TYPE                                                    123
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 27(11P15.4) MUTATED                                                                  13
  DEL PEAK 27(11P15.4) WILD-TYPE                                                                41
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 27(11P15.4) MUTATED                                                  9
  DEL PEAK 27(11P15.4) WILD-TYPE                                               36
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 27(11P15.4) MUTATED                                                           1
  DEL PEAK 27(11P15.4) WILD-TYPE                                                         0
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 27(11P15.4) MUTATED                                                          5
  DEL PEAK 27(11P15.4) WILD-TYPE                                                       14
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 27(11P15.4) MUTATED                                                           4
  DEL PEAK 27(11P15.4) WILD-TYPE                                                         1
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 27(11P15.4) MUTATED                                          1
  DEL PEAK 27(11P15.4) WILD-TYPE                                        3
D60V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 27(11P15.4) 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                                             9
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     1
                                                                   clus
vv                                                                  DEL PEAK 27(11P15.4) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         54
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       123
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             41
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              36
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V9, binary
                                cls
clus                               0   1
  DEL PEAK 27(11P15.4) MUTATED     3  69
  DEL PEAK 27(11P15.4) WILD-TYPE   4 270
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(11P15.4) MUTATED      3   69
  DEL PEAK 27(11P15.4) WILD-TYPE    4  270
     clus
vv    DEL PEAK 27(11P15.4) MUTATED DEL PEAK 27(11P15.4) WILD-TYPE
  NO                             3                              4
  YES                           69                            270
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 27(11P15.4) MUTATED    52   4   4   8
  DEL PEAK 27(11P15.4) WILD-TYPE 225   9   9  17
D60V10, multiclass
    clus
vv   DEL PEAK 27(11P15.4) MUTATED DEL PEAK 27(11P15.4) WILD-TYPE
  R0                           52                            225
  R1                            4                              9
  R2                            4                              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"
D60V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 27(11P15.4) MUTATED      16                         1
  DEL PEAK 27(11P15.4) WILD-TYPE    68                         2
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 27(11P15.4) MUTATED                                           0
  DEL PEAK 27(11P15.4) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 27(11P15.4) MUTATED      41
  DEL PEAK 27(11P15.4) WILD-TYPE   167
D60V12, multiclass
                                           clus
vv                                          DEL PEAK 27(11P15.4) MUTATED
  ASIAN                                                               16
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               41
                                           clus
vv                                          DEL PEAK 27(11P15.4) WILD-TYPE
  ASIAN                                                                 68
  BLACK OR AFRICAN AMERICAN                                              2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(61) Variable = DEL PEAK 28(11Q23.2) MUTATION ANALYSIS
D61V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 28(11Q23.2) MUTATED    43  25
  DEL PEAK 28(11Q23.2) WILD-TYPE 179  68
  DEL PEAK 28(11Q23.2) MUTATED DEL PEAK 28(11Q23.2) WILD-TYPE 
                            68                            247 
  DEL PEAK 28(11Q23.2) MUTATED DEL PEAK 28(11Q23.2) WILD-TYPE 
                            25                             68 
$`DEL PEAK 28(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         2.27         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        10.26 
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 
      115.69         8.94 

$`DEL PEAK 28(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         0.07         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        13.35        17.19        15.22 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        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-A6RS TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG 
       13.08         6.87         1.81         5.56        60.56         3.72 
TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        4.50        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-SW-A7EB 
       37.91        40.64       116.38        71.38        57.44         5.79 
TCGA-ZA-A8F6 
        4.21 

  DEL PEAK 28(11Q23.2) MUTATED DEL PEAK 28(11Q23.2) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 28(11Q23.2) MUTATED DEL PEAK 28(11Q23.2) WILD-TYPE 
                        115.69                         122.30 
  DEL PEAK 28(11Q23.2) MUTATED DEL PEAK 28(11Q23.2) WILD-TYPE 
                         6.705                         12.000 
[1] "0.1 - 115.7 (6.7)"  "0.1 - 122.3 (12.0)"
[1] "hr=" "1.8"
D61V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 28(11Q23.2) MUTATED         1        5        4       10         5
  DEL PEAK 28(11Q23.2) WILD-TYPE       1        7       34       17        27
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 28(11Q23.2) MUTATED           8         0         16          7
  DEL PEAK 28(11Q23.2) WILD-TYPE        39         3         45         38
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 28(11Q23.2) MUTATED            8        8
  DEL PEAK 28(11Q23.2) WILD-TYPE         24       23
D61V3, multiclass
            clus
vv           DEL PEAK 28(11Q23.2) MUTATED DEL PEAK 28(11Q23.2) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                              5                              7
  STAGE IB                              4                             34
  STAGE II                             10                             17
  STAGE IIA                             5                             27
  STAGE IIB                             8                             39
  STAGE III                             0                              3
  STAGE IIIA                           16                             45
  STAGE IIIB                            7                             38
  STAGE IIIC                            8                             24
  STAGE IV                              8                             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 28(11Q23.2) MUTATED     7  19  29  18
  DEL PEAK 28(11Q23.2) WILD-TYPE  13  66 117  67
D61V4, multiclass
    clus
vv   DEL PEAK 28(11Q23.2) MUTATED DEL PEAK 28(11Q23.2) WILD-TYPE
  T1                            7                             13
  T2                           19                             66
  T3                           29                            117
  T4                           18                             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 28(11Q23.2) MUTATED   20 18 21 14
  DEL PEAK 28(11Q23.2) WILD-TYPE 89 74 45 53
D61V5, multiclass
    clus
vv   DEL PEAK 28(11Q23.2) MUTATED DEL PEAK 28(11Q23.2) WILD-TYPE
  N0                           20                             89
  N1                           18                             74
  N2                           21                             45
  N3                           14                             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
  DEL PEAK 28(11Q23.2) MUTATED    59   7   8
  DEL PEAK 28(11Q23.2) WILD-TYPE 249  14   9
D61V6, multiclass
    clus
vv   DEL PEAK 28(11Q23.2) MUTATED DEL PEAK 28(11Q23.2) WILD-TYPE
  M0                           59                            249
  M1                            7                             14
  MX                            8                              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"
D61V7, binary
                                cls
clus                               0   1
  DEL PEAK 28(11Q23.2) MUTATED    26  48
  DEL PEAK 28(11Q23.2) WILD-TYPE 111 161
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(11Q23.2) MUTATED     26   48
  DEL PEAK 28(11Q23.2) WILD-TYPE  111  161
        clus
vv       DEL PEAK 28(11Q23.2) MUTATED DEL PEAK 28(11Q23.2) WILD-TYPE
  FEMALE                           26                            111
  MALE                             48                            161
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 28(11Q23.2) MUTATED                                       9
  DEL PEAK 28(11Q23.2) WILD-TYPE                                    53
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 28(11Q23.2) MUTATED                                                       33
  DEL PEAK 28(11Q23.2) WILD-TYPE                                                    121
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 28(11Q23.2) MUTATED                                                                  11
  DEL PEAK 28(11Q23.2) WILD-TYPE                                                                43
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 28(11Q23.2) MUTATED                                                 12
  DEL PEAK 28(11Q23.2) WILD-TYPE                                               33
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 28(11Q23.2) MUTATED                                                           1
  DEL PEAK 28(11Q23.2) WILD-TYPE                                                         0
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 28(11Q23.2) MUTATED                                                          5
  DEL PEAK 28(11Q23.2) WILD-TYPE                                                       14
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 28(11Q23.2) MUTATED                                                           1
  DEL PEAK 28(11Q23.2) WILD-TYPE                                                         4
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 28(11Q23.2) MUTATED                                          2
  DEL PEAK 28(11Q23.2) WILD-TYPE                                        2
D61V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 28(11Q23.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      33
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            12
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
                                                                   clus
vv                                                                  DEL PEAK 28(11Q23.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         53
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       121
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             43
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              33
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V9, binary
                                cls
clus                               0   1
  DEL PEAK 28(11Q23.2) MUTATED     2  72
  DEL PEAK 28(11Q23.2) WILD-TYPE   5 267
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(11Q23.2) MUTATED      2   72
  DEL PEAK 28(11Q23.2) WILD-TYPE    5  267
     clus
vv    DEL PEAK 28(11Q23.2) MUTATED DEL PEAK 28(11Q23.2) WILD-TYPE
  NO                             2                              5
  YES                           72                            267
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 28(11Q23.2) MUTATED    55   6   4   5
  DEL PEAK 28(11Q23.2) WILD-TYPE 222   7   9  20
D61V10, multiclass
    clus
vv   DEL PEAK 28(11Q23.2) MUTATED DEL PEAK 28(11Q23.2) WILD-TYPE
  R0                           55                            222
  R1                            6                              7
  R2                            4                              9
  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 28(11Q23.2) MUTATED      19                         0
  DEL PEAK 28(11Q23.2) WILD-TYPE    65                         3
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 28(11Q23.2) MUTATED                                           0
  DEL PEAK 28(11Q23.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 28(11Q23.2) MUTATED      43
  DEL PEAK 28(11Q23.2) WILD-TYPE   165
D61V12, multiclass
                                           clus
vv                                          DEL PEAK 28(11Q23.2) MUTATED
  ASIAN                                                               19
  BLACK OR AFRICAN AMERICAN                                            0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               43
                                           clus
vv                                          DEL PEAK 28(11Q23.2) WILD-TYPE
  ASIAN                                                                 65
  BLACK OR AFRICAN AMERICAN                                              3
  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(62) Variable = DEL PEAK 29(12P13.1) MUTATION ANALYSIS
D62V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(12P13.1) MUTATED    31  17
  DEL PEAK 29(12P13.1) WILD-TYPE 191  76
  DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE 
                            48                            267 
  DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE 
                            17                             76 
$`DEL PEAK 29(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         2.27        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         0.07         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 

$`DEL PEAK 29(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        13.35        17.19        10.26        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-A6RS TCGA-IN-A7NT TCGA-KB-A6F5 TCGA-KB-A6F7 
        1.41         6.44         6.87         5.56         5.56        60.56 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        3.72         4.50        11.05         8.61         4.67        16.67 
TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
      122.30        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-ZA-A8F6 
        8.94         5.79         4.21 

  DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE 
                         72.23                         122.30 
  DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE 
                          7.20                          11.41 
[1] "0.1 - 72.2 (7.2)"   "0.1 - 122.3 (11.4)"
[1] "hr=" "1.5"
D62V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 29(12P13.1) MUTATED         0        1       10        4         6
  DEL PEAK 29(12P13.1) WILD-TYPE       2       11       28       23        26
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 29(12P13.1) MUTATED           7         0         11          6
  DEL PEAK 29(12P13.1) WILD-TYPE        40         3         50         39
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 29(12P13.1) MUTATED            2        4
  DEL PEAK 29(12P13.1) WILD-TYPE         30       27
D62V3, multiclass
            clus
vv           DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              1                             11
  STAGE IB                             10                             28
  STAGE II                              4                             23
  STAGE IIA                             6                             26
  STAGE IIB                             7                             40
  STAGE III                             0                              3
  STAGE IIIA                           11                             50
  STAGE IIIB                            6                             39
  STAGE IIIC                            2                             30
  STAGE IV                              4                             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 29(12P13.1) MUTATED     1  20  24   6
  DEL PEAK 29(12P13.1) WILD-TYPE  19  65 122  79
D62V4, multiclass
    clus
vv   DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE
  T1                            1                             19
  T2                           20                             65
  T3                           24                            122
  T4                            6                             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 29(12P13.1) MUTATED   20 13  9  9
  DEL PEAK 29(12P13.1) WILD-TYPE 89 79 57 58
D62V5, multiclass
    clus
vv   DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE
  N0                           20                             89
  N1                           13                             79
  N2                            9                             57
  N3                            9                             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 29(12P13.1) MUTATED    47   3   3
  DEL PEAK 29(12P13.1) WILD-TYPE 261  18  14
D62V6, multiclass
    clus
vv   DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE
  M0                           47                            261
  M1                            3                             18
  MX                            3                             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 29(12P13.1) MUTATED    22  31
  DEL PEAK 29(12P13.1) WILD-TYPE 115 178
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(12P13.1) MUTATED     22   31
  DEL PEAK 29(12P13.1) WILD-TYPE  115  178
        clus
vv       DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE
  FEMALE                           22                            115
  MALE                             31                            178
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 29(12P13.1) MUTATED                                       2
  DEL PEAK 29(12P13.1) WILD-TYPE                                    60
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 29(12P13.1) MUTATED                                                       30
  DEL PEAK 29(12P13.1) WILD-TYPE                                                    124
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 29(12P13.1) MUTATED                                                                  11
  DEL PEAK 29(12P13.1) WILD-TYPE                                                                43
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 29(12P13.1) MUTATED                                                  7
  DEL PEAK 29(12P13.1) WILD-TYPE                                               38
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 29(12P13.1) MUTATED                                                           0
  DEL PEAK 29(12P13.1) WILD-TYPE                                                         1
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 29(12P13.1) MUTATED                                                          0
  DEL PEAK 29(12P13.1) WILD-TYPE                                                       19
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 29(12P13.1) MUTATED                                                           3
  DEL PEAK 29(12P13.1) WILD-TYPE                                                         2
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 29(12P13.1) MUTATED                                          0
  DEL PEAK 29(12P13.1) WILD-TYPE                                        4
D62V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 29(12P13.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      30
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             7
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     0
                                                                   clus
vv                                                                  DEL PEAK 29(12P13.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         60
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             43
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              38
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       4
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V9, binary
                                cls
clus                               0   1
  DEL PEAK 29(12P13.1) MUTATED     3  50
  DEL PEAK 29(12P13.1) WILD-TYPE   4 289
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(12P13.1) MUTATED      3   50
  DEL PEAK 29(12P13.1) WILD-TYPE    4  289
     clus
vv    DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE
  NO                             3                              4
  YES                           50                            289
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 29(12P13.1) MUTATED    39   2   2   5
  DEL PEAK 29(12P13.1) WILD-TYPE 238  11  11  20
D62V10, multiclass
    clus
vv   DEL PEAK 29(12P13.1) MUTATED DEL PEAK 29(12P13.1) WILD-TYPE
  R0                           39                            238
  R1                            2                             11
  R2                            2                             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"
D62V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 29(12P13.1) MUTATED      12                         1
  DEL PEAK 29(12P13.1) WILD-TYPE    72                         2
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 29(12P13.1) MUTATED                                           0
  DEL PEAK 29(12P13.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 29(12P13.1) MUTATED      32
  DEL PEAK 29(12P13.1) WILD-TYPE   176
D62V12, multiclass
                                           clus
vv                                          DEL PEAK 29(12P13.1) MUTATED
  ASIAN                                                               12
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               32
                                           clus
vv                                          DEL PEAK 29(12P13.1) WILD-TYPE
  ASIAN                                                                 72
  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(63) Variable = DEL PEAK 30(13Q12.11) MUTATION ANALYSIS
D63V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 30(13Q12.11) MUTATED    26  16
  DEL PEAK 30(13Q12.11) WILD-TYPE 196  77
  DEL PEAK 30(13Q12.11) MUTATED DEL PEAK 30(13Q12.11) WILD-TYPE 
                             42                             273 
  DEL PEAK 30(13Q12.11) MUTATED DEL PEAK 30(13Q12.11) WILD-TYPE 
                             16                              77 
$`DEL PEAK 30(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         0.07        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        13.35 
TCGA-D7-6527 TCGA-D7-6818 TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A6F2 TCGA-FP-7916 
       10.26        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-RD-A7BS TCGA-RD-A8N1 
       18.81         3.39         5.36         5.19        11.05       115.69 

$`DEL PEAK 30(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         2.27        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-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
       60.56         3.72         4.50         8.61         4.67        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
      122.30        37.91        40.64       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-ZA-A8F6 
        8.94         5.79         4.21 

  DEL PEAK 30(13Q12.11) MUTATED DEL PEAK 30(13Q12.11) WILD-TYPE 
                           0.07                            0.07 
  DEL PEAK 30(13Q12.11) MUTATED DEL PEAK 30(13Q12.11) WILD-TYPE 
                         115.69                          122.30 
  DEL PEAK 30(13Q12.11) MUTATED DEL PEAK 30(13Q12.11) WILD-TYPE 
                         10.405                          11.310 
[1] "0.1 - 115.7 (10.4)" "0.1 - 122.3 (11.3)"
[1] "hr=" "1.3"
D63V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 30(13Q12.11) MUTATED         0        1        6        3         5
  DEL PEAK 30(13Q12.11) WILD-TYPE       2       11       32       24        27
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 30(13Q12.11) MUTATED           8         0         10          6
  DEL PEAK 30(13Q12.11) WILD-TYPE        39         3         51         39
                                 vv
clus                              STAGE IIIC STAGE IV
  DEL PEAK 30(13Q12.11) MUTATED            4        4
  DEL PEAK 30(13Q12.11) WILD-TYPE         28       27
D63V3, multiclass
            clus
vv           DEL PEAK 30(13Q12.11) MUTATED DEL PEAK 30(13Q12.11) WILD-TYPE
  STAGE I                                0                               2
  STAGE IA                               1                              11
  STAGE IB                               6                              32
  STAGE II                               3                              24
  STAGE IIA                              5                              27
  STAGE IIB                              8                              39
  STAGE III                              0                               3
  STAGE IIIA                            10                              51
  STAGE IIIB                             6                              39
  STAGE IIIC                             4                              28
  STAGE IV                               4                              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 30(13Q12.11) MUTATED     2  15  22   9
  DEL PEAK 30(13Q12.11) WILD-TYPE  18  70 124  76
D63V4, multiclass
    clus
vv   DEL PEAK 30(13Q12.11) MUTATED DEL PEAK 30(13Q12.11) WILD-TYPE
  T1                             2                              18
  T2                            15                              70
  T3                            22                             124
  T4                             9                              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 30(13Q12.11) MUTATED   14 14  9 11
  DEL PEAK 30(13Q12.11) WILD-TYPE 95 78 57 56
D63V5, multiclass
    clus
vv   DEL PEAK 30(13Q12.11) MUTATED DEL PEAK 30(13Q12.11) WILD-TYPE
  N0                            14                              95
  N1                            14                              78
  N2                             9                              57
  N3                            11                              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 30(13Q12.11) MUTATED    44   2   3
  DEL PEAK 30(13Q12.11) WILD-TYPE 264  19  14
D63V6, multiclass
    clus
vv   DEL PEAK 30(13Q12.11) MUTATED DEL PEAK 30(13Q12.11) WILD-TYPE
  M0                            44                             264
  M1                             2                              19
  MX                             3                              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"
D63V7, binary
                                 cls
clus                                0   1
  DEL PEAK 30(13Q12.11) MUTATED    13  36
  DEL PEAK 30(13Q12.11) WILD-TYPE 124 173
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(13Q12.11) MUTATED     13   36
  DEL PEAK 30(13Q12.11) WILD-TYPE  124  173
        clus
vv       DEL PEAK 30(13Q12.11) MUTATED DEL PEAK 30(13Q12.11) WILD-TYPE
  FEMALE                            13                             124
  MALE                              36                             173
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 30(13Q12.11) MUTATED                                      11
  DEL PEAK 30(13Q12.11) WILD-TYPE                                    51
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 30(13Q12.11) MUTATED                                                       19
  DEL PEAK 30(13Q12.11) WILD-TYPE                                                    135
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 30(13Q12.11) MUTATED                                                                   5
  DEL PEAK 30(13Q12.11) WILD-TYPE                                                                49
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 30(13Q12.11) MUTATED                                                  9
  DEL PEAK 30(13Q12.11) WILD-TYPE                                               36
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 30(13Q12.11) MUTATED                                                           1
  DEL PEAK 30(13Q12.11) WILD-TYPE                                                         0
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 30(13Q12.11) MUTATED                                                          3
  DEL PEAK 30(13Q12.11) WILD-TYPE                                                       16
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 30(13Q12.11) MUTATED                                                           0
  DEL PEAK 30(13Q12.11) WILD-TYPE                                                         5
                                 vv
clus                              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 30(13Q12.11) MUTATED                                          0
  DEL PEAK 30(13Q12.11) WILD-TYPE                                        4
D63V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 30(13Q12.11) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        11
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       19
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              9
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      0
                                                                   clus
vv                                                                  DEL PEAK 30(13Q12.11) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          51
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        135
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              49
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               36
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                        4
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V9, binary
                                 cls
clus                                0   1
  DEL PEAK 30(13Q12.11) MUTATED     4  45
  DEL PEAK 30(13Q12.11) WILD-TYPE   3 294
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(13Q12.11) MUTATED      4   45
  DEL PEAK 30(13Q12.11) WILD-TYPE    3  294
     clus
vv    DEL PEAK 30(13Q12.11) MUTATED DEL PEAK 30(13Q12.11) WILD-TYPE
  NO                              4                               3
  YES                            45                             294
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 30(13Q12.11) MUTATED    38   4   1   4
  DEL PEAK 30(13Q12.11) WILD-TYPE 239   9  12  21
D63V10, multiclass
    clus
vv   DEL PEAK 30(13Q12.11) MUTATED DEL PEAK 30(13Q12.11) WILD-TYPE
  R0                            38                             239
  R1                             4                               9
  R2                             1                              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"
D63V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 30(13Q12.11) MUTATED      12                         0
  DEL PEAK 30(13Q12.11) WILD-TYPE    72                         3
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 30(13Q12.11) MUTATED                                           0
  DEL PEAK 30(13Q12.11) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 30(13Q12.11) MUTATED      29
  DEL PEAK 30(13Q12.11) WILD-TYPE   179
D63V12, multiclass
                                           clus
vv                                          DEL PEAK 30(13Q12.11) MUTATED
  ASIAN                                                                12
  BLACK OR AFRICAN AMERICAN                                             0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                29
                                           clus
vv                                          DEL PEAK 30(13Q12.11) WILD-TYPE
  ASIAN                                                                  72
  BLACK OR AFRICAN AMERICAN                                               3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 179
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(64) Variable = DEL PEAK 31(14Q23.3) MUTATION ANALYSIS
D64V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(14Q23.3) MUTATED    64  27
  DEL PEAK 31(14Q23.3) WILD-TYPE 158  66
  DEL PEAK 31(14Q23.3) MUTATED DEL PEAK 31(14Q23.3) WILD-TYPE 
                            91                            224 
  DEL PEAK 31(14Q23.3) MUTATED DEL PEAK 31(14Q23.3) WILD-TYPE 
                            27                             66 
$`DEL PEAK 31(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         2.27         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 
       13.35        17.19        10.26        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-A7NU 
       27.42        21.21         5.19        13.08         6.44         1.81 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 
        2.53         5.56        16.67       122.30        37.91       115.69 
TCGA-RD-A8N6 
        8.94 

$`DEL PEAK 31(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         0.07         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-RD-A7BS 
        6.87         5.56        60.56         3.72         4.50        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
        8.61         4.67        40.64       116.38        71.38        57.44 
TCGA-SW-A7EB TCGA-ZA-A8F6 
        5.79         4.21 

  DEL PEAK 31(14Q23.3) MUTATED DEL PEAK 31(14Q23.3) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 31(14Q23.3) MUTATED DEL PEAK 31(14Q23.3) WILD-TYPE 
                        122.30                         116.38 
  DEL PEAK 31(14Q23.3) MUTATED DEL PEAK 31(14Q23.3) WILD-TYPE 
                        10.260                         11.145 
[1] "0.1 - 122.3 (10.3)" "0.1 - 116.4 (11.1)"
[1] "hr=" "1"  
D64V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 31(14Q23.3) MUTATED         0        1       10       10        11
  DEL PEAK 31(14Q23.3) WILD-TYPE       2       11       28       17        21
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 31(14Q23.3) MUTATED          11         0         24         17
  DEL PEAK 31(14Q23.3) WILD-TYPE        36         3         37         28
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 31(14Q23.3) MUTATED            8        3
  DEL PEAK 31(14Q23.3) WILD-TYPE         24       28
D64V3, multiclass
            clus
vv           DEL PEAK 31(14Q23.3) MUTATED DEL PEAK 31(14Q23.3) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              1                             11
  STAGE IB                             10                             28
  STAGE II                             10                             17
  STAGE IIA                            11                             21
  STAGE IIB                            11                             36
  STAGE III                             0                              3
  STAGE IIIA                           24                             37
  STAGE IIIB                           17                             28
  STAGE IIIC                            8                             24
  STAGE IV                              3                             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(14Q23.3) MUTATED     3  25  45  22
  DEL PEAK 31(14Q23.3) WILD-TYPE  17  60 101  63
D64V4, multiclass
    clus
vv   DEL PEAK 31(14Q23.3) MUTATED DEL PEAK 31(14Q23.3) WILD-TYPE
  T1                            3                             17
  T2                           25                             60
  T3                           45                            101
  T4                           22                             63
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 31(14Q23.3) MUTATED   29 27 26 13
  DEL PEAK 31(14Q23.3) WILD-TYPE 80 65 40 54
D64V5, multiclass
    clus
vv   DEL PEAK 31(14Q23.3) MUTATED DEL PEAK 31(14Q23.3) WILD-TYPE
  N0                           29                             80
  N1                           27                             65
  N2                           26                             40
  N3                           13                             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
  DEL PEAK 31(14Q23.3) MUTATED    89   2   8
  DEL PEAK 31(14Q23.3) WILD-TYPE 219  19   9
D64V6, multiclass
    clus
vv   DEL PEAK 31(14Q23.3) MUTATED DEL PEAK 31(14Q23.3) WILD-TYPE
  M0                           89                            219
  M1                            2                             19
  MX                            8                              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"
D64V7, binary
                                cls
clus                               0   1
  DEL PEAK 31(14Q23.3) MUTATED    36  63
  DEL PEAK 31(14Q23.3) WILD-TYPE 101 146
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(14Q23.3) MUTATED     36   63
  DEL PEAK 31(14Q23.3) WILD-TYPE  101  146
        clus
vv       DEL PEAK 31(14Q23.3) MUTATED DEL PEAK 31(14Q23.3) WILD-TYPE
  FEMALE                           36                            101
  MALE                             63                            146
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 31(14Q23.3) MUTATED                                      14
  DEL PEAK 31(14Q23.3) WILD-TYPE                                    48
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 31(14Q23.3) MUTATED                                                       46
  DEL PEAK 31(14Q23.3) WILD-TYPE                                                    108
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 31(14Q23.3) MUTATED                                                                  21
  DEL PEAK 31(14Q23.3) WILD-TYPE                                                                33
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 31(14Q23.3) MUTATED                                                 12
  DEL PEAK 31(14Q23.3) WILD-TYPE                                               33
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 31(14Q23.3) MUTATED                                                           1
  DEL PEAK 31(14Q23.3) WILD-TYPE                                                         0
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 31(14Q23.3) MUTATED                                                          2
  DEL PEAK 31(14Q23.3) WILD-TYPE                                                       17
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 31(14Q23.3) MUTATED                                                           2
  DEL PEAK 31(14Q23.3) WILD-TYPE                                                         3
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 31(14Q23.3) MUTATED                                          1
  DEL PEAK 31(14Q23.3) WILD-TYPE                                        3
D64V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 31(14Q23.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       14
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      46
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           21
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            12
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     1
                                                                   clus
vv                                                                  DEL PEAK 31(14Q23.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       108
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             33
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              33
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V9, binary
                                cls
clus                               0   1
  DEL PEAK 31(14Q23.3) MUTATED     2  97
  DEL PEAK 31(14Q23.3) WILD-TYPE   5 242
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(14Q23.3) MUTATED      2   97
  DEL PEAK 31(14Q23.3) WILD-TYPE    5  242
     clus
vv    DEL PEAK 31(14Q23.3) MUTATED DEL PEAK 31(14Q23.3) WILD-TYPE
  NO                             2                              5
  YES                           97                            242
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 31(14Q23.3) MUTATED    85   1   1   7
  DEL PEAK 31(14Q23.3) WILD-TYPE 192  12  12  18
D64V10, multiclass
    clus
vv   DEL PEAK 31(14Q23.3) MUTATED DEL PEAK 31(14Q23.3) WILD-TYPE
  R0                           85                            192
  R1                            1                             12
  R2                            1                             12
  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"
D64V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 31(14Q23.3) MUTATED      24                         0
  DEL PEAK 31(14Q23.3) WILD-TYPE    60                         3
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 31(14Q23.3) MUTATED                                           0
  DEL PEAK 31(14Q23.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 31(14Q23.3) MUTATED      64
  DEL PEAK 31(14Q23.3) WILD-TYPE   144
D64V12, multiclass
                                           clus
vv                                          DEL PEAK 31(14Q23.3) MUTATED
  ASIAN                                                               24
  BLACK OR AFRICAN AMERICAN                                            0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               64
                                           clus
vv                                          DEL PEAK 31(14Q23.3) WILD-TYPE
  ASIAN                                                                 60
  BLACK OR AFRICAN AMERICAN                                              3
  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(65) Variable = DEL PEAK 32(14Q32.33) MUTATION ANALYSIS
D65V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 32(14Q32.33) MUTATED    67  25
  DEL PEAK 32(14Q32.33) WILD-TYPE 155  68
  DEL PEAK 32(14Q32.33) MUTATED DEL PEAK 32(14Q32.33) WILD-TYPE 
                             92                             223 
  DEL PEAK 32(14Q32.33) MUTATED DEL PEAK 32(14Q32.33) WILD-TYPE 
                             25                              68 
$`DEL PEAK 32(14Q32.33) MUTATED`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4279 TCGA-BR-6458 TCGA-BR-6564 
       11.70         6.61        18.35         9.57         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-8677 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A4CS 
       15.81         0.49        11.54        15.68        10.68         0.92 
TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PF 
       12.89         0.72         0.66        19.36         0.46         1.15 
TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A489 
       13.18         0.07         0.07         0.13         0.13         0.13 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4443 
        0.13         0.10        20.02         7.99        54.08        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4477 TCGA-CG-5733 TCGA-D7-6519 TCGA-D7-6520 
       47.05        19.07        30.97        21.07        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6822 TCGA-D7-8575 
       18.54        13.35        10.26        15.98        12.33         0.23 
TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
        6.97        14.27        16.44        11.31         9.76         2.96 
TCGA-D7-A74A TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 
        7.40         7.79        16.24         8.12         3.02        17.06 
TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
       26.47        12.59        14.17        25.81        11.77         8.98 
TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
        2.10        17.69        12.30        27.42        21.21        18.81 
TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NU TCGA-IP-7968 TCGA-RD-A7C1 TCGA-RD-A8MV 
        5.19         6.44         1.81         2.53        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N6 
       37.91         8.94 

$`DEL PEAK 32(14Q32.33) 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-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-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-8680 TCGA-BR-8682 
        2.14        13.45         0.20         7.53        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        0.59         0.62        12.56         1.15         0.66         3.02 
TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
        2.27        13.41        13.51         0.79        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL 
       12.82        13.51        20.65        20.42        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8525 
        5.13         2.83         3.25        13.15         0.30         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-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A4MG 
        0.10         0.10         0.07         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-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 
        8.05         4.01        14.01        12.03        21.99         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-5732 
       15.02        28.96        79.07        65.10         4.01        55.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6522 
        7.99        12.36        12.66        11.93        19.13        18.61 
TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.85        17.19        15.22        12.79        10.55        11.31 
TCGA-D7-8570 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-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-A6F2 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6177 
       11.44        15.65         4.34         7.13         0.62         6.58 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
       14.47        72.23        21.27         0.39        19.53        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX 
       59.54         5.03        13.58         0.56         1.55         0.23 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 
       18.08         1.51         5.92        14.27        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
       24.20         3.25        22.75        21.37        29.98         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-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-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
       60.56         3.72         4.50        11.05         8.61         4.67 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-SW-A7EB 
       40.64       115.69       116.38        71.38        57.44         5.79 
TCGA-ZA-A8F6 
        4.21 

  DEL PEAK 32(14Q32.33) MUTATED DEL PEAK 32(14Q32.33) WILD-TYPE 
                           0.07                            0.07 
  DEL PEAK 32(14Q32.33) MUTATED DEL PEAK 32(14Q32.33) WILD-TYPE 
                         122.30                          116.38 
  DEL PEAK 32(14Q32.33) MUTATED DEL PEAK 32(14Q32.33) WILD-TYPE 
                          11.62                           10.55 
[1] "0.1 - 122.3 (11.6)" "0.1 - 116.4 (10.6)"
[1] "hr=" "1.1"
D65V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 32(14Q32.33) MUTATED         0        2       10        9        12
  DEL PEAK 32(14Q32.33) WILD-TYPE       2       10       28       18        20
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 32(14Q32.33) MUTATED          12         0         26         15
  DEL PEAK 32(14Q32.33) WILD-TYPE        35         3         35         30
                                 vv
clus                              STAGE IIIC STAGE IV
  DEL PEAK 32(14Q32.33) MUTATED            8        3
  DEL PEAK 32(14Q32.33) WILD-TYPE         24       28
D65V3, multiclass
            clus
vv           DEL PEAK 32(14Q32.33) MUTATED DEL PEAK 32(14Q32.33) WILD-TYPE
  STAGE I                                0                               2
  STAGE IA                               2                              10
  STAGE IB                              10                              28
  STAGE II                               9                              18
  STAGE IIA                             12                              20
  STAGE IIB                             12                              35
  STAGE III                              0                               3
  STAGE IIIA                            26                              35
  STAGE IIIB                            15                              30
  STAGE IIIC                             8                              24
  STAGE IV                               3                              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 32(14Q32.33) MUTATED     3  28  46  20
  DEL PEAK 32(14Q32.33) WILD-TYPE  17  57 100  65
D65V4, multiclass
    clus
vv   DEL PEAK 32(14Q32.33) MUTATED DEL PEAK 32(14Q32.33) WILD-TYPE
  T1                             3                              17
  T2                            28                              57
  T3                            46                             100
  T4                            20                              65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2 N3
  DEL PEAK 32(14Q32.33) MUTATED   31 26 25 15
  DEL PEAK 32(14Q32.33) WILD-TYPE 78 66 41 52
D65V5, multiclass
    clus
vv   DEL PEAK 32(14Q32.33) MUTATED DEL PEAK 32(14Q32.33) WILD-TYPE
  N0                            31                              78
  N1                            26                              66
  N2                            25                              41
  N3                            15                              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 32(14Q32.33) MUTATED    92   1   7
  DEL PEAK 32(14Q32.33) WILD-TYPE 216  20  10
D65V6, multiclass
    clus
vv   DEL PEAK 32(14Q32.33) MUTATED DEL PEAK 32(14Q32.33) WILD-TYPE
  M0                            92                             216
  M1                             1                              20
  MX                             7                              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"
D65V7, binary
                                 cls
clus                                0   1
  DEL PEAK 32(14Q32.33) MUTATED    37  63
  DEL PEAK 32(14Q32.33) WILD-TYPE 100 146
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(14Q32.33) MUTATED     37   63
  DEL PEAK 32(14Q32.33) WILD-TYPE  100  146
        clus
vv       DEL PEAK 32(14Q32.33) MUTATED DEL PEAK 32(14Q32.33) WILD-TYPE
  FEMALE                            37                             100
  MALE                              63                             146
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 32(14Q32.33) MUTATED                                      14
  DEL PEAK 32(14Q32.33) WILD-TYPE                                    48
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 32(14Q32.33) MUTATED                                                       46
  DEL PEAK 32(14Q32.33) WILD-TYPE                                                    108
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 32(14Q32.33) MUTATED                                                                  17
  DEL PEAK 32(14Q32.33) WILD-TYPE                                                                37
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 32(14Q32.33) MUTATED                                                 14
  DEL PEAK 32(14Q32.33) WILD-TYPE                                               31
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 32(14Q32.33) MUTATED                                                           1
  DEL PEAK 32(14Q32.33) WILD-TYPE                                                         0
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 32(14Q32.33) MUTATED                                                          5
  DEL PEAK 32(14Q32.33) WILD-TYPE                                                       14
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 32(14Q32.33) MUTATED                                                           2
  DEL PEAK 32(14Q32.33) WILD-TYPE                                                         3
                                 vv
clus                              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 32(14Q32.33) MUTATED                                          1
  DEL PEAK 32(14Q32.33) WILD-TYPE                                        3
D65V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 32(14Q32.33) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        14
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       46
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             14
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      1
                                                                   clus
vv                                                                  DEL PEAK 32(14Q32.33) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        108
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               31
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                        3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V9, binary
                                 cls
clus                                0   1
  DEL PEAK 32(14Q32.33) MUTATED     3  97
  DEL PEAK 32(14Q32.33) WILD-TYPE   4 242
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(14Q32.33) MUTATED      3   97
  DEL PEAK 32(14Q32.33) WILD-TYPE    4  242
     clus
vv    DEL PEAK 32(14Q32.33) MUTATED DEL PEAK 32(14Q32.33) WILD-TYPE
  NO                              3                               4
  YES                            97                             242
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 32(14Q32.33) MUTATED    86   2   0   6
  DEL PEAK 32(14Q32.33) WILD-TYPE 191  11  13  19
D65V10, multiclass
    clus
vv   DEL PEAK 32(14Q32.33) MUTATED DEL PEAK 32(14Q32.33) WILD-TYPE
  R0                            86                             191
  R1                             2                              11
  R2                             0                              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"
D65V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 32(14Q32.33) MUTATED      25                         0
  DEL PEAK 32(14Q32.33) WILD-TYPE    59                         3
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 32(14Q32.33) MUTATED                                           0
  DEL PEAK 32(14Q32.33) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 32(14Q32.33) MUTATED      65
  DEL PEAK 32(14Q32.33) WILD-TYPE   143
D65V12, multiclass
                                           clus
vv                                          DEL PEAK 32(14Q32.33) MUTATED
  ASIAN                                                                25
  BLACK OR AFRICAN AMERICAN                                             0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                65
                                           clus
vv                                          DEL PEAK 32(14Q32.33) WILD-TYPE
  ASIAN                                                                  59
  BLACK OR AFRICAN AMERICAN                                               3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  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(66) Variable = DEL PEAK 33(15Q11.2) MUTATION ANALYSIS
D66V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 33(15Q11.2) MUTATED    61  23
  DEL PEAK 33(15Q11.2) WILD-TYPE 161  70
  DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE 
                            84                            231 
  DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE 
                            23                             70 
$`DEL PEAK 33(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         2.27         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        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8575 
       17.19        10.26        15.22        15.98        12.79         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-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-SW-A7EB 
       60.56        11.05        16.67        37.91       115.69         5.79 

$`DEL PEAK 33(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         0.07         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-A6RS TCGA-KB-A6F5 TCGA-MX-A5UG TCGA-MX-A5UJ 
       13.08         6.44         6.87         5.56         3.72         4.50 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
        8.61         4.67       122.30        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-ZA-A8F6 
       57.44         8.94         4.21 

  DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE 
                        115.69                         122.30 
  DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE 
                         11.18                          10.62 
[1] "0.1 - 115.7 (11.2)" "0.1 - 122.3 (10.6)"
[1] "hr=" "1.1"
D66V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 33(15Q11.2) MUTATED         0        4       12        5         9
  DEL PEAK 33(15Q11.2) WILD-TYPE       2        8       26       22        23
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 33(15Q11.2) MUTATED          10         0         26         10
  DEL PEAK 33(15Q11.2) WILD-TYPE        37         3         35         35
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 33(15Q11.2) MUTATED            5        9
  DEL PEAK 33(15Q11.2) WILD-TYPE         27       22
D66V3, multiclass
            clus
vv           DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              4                              8
  STAGE IB                             12                             26
  STAGE II                              5                             22
  STAGE IIA                             9                             23
  STAGE IIB                            10                             37
  STAGE III                             0                              3
  STAGE IIIA                           26                             35
  STAGE IIIB                           10                             35
  STAGE IIIC                            5                             27
  STAGE IV                              9                             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 33(15Q11.2) MUTATED     6  25  45  15
  DEL PEAK 33(15Q11.2) WILD-TYPE  14  60 101  70
D66V4, multiclass
    clus
vv   DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE
  T1                            6                             14
  T2                           25                             60
  T3                           45                            101
  T4                           15                             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 33(15Q11.2) MUTATED   30 24 22 14
  DEL PEAK 33(15Q11.2) WILD-TYPE 79 68 44 53
D66V5, multiclass
    clus
vv   DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE
  N0                           30                             79
  N1                           24                             68
  N2                           22                             44
  N3                           14                             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
  DEL PEAK 33(15Q11.2) MUTATED    83   5   6
  DEL PEAK 33(15Q11.2) WILD-TYPE 225  16  11
D66V6, multiclass
    clus
vv   DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE
  M0                           83                            225
  M1                            5                             16
  MX                            6                             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"
D66V7, binary
                                cls
clus                               0   1
  DEL PEAK 33(15Q11.2) MUTATED    35  59
  DEL PEAK 33(15Q11.2) WILD-TYPE 102 150
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q11.2) MUTATED     35   59
  DEL PEAK 33(15Q11.2) WILD-TYPE  102  150
        clus
vv       DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE
  FEMALE                           35                            102
  MALE                             59                            150
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 33(15Q11.2) MUTATED                                      13
  DEL PEAK 33(15Q11.2) WILD-TYPE                                    49
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 33(15Q11.2) MUTATED                                                       36
  DEL PEAK 33(15Q11.2) WILD-TYPE                                                    118
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 33(15Q11.2) MUTATED                                                                  16
  DEL PEAK 33(15Q11.2) WILD-TYPE                                                                38
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 33(15Q11.2) MUTATED                                                 19
  DEL PEAK 33(15Q11.2) WILD-TYPE                                               26
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 33(15Q11.2) MUTATED                                                           1
  DEL PEAK 33(15Q11.2) WILD-TYPE                                                         0
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 33(15Q11.2) MUTATED                                                          4
  DEL PEAK 33(15Q11.2) WILD-TYPE                                                       15
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 33(15Q11.2) MUTATED                                                           2
  DEL PEAK 33(15Q11.2) WILD-TYPE                                                         3
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 33(15Q11.2) MUTATED                                          3
  DEL PEAK 33(15Q11.2) WILD-TYPE                                        1
D66V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 33(15Q11.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       13
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      36
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           16
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            19
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     3
                                                                   clus
vv                                                                  DEL PEAK 33(15Q11.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       118
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              26
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V9, binary
                                cls
clus                               0   1
  DEL PEAK 33(15Q11.2) MUTATED     5  89
  DEL PEAK 33(15Q11.2) WILD-TYPE   2 250
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q11.2) MUTATED      5   89
  DEL PEAK 33(15Q11.2) WILD-TYPE    2  250
     clus
vv    DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE
  NO                             5                              2
  YES                           89                            250
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 33(15Q11.2) MUTATED    78   6   2   4
  DEL PEAK 33(15Q11.2) WILD-TYPE 199   7  11  21
D66V10, multiclass
    clus
vv   DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE
  R0                           78                            199
  R1                            6                              7
  R2                            2                             11
  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"
D66V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 33(15Q11.2) MUTATED      26                         1
  DEL PEAK 33(15Q11.2) WILD-TYPE    58                         2
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 33(15Q11.2) MUTATED                                           0
  DEL PEAK 33(15Q11.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 33(15Q11.2) MUTATED      53
  DEL PEAK 33(15Q11.2) WILD-TYPE   155
D66V12, multiclass
                                           clus
vv                                          DEL PEAK 33(15Q11.2) MUTATED
  ASIAN                                                               26
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               53
                                           clus
vv                                          DEL PEAK 33(15Q11.2) WILD-TYPE
  ASIAN                                                                 58
  BLACK OR AFRICAN AMERICAN                                              2
  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(67) Variable = DEL PEAK 34(15Q15.1) MUTATION ANALYSIS
D67V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 34(15Q15.1) MUTATED    63  24
  DEL PEAK 34(15Q15.1) WILD-TYPE 159  69
  DEL PEAK 34(15Q15.1) MUTATED DEL PEAK 34(15Q15.1) WILD-TYPE 
                            87                            228 
  DEL PEAK 34(15Q15.1) MUTATED DEL PEAK 34(15Q15.1) WILD-TYPE 
                            24                             69 
$`DEL PEAK 34(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 
        2.27         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        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8575 
       17.19        10.26        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-RD-A7BS TCGA-RD-A7C1 
        6.44         5.56         1.81         2.53        11.05        16.67 
TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-SW-A7EB 
       37.91       115.69         5.79 

$`DEL PEAK 34(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         0.07         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-A6RS TCGA-KB-A6F5 
       21.21         3.45         3.39        13.08         6.87         5.56 
TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV 
       60.56         3.72         4.50         8.61         4.67       122.30 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-ZA-A8F6 
       40.64       116.38        71.38        57.44         8.94         4.21 

  DEL PEAK 34(15Q15.1) MUTATED DEL PEAK 34(15Q15.1) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 34(15Q15.1) MUTATED DEL PEAK 34(15Q15.1) WILD-TYPE 
                        115.69                         122.30 
  DEL PEAK 34(15Q15.1) MUTATED DEL PEAK 34(15Q15.1) WILD-TYPE 
                        11.310                         10.585 
[1] "0.1 - 115.7 (11.3)" "0.1 - 122.3 (10.6)"
[1] "hr=" "1.1"
D67V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 34(15Q15.1) MUTATED         0        2       14        5         7
  DEL PEAK 34(15Q15.1) WILD-TYPE       2       10       24       22        25
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 34(15Q15.1) MUTATED          11         0         25         13
  DEL PEAK 34(15Q15.1) WILD-TYPE        36         3         36         32
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 34(15Q15.1) MUTATED            6        9
  DEL PEAK 34(15Q15.1) WILD-TYPE         26       22
D67V3, multiclass
            clus
vv           DEL PEAK 34(15Q15.1) MUTATED DEL PEAK 34(15Q15.1) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              2                             10
  STAGE IB                             14                             24
  STAGE II                              5                             22
  STAGE IIA                             7                             25
  STAGE IIB                            11                             36
  STAGE III                             0                              3
  STAGE IIIA                           25                             36
  STAGE IIIB                           13                             32
  STAGE IIIC                            6                             26
  STAGE IV                              9                             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 34(15Q15.1) MUTATED     4  29  45  16
  DEL PEAK 34(15Q15.1) WILD-TYPE  16  56 101  69
D67V4, multiclass
    clus
vv   DEL PEAK 34(15Q15.1) MUTATED DEL PEAK 34(15Q15.1) WILD-TYPE
  T1                            4                             16
  T2                           29                             56
  T3                           45                            101
  T4                           16                             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 34(15Q15.1) MUTATED   29 25 21 17
  DEL PEAK 34(15Q15.1) WILD-TYPE 80 67 45 50
D67V5, multiclass
    clus
vv   DEL PEAK 34(15Q15.1) MUTATED DEL PEAK 34(15Q15.1) WILD-TYPE
  N0                           29                             80
  N1                           25                             67
  N2                           21                             45
  N3                           17                             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
  DEL PEAK 34(15Q15.1) MUTATED    83   5   9
  DEL PEAK 34(15Q15.1) WILD-TYPE 225  16   8
D67V6, multiclass
    clus
vv   DEL PEAK 34(15Q15.1) MUTATED DEL PEAK 34(15Q15.1) WILD-TYPE
  M0                           83                            225
  M1                            5                             16
  MX                            9                              8
[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 34(15Q15.1) MUTATED    35  62
  DEL PEAK 34(15Q15.1) WILD-TYPE 102 147
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(15Q15.1) MUTATED     35   62
  DEL PEAK 34(15Q15.1) WILD-TYPE  102  147
        clus
vv       DEL PEAK 34(15Q15.1) MUTATED DEL PEAK 34(15Q15.1) WILD-TYPE
  FEMALE                           35                            102
  MALE                             62                            147
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 34(15Q15.1) MUTATED                                      13
  DEL PEAK 34(15Q15.1) WILD-TYPE                                    49
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 34(15Q15.1) MUTATED                                                       37
  DEL PEAK 34(15Q15.1) WILD-TYPE                                                    117
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 34(15Q15.1) MUTATED                                                                  18
  DEL PEAK 34(15Q15.1) WILD-TYPE                                                                36
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 34(15Q15.1) MUTATED                                                 19
  DEL PEAK 34(15Q15.1) WILD-TYPE                                               26
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 34(15Q15.1) MUTATED                                                           1
  DEL PEAK 34(15Q15.1) WILD-TYPE                                                         0
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 34(15Q15.1) MUTATED                                                          4
  DEL PEAK 34(15Q15.1) WILD-TYPE                                                       15
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 34(15Q15.1) MUTATED                                                           2
  DEL PEAK 34(15Q15.1) WILD-TYPE                                                         3
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 34(15Q15.1) MUTATED                                          3
  DEL PEAK 34(15Q15.1) WILD-TYPE                                        1
D67V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 34(15Q15.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       13
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      37
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           18
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            19
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     3
                                                                   clus
vv                                                                  DEL PEAK 34(15Q15.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       117
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              26
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V9, binary
                                cls
clus                               0   1
  DEL PEAK 34(15Q15.1) MUTATED     5  92
  DEL PEAK 34(15Q15.1) WILD-TYPE   2 247
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(15Q15.1) MUTATED      5   92
  DEL PEAK 34(15Q15.1) WILD-TYPE    2  247
     clus
vv    DEL PEAK 34(15Q15.1) MUTATED DEL PEAK 34(15Q15.1) WILD-TYPE
  NO                             5                              2
  YES                           92                            247
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 34(15Q15.1) MUTATED    78   7   2   6
  DEL PEAK 34(15Q15.1) WILD-TYPE 199   6  11  19
D67V10, multiclass
    clus
vv   DEL PEAK 34(15Q15.1) MUTATED DEL PEAK 34(15Q15.1) WILD-TYPE
  R0                           78                            199
  R1                            7                              6
  R2                            2                             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"
D67V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 34(15Q15.1) MUTATED      25                         1
  DEL PEAK 34(15Q15.1) WILD-TYPE    59                         2
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 34(15Q15.1) MUTATED                                           0
  DEL PEAK 34(15Q15.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 34(15Q15.1) MUTATED      57
  DEL PEAK 34(15Q15.1) WILD-TYPE   151
D67V12, multiclass
                                           clus
vv                                          DEL PEAK 34(15Q15.1) MUTATED
  ASIAN                                                               25
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               57
                                           clus
vv                                          DEL PEAK 34(15Q15.1) WILD-TYPE
  ASIAN                                                                 59
  BLACK OR AFRICAN AMERICAN                                              2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                151
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(68) Variable = DEL PEAK 35(16P13.3) MUTATION ANALYSIS
D68V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 35(16P13.3) MUTATED    46  14
  DEL PEAK 35(16P13.3) WILD-TYPE 176  79
  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                            60                            255 
  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                            14                             79 
$`DEL PEAK 35(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         2.27         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         0.07         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-A6RS TCGA-KB-A6F5 TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-SW-A7EB 
        3.39         6.87         5.56        11.05        16.67         5.79 

$`DEL PEAK 35(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        13.35        17.19        10.26 
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-RD-A7BT TCGA-RD-A7BW 
        2.53        60.56         3.72         4.50         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-A8N6 TCGA-ZA-A8F6 
       57.44         8.94         4.21 

  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                         72.23                         122.30 
  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                          8.50                          11.41 
[1] "0.1 - 72.2 (8.5)"   "0.1 - 122.3 (11.4)"
[1] "hr=" "1.1"
D68V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 35(16P13.3) MUTATED         0        4        6        8         8
  DEL PEAK 35(16P13.3) WILD-TYPE       2        8       32       19        24
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 35(16P13.3) MUTATED          11         0         19          2
  DEL PEAK 35(16P13.3) WILD-TYPE        36         3         42         43
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 35(16P13.3) MUTATED            3        3
  DEL PEAK 35(16P13.3) WILD-TYPE         29       28
D68V3, multiclass
            clus
vv           DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              4                              8
  STAGE IB                              6                             32
  STAGE II                              8                             19
  STAGE IIA                             8                             24
  STAGE IIB                            11                             36
  STAGE III                             0                              3
  STAGE IIIA                           19                             42
  STAGE IIIB                            2                             43
  STAGE IIIC                            3                             29
  STAGE IV                              3                             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 35(16P13.3) MUTATED     3  14  38  10
  DEL PEAK 35(16P13.3) WILD-TYPE  17  71 108  75
D68V4, multiclass
    clus
vv   DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  T1                            3                             17
  T2                           14                             71
  T3                           38                            108
  T4                           10                             75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 35(16P13.3) MUTATED   24 23 11  7
  DEL PEAK 35(16P13.3) WILD-TYPE 85 69 55 60
D68V5, multiclass
    clus
vv   DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  N0                           24                             85
  N1                           23                             69
  N2                           11                             55
  N3                            7                             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 35(16P13.3) MUTATED    64   2   2
  DEL PEAK 35(16P13.3) WILD-TYPE 244  19  15
D68V6, multiclass
    clus
vv   DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  M0                           64                            244
  M1                            2                             19
  MX                            2                             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 35(16P13.3) MUTATED    23  45
  DEL PEAK 35(16P13.3) WILD-TYPE 114 164
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(16P13.3) MUTATED     23   45
  DEL PEAK 35(16P13.3) WILD-TYPE  114  164
        clus
vv       DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  FEMALE                           23                            114
  MALE                             45                            164
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 35(16P13.3) MUTATED                                       7
  DEL PEAK 35(16P13.3) WILD-TYPE                                    55
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 35(16P13.3) MUTATED                                                       30
  DEL PEAK 35(16P13.3) WILD-TYPE                                                    124
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 35(16P13.3) MUTATED                                                                   8
  DEL PEAK 35(16P13.3) WILD-TYPE                                                                46
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 35(16P13.3) MUTATED                                                 14
  DEL PEAK 35(16P13.3) WILD-TYPE                                               31
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 35(16P13.3) MUTATED                                                           0
  DEL PEAK 35(16P13.3) WILD-TYPE                                                         1
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 35(16P13.3) MUTATED                                                          7
  DEL PEAK 35(16P13.3) WILD-TYPE                                                       12
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 35(16P13.3) MUTATED                                                           2
  DEL PEAK 35(16P13.3) WILD-TYPE                                                         3
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 35(16P13.3) MUTATED                                          0
  DEL PEAK 35(16P13.3) WILD-TYPE                                        4
D68V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 35(16P13.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      30
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            8
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            14
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     0
                                                                   clus
vv                                                                  DEL PEAK 35(16P13.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         55
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             46
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              31
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       4
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V9, binary
                                cls
clus                               0   1
  DEL PEAK 35(16P13.3) MUTATED     2  66
  DEL PEAK 35(16P13.3) WILD-TYPE   5 273
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(16P13.3) MUTATED      2   66
  DEL PEAK 35(16P13.3) WILD-TYPE    5  273
     clus
vv    DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  NO                             2                              5
  YES                           66                            273
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 35(16P13.3) MUTATED    50   4   1   6
  DEL PEAK 35(16P13.3) WILD-TYPE 227   9  12  19
D68V10, multiclass
    clus
vv   DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  R0                           50                            227
  R1                            4                              9
  R2                            1                             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"
D68V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 35(16P13.3) MUTATED      24                         1
  DEL PEAK 35(16P13.3) WILD-TYPE    60                         2
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 35(16P13.3) MUTATED                                           0
  DEL PEAK 35(16P13.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 35(16P13.3) MUTATED      36
  DEL PEAK 35(16P13.3) WILD-TYPE   172
D68V12, multiclass
                                           clus
vv                                          DEL PEAK 35(16P13.3) MUTATED
  ASIAN                                                               24
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               36
                                           clus
vv                                          DEL PEAK 35(16P13.3) WILD-TYPE
  ASIAN                                                                 60
  BLACK OR AFRICAN AMERICAN                                              2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                172
[1] 4 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 36(16Q23.1) MUTATION ANALYSIS
D69V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 36(16Q23.1) MUTATED    87  35
  DEL PEAK 36(16Q23.1) WILD-TYPE 135  58
  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                           122                            193 
  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                            35                             58 
$`DEL PEAK 36(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         2.27         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         0.07         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 
       13.35        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-RD-A7BS TCGA-RD-A7C1 
        6.44         1.81         5.56        60.56        11.05        16.67 
TCGA-RD-A8N6 TCGA-SW-A7EB 
        8.94         5.79 

$`DEL PEAK 36(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        10.26        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-A6RS TCGA-IN-A7NT 
        3.39         5.36         5.19         1.41         6.87         5.56 
TCGA-IP-7968 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV 
        2.53         3.72         4.50         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-ZA-A8F6 
        4.21 

  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                        105.07                         122.30 
  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                        11.145                         10.680 
[1] "0.1 - 105.1 (11.1)" "0.1 - 122.3 (10.7)"
[1] "hr=" "1"  
D69V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 36(16Q23.1) MUTATED         0        5       16       16        10
  DEL PEAK 36(16Q23.1) WILD-TYPE       2        7       22       11        22
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 36(16Q23.1) MUTATED          18         2         32          8
  DEL PEAK 36(16Q23.1) WILD-TYPE        29         1         29         37
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 36(16Q23.1) MUTATED           17        7
  DEL PEAK 36(16Q23.1) WILD-TYPE         15       24
D69V3, multiclass
            clus
vv           DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              5                              7
  STAGE IB                             16                             22
  STAGE II                             16                             11
  STAGE IIA                            10                             22
  STAGE IIB                            18                             29
  STAGE III                             2                              1
  STAGE IIIA                           32                             29
  STAGE IIIB                            8                             37
  STAGE IIIC                           17                             15
  STAGE IV                              7                             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 36(16Q23.1) MUTATED    8 38 57 30
  DEL PEAK 36(16Q23.1) WILD-TYPE 12 47 89 55
D69V4, multiclass
    clus
vv   DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  T1                            8                             12
  T2                           38                             47
  T3                           57                             89
  T4                           30                             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
  DEL PEAK 36(16Q23.1) MUTATED   41 40 24 27
  DEL PEAK 36(16Q23.1) WILD-TYPE 68 52 42 40
D69V5, multiclass
    clus
vv   DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  N0                           41                             68
  N1                           40                             52
  N2                           24                             42
  N3                           27                             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 36(16Q23.1) MUTATED   127   3   5
  DEL PEAK 36(16Q23.1) WILD-TYPE 181  18  12
D69V6, multiclass
    clus
vv   DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  M0                          127                            181
  M1                            3                             18
  MX                            5                             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"
D69V7, binary
                                cls
clus                               0   1
  DEL PEAK 36(16Q23.1) MUTATED    48  87
  DEL PEAK 36(16Q23.1) WILD-TYPE  89 122
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16Q23.1) MUTATED     48   87
  DEL PEAK 36(16Q23.1) WILD-TYPE   89  122
        clus
vv       DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  FEMALE                           48                             89
  MALE                             87                            122
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 36(16Q23.1) MUTATED                                      21
  DEL PEAK 36(16Q23.1) WILD-TYPE                                    41
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 36(16Q23.1) MUTATED                                                       58
  DEL PEAK 36(16Q23.1) WILD-TYPE                                                     96
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 36(16Q23.1) MUTATED                                                                  18
  DEL PEAK 36(16Q23.1) WILD-TYPE                                                                36
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 36(16Q23.1) MUTATED                                                 21
  DEL PEAK 36(16Q23.1) WILD-TYPE                                               24
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 36(16Q23.1) MUTATED                                                           0
  DEL PEAK 36(16Q23.1) WILD-TYPE                                                         1
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 36(16Q23.1) MUTATED                                                         10
  DEL PEAK 36(16Q23.1) WILD-TYPE                                                        9
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 36(16Q23.1) MUTATED                                                           5
  DEL PEAK 36(16Q23.1) WILD-TYPE                                                         0
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 36(16Q23.1) MUTATED                                          1
  DEL PEAK 36(16Q23.1) WILD-TYPE                                        3
D69V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 36(16Q23.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       21
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      58
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           18
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            21
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     1
                                                                   clus
vv                                                                  DEL PEAK 36(16Q23.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         41
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        96
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              24
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V9, binary
                                cls
clus                               0   1
  DEL PEAK 36(16Q23.1) MUTATED     5 130
  DEL PEAK 36(16Q23.1) WILD-TYPE   2 209
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16Q23.1) MUTATED      5  130
  DEL PEAK 36(16Q23.1) WILD-TYPE    2  209
     clus
vv    DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  NO                             5                              2
  YES                          130                            209
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 36(16Q23.1) MUTATED   109   7   1  10
  DEL PEAK 36(16Q23.1) WILD-TYPE 168   6  12  15
D69V10, multiclass
    clus
vv   DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  R0                          109                            168
  R1                            7                              6
  R2                            1                             12
  RX                           10                             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 36(16Q23.1) MUTATED      34                         1
  DEL PEAK 36(16Q23.1) WILD-TYPE    50                         2
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 36(16Q23.1) MUTATED                                           0
  DEL PEAK 36(16Q23.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 36(16Q23.1) MUTATED      78
  DEL PEAK 36(16Q23.1) WILD-TYPE   130
D69V12, multiclass
                                           clus
vv                                          DEL PEAK 36(16Q23.1) MUTATED
  ASIAN                                                               34
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               78
                                           clus
vv                                          DEL PEAK 36(16Q23.1) WILD-TYPE
  ASIAN                                                                 50
  BLACK OR AFRICAN AMERICAN                                              2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                130
[1] 4 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 37(17P12) MUTATION ANALYSIS
D70V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 37(17P12) MUTATED    89  34
  DEL PEAK 37(17P12) WILD-TYPE 133  59
  DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE 
                         123                          192 
  DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE 
                          34                           59 
$`DEL PEAK 37(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         2.27         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         0.07 
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        13.35        17.19        10.26        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-RD-A7BT 
        6.44         6.87         1.81         2.53         5.56         8.61 
TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N6 
       16.67       115.69         8.94 

$`DEL PEAK 37(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-A7NT TCGA-KB-A6F7 
        8.81         3.45         5.36        13.08         5.56        60.56 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
        3.72         4.50        11.05         4.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-SW-A7EB TCGA-ZA-A8F6 
       40.64       116.38        71.38        57.44         5.79         4.21 

  DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE 
                        0.07                         0.07 
  DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE 
                      115.69                       122.30 
  DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE 
                       8.980                       11.705 
[1] "0.1 - 115.7 (9.0)"  "0.1 - 122.3 (11.7)"
[1] "hr=" "1"  
D70V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 37(17P12) MUTATED         0        5       16       14        11
  DEL PEAK 37(17P12) WILD-TYPE       2        7       22       13        21
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 37(17P12) MUTATED          17         0         26         18
  DEL PEAK 37(17P12) WILD-TYPE        30         3         35         27
                              vv
clus                           STAGE IIIC STAGE IV
  DEL PEAK 37(17P12) MUTATED           10       11
  DEL PEAK 37(17P12) WILD-TYPE         22       20
D70V3, multiclass
            clus
vv           DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE
  STAGE I                             0                            2
  STAGE IA                            5                            7
  STAGE IB                           16                           22
  STAGE II                           14                           13
  STAGE IIA                          11                           21
  STAGE IIB                          17                           30
  STAGE III                           0                            3
  STAGE IIIA                         26                           35
  STAGE IIIB                         18                           27
  STAGE IIIC                         10                           22
  STAGE IV                           11                           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 37(17P12) MUTATED    6 40 56 27
  DEL PEAK 37(17P12) WILD-TYPE 14 45 90 58
D70V4, multiclass
    clus
vv   DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE
  T1                          6                           14
  T2                         40                           45
  T3                         56                           90
  T4                         27                           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
  DEL PEAK 37(17P12) MUTATED   44 36 26 23
  DEL PEAK 37(17P12) WILD-TYPE 65 56 40 44
D70V5, multiclass
    clus
vv   DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE
  N0                         44                           65
  N1                         36                           56
  N2                         26                           40
  N3                         23                           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
  DEL PEAK 37(17P12) MUTATED   115   6  10
  DEL PEAK 37(17P12) WILD-TYPE 193  15   7
D70V6, multiclass
    clus
vv   DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE
  M0                        115                          193
  M1                          6                           15
  MX                         10                            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"
D70V7, binary
                              cls
clus                             0   1
  DEL PEAK 37(17P12) MUTATED    45  86
  DEL PEAK 37(17P12) WILD-TYPE  92 123
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 37(17P12) MUTATED     45   86
  DEL PEAK 37(17P12) WILD-TYPE   92  123
        clus
vv       DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE
  FEMALE                         45                           92
  MALE                           86                          123
[1] 2 2
[1] FALSE
                              vv
clus                           STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 37(17P12) MUTATED                                      14
  DEL PEAK 37(17P12) WILD-TYPE                                    48
                              vv
clus                           STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 37(17P12) MUTATED                                                       55
  DEL PEAK 37(17P12) WILD-TYPE                                                     99
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 37(17P12) MUTATED                                                                  27
  DEL PEAK 37(17P12) WILD-TYPE                                                                27
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 37(17P12) MUTATED                                                 20
  DEL PEAK 37(17P12) WILD-TYPE                                               25
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 37(17P12) MUTATED                                                           1
  DEL PEAK 37(17P12) WILD-TYPE                                                         0
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 37(17P12) MUTATED                                                          9
  DEL PEAK 37(17P12) WILD-TYPE                                                       10
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 37(17P12) MUTATED                                                           3
  DEL PEAK 37(17P12) WILD-TYPE                                                         2
                              vv
clus                           STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 37(17P12) MUTATED                                          2
  DEL PEAK 37(17P12) WILD-TYPE                                        2
D70V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 37(17P12) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     14
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    55
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         27
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                          20
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                  1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                  3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   2
                                                                   clus
vv                                                                  DEL PEAK 37(17P12) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      99
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           27
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            25
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V9, binary
                              cls
clus                             0   1
  DEL PEAK 37(17P12) MUTATED     5 126
  DEL PEAK 37(17P12) WILD-TYPE   2 213
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 37(17P12) MUTATED      5  126
  DEL PEAK 37(17P12) WILD-TYPE    2  213
     clus
vv    DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE
  NO                           5                            2
  YES                        126                          213
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 37(17P12) MUTATED   107   7   4   5
  DEL PEAK 37(17P12) WILD-TYPE 170   6   9  20
D70V10, multiclass
    clus
vv   DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE
  R0                        107                          170
  R1                          7                            6
  R2                          4                            9
  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"
D70V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 37(17P12) MUTATED      33                         1
  DEL PEAK 37(17P12) WILD-TYPE    51                         2
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 37(17P12) MUTATED                                           1    73
  DEL PEAK 37(17P12) WILD-TYPE                                         0   135
D70V12, multiclass
                                           clus
vv                                          DEL PEAK 37(17P12) MUTATED
  ASIAN                                                             33
  BLACK OR AFRICAN AMERICAN                                          1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                             73
                                           clus
vv                                          DEL PEAK 37(17P12) WILD-TYPE
  ASIAN                                                               51
  BLACK OR AFRICAN AMERICAN                                            2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              135
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(71) Variable = DEL PEAK 38(17Q24.3) MUTATION ANALYSIS
D71V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 38(17Q24.3) MUTATED    40  17
  DEL PEAK 38(17Q24.3) WILD-TYPE 182  76
  DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE 
                            57                            258 
  DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE 
                            17                             76 
$`DEL PEAK 38(17Q24.3) MUTATED`
TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7723 TCGA-BR-7959 
        7.00         0.62        35.24        15.42        18.54        18.71 
TCGA-BR-8077 TCGA-BR-8291 TCGA-BR-8361 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8485 
        0.69        16.31        19.50        14.79         3.72         9.21 
TCGA-BR-8683 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.59         1.15         0.66         0.72        13.51        20.65 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-8524 TCGA-CD-8528 TCGA-CD-8533 TCGA-CD-A489 
        1.15        13.64         0.07         0.10         0.13         0.13 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        0.13         0.10        20.02        54.08         4.01        14.01 
TCGA-CG-4444 TCGA-CG-4469 TCGA-CG-5730 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6528 
       47.05         7.07         4.01        11.93        17.19        15.22 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8576 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A74A 
       11.31        12.33         6.97        16.44        11.31         7.40 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GH 
       16.24         0.23         5.92        12.59        14.17        11.77 
TCGA-HU-A4GP TCGA-HU-A4H2 TCGA-IN-8462 TCGA-IN-8663 TCGA-RD-A7BT TCGA-RD-A7C1 
        8.98        12.95        18.81         3.39         8.61        16.67 
TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB 
      115.69         8.94         5.79 

$`DEL PEAK 38(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-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-8060 
        0.95         0.69        12.76        17.49         0.82         1.32 
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-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 
        0.26         1.55         1.48         7.40         6.18         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-8380 TCGA-BR-8381 
       14.04         3.32         0.36        19.17         0.69         0.26 
TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
       15.85         5.39         0.72        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-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        15.81        16.44        15.68         0.62        10.68 
TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       12.56         3.02         2.27         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-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       19.36         0.46        20.42        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 
        3.25        13.15        13.18         0.30         0.07         0.07 
TCGA-CD-8526 TCGA-CD-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-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A4MG 
        0.13         0.10         0.07         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-4436 TCGA-CG-4437 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
        7.99         8.05        29.98        19.07        12.03        21.99 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97        12.00        22.98        30.97         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-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-D7-6518 TCGA-D7-6519 
       21.07         7.99        12.36        12.66        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 
       18.84        18.54        18.61        17.85        13.35        10.26 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       15.98        12.79        10.55        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       17.19         0.23        21.14        20.91        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
       15.16        13.78        14.76        13.71        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 
        9.76         2.96        15.65         4.34         7.13         0.62 
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-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-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HJ-7597 
        5.03        13.58         0.56         1.55        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        1.51        14.27        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-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-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.25        10.19         0.26         2.10        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-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO 
        3.45        18.38         5.36         5.19        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-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV 
       60.56         3.72         4.50        11.05         4.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-ZA-A8F6 
       37.91        40.64       116.38        71.38        57.44         4.21 

  DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE 
                        115.69                         122.30 
  DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE 
                        11.310                         10.865 
[1] "0.1 - 115.7 (11.3)" "0.1 - 122.3 (10.9)"
[1] "hr=" "1.1"
D71V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 38(17Q24.3) MUTATED         0        1        3        3         6
  DEL PEAK 38(17Q24.3) WILD-TYPE       2       11       35       24        26
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 38(17Q24.3) MUTATED           9         0         13         13
  DEL PEAK 38(17Q24.3) WILD-TYPE        38         3         48         32
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 38(17Q24.3) MUTATED            5        6
  DEL PEAK 38(17Q24.3) WILD-TYPE         27       25
D71V3, multiclass
            clus
vv           DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              1                             11
  STAGE IB                              3                             35
  STAGE II                              3                             24
  STAGE IIA                             6                             26
  STAGE IIB                             9                             38
  STAGE III                             0                              3
  STAGE IIIA                           13                             48
  STAGE IIIB                           13                             32
  STAGE IIIC                            5                             27
  STAGE IV                              6                             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 38(17Q24.3) MUTATED     1  12  28  19
  DEL PEAK 38(17Q24.3) WILD-TYPE  19  73 118  66
D71V4, multiclass
    clus
vv   DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  T1                            1                             19
  T2                           12                             73
  T3                           28                            118
  T4                           19                             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 38(17Q24.3) MUTATED   16 14 18 12
  DEL PEAK 38(17Q24.3) WILD-TYPE 93 78 48 55
D71V5, multiclass
    clus
vv   DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  N0                           16                             93
  N1                           14                             78
  N2                           18                             48
  N3                           12                             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                              M0  M1  MX
  DEL PEAK 38(17Q24.3) MUTATED    59   3   2
  DEL PEAK 38(17Q24.3) WILD-TYPE 249  18  15
D71V6, multiclass
    clus
vv   DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  M0                           59                            249
  M1                            3                             18
  MX                            2                             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"
D71V7, binary
                                cls
clus                               0   1
  DEL PEAK 38(17Q24.3) MUTATED    26  38
  DEL PEAK 38(17Q24.3) WILD-TYPE 111 171
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(17Q24.3) MUTATED     26   38
  DEL PEAK 38(17Q24.3) WILD-TYPE  111  171
        clus
vv       DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  FEMALE                           26                            111
  MALE                             38                            171
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 38(17Q24.3) MUTATED                                       7
  DEL PEAK 38(17Q24.3) WILD-TYPE                                    55
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 38(17Q24.3) MUTATED                                                       27
  DEL PEAK 38(17Q24.3) WILD-TYPE                                                    127
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 38(17Q24.3) MUTATED                                                                  11
  DEL PEAK 38(17Q24.3) WILD-TYPE                                                                43
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 38(17Q24.3) MUTATED                                                 14
  DEL PEAK 38(17Q24.3) WILD-TYPE                                               31
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 38(17Q24.3) MUTATED                                                           0
  DEL PEAK 38(17Q24.3) WILD-TYPE                                                         1
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 38(17Q24.3) MUTATED                                                          3
  DEL PEAK 38(17Q24.3) WILD-TYPE                                                       16
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 38(17Q24.3) MUTATED                                                           1
  DEL PEAK 38(17Q24.3) WILD-TYPE                                                         4
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 38(17Q24.3) MUTATED                                          1
  DEL PEAK 38(17Q24.3) WILD-TYPE                                        3
D71V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 38(17Q24.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      27
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            14
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     1
                                                                   clus
vv                                                                  DEL PEAK 38(17Q24.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         55
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             43
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              31
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V9, binary
                                cls
clus                               0   1
  DEL PEAK 38(17Q24.3) MUTATED     0  64
  DEL PEAK 38(17Q24.3) WILD-TYPE   7 275
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(17Q24.3) MUTATED      0   64
  DEL PEAK 38(17Q24.3) WILD-TYPE    7  275
     clus
vv    DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  NO                             0                              7
  YES                           64                            275
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 38(17Q24.3) MUTATED    48   3   4   6
  DEL PEAK 38(17Q24.3) WILD-TYPE 229  10   9  19
D71V10, multiclass
    clus
vv   DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  R0                           48                            229
  R1                            3                             10
  R2                            4                              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"
D71V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 38(17Q24.3) MUTATED      15                         0
  DEL PEAK 38(17Q24.3) WILD-TYPE    69                         3
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 38(17Q24.3) MUTATED                                           1
  DEL PEAK 38(17Q24.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 38(17Q24.3) MUTATED      40
  DEL PEAK 38(17Q24.3) WILD-TYPE   168
D71V12, multiclass
                                           clus
vv                                          DEL PEAK 38(17Q24.3) MUTATED
  ASIAN                                                               15
  BLACK OR AFRICAN AMERICAN                                            0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               40
                                           clus
vv                                          DEL PEAK 38(17Q24.3) WILD-TYPE
  ASIAN                                                                 69
  BLACK OR AFRICAN AMERICAN                                              3
  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(72) Variable = DEL PEAK 39(18Q21.2) MUTATION ANALYSIS
D72V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 39(18Q21.2) MUTATED   106  37
  DEL PEAK 39(18Q21.2) WILD-TYPE 116  56
  DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE 
                           143                            172 
  DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE 
                            37                             56 
$`DEL PEAK 39(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         2.27         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         0.07         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        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 
       17.19        10.26        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-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 
        1.41         6.44         5.56         1.81         2.53         5.56 
TCGA-KB-A6F7 TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-SW-A7EB 
       60.56        16.67        37.91       115.69         5.79 

$`DEL PEAK 39(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         4.50 
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-ZA-A8F6 
       71.38        57.44         8.94         4.21 

  DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE 
                        115.69                         122.30 
  DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE 
                         9.670                         11.555 
[1] "0.1 - 115.7 (9.7)"  "0.1 - 122.3 (11.6)"
[1] "hr=" "1.1"
D72V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 39(18Q21.2) MUTATED         0        4       15       15        15
  DEL PEAK 39(18Q21.2) WILD-TYPE       2        8       23       12        17
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 39(18Q21.2) MUTATED          21         1         29         22
  DEL PEAK 39(18Q21.2) WILD-TYPE        26         2         32         23
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 39(18Q21.2) MUTATED           12       16
  DEL PEAK 39(18Q21.2) WILD-TYPE         20       15
D72V3, multiclass
            clus
vv           DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              4                              8
  STAGE IB                             15                             23
  STAGE II                             15                             12
  STAGE IIA                            15                             17
  STAGE IIB                            21                             26
  STAGE III                             1                              2
  STAGE IIIA                           29                             32
  STAGE IIIB                           22                             23
  STAGE IIIC                           12                             20
  STAGE IV                             16                             15
[1] 11  2
[1] TRUE
[1] "dimension of 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(18Q21.2) MUTATED    7 38 81 27
  DEL PEAK 39(18Q21.2) WILD-TYPE 13 47 65 58
D72V4, multiclass
    clus
vv   DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE
  T1                            7                             13
  T2                           38                             47
  T3                           81                             65
  T4                           27                             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
  DEL PEAK 39(18Q21.2) MUTATED   45 43 29 34
  DEL PEAK 39(18Q21.2) WILD-TYPE 64 49 37 33
D72V5, multiclass
    clus
vv   DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE
  N0                           45                             64
  N1                           43                             49
  N2                           29                             37
  N3                           34                             33
[1] 4 2
[1] 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(18Q21.2) MUTATED   135  11  10
  DEL PEAK 39(18Q21.2) WILD-TYPE 173  10   7
D72V6, multiclass
    clus
vv   DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE
  M0                          135                            173
  M1                           11                             10
  MX                           10                              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"
D72V7, binary
                                cls
clus                               0   1
  DEL PEAK 39(18Q21.2) MUTATED    57  99
  DEL PEAK 39(18Q21.2) WILD-TYPE  80 110
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(18Q21.2) MUTATED     57   99
  DEL PEAK 39(18Q21.2) WILD-TYPE   80  110
        clus
vv       DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE
  FEMALE                           57                             80
  MALE                             99                            110
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 39(18Q21.2) MUTATED                                      24
  DEL PEAK 39(18Q21.2) WILD-TYPE                                    38
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 39(18Q21.2) MUTATED                                                       66
  DEL PEAK 39(18Q21.2) WILD-TYPE                                                     88
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 39(18Q21.2) MUTATED                                                                  27
  DEL PEAK 39(18Q21.2) WILD-TYPE                                                                27
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 39(18Q21.2) MUTATED                                                 25
  DEL PEAK 39(18Q21.2) WILD-TYPE                                               20
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 39(18Q21.2) MUTATED                                                           1
  DEL PEAK 39(18Q21.2) WILD-TYPE                                                         0
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 39(18Q21.2) MUTATED                                                          6
  DEL PEAK 39(18Q21.2) WILD-TYPE                                                       13
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 39(18Q21.2) MUTATED                                                           3
  DEL PEAK 39(18Q21.2) WILD-TYPE                                                         2
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 39(18Q21.2) MUTATED                                          2
  DEL PEAK 39(18Q21.2) WILD-TYPE                                        2
D72V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 39(18Q21.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       24
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      66
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           27
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            25
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
                                                                   clus
vv                                                                  DEL PEAK 39(18Q21.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         38
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        88
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             27
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              20
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V9, binary
                                cls
clus                               0   1
  DEL PEAK 39(18Q21.2) MUTATED     3 153
  DEL PEAK 39(18Q21.2) WILD-TYPE   4 186
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(18Q21.2) MUTATED      3  153
  DEL PEAK 39(18Q21.2) WILD-TYPE    4  186
     clus
vv    DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE
  NO                             3                              4
  YES                          153                            186
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 39(18Q21.2) MUTATED   121  10   5  10
  DEL PEAK 39(18Q21.2) WILD-TYPE 156   3   8  15
D72V10, multiclass
    clus
vv   DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE
  R0                          121                            156
  R1                           10                              3
  R2                            5                              8
  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"
D72V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 39(18Q21.2) MUTATED      42                         0
  DEL PEAK 39(18Q21.2) WILD-TYPE    42                         3
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 39(18Q21.2) MUTATED                                           0
  DEL PEAK 39(18Q21.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 39(18Q21.2) MUTATED      92
  DEL PEAK 39(18Q21.2) WILD-TYPE   116
D72V12, multiclass
                                           clus
vv                                          DEL PEAK 39(18Q21.2) MUTATED
  ASIAN                                                               42
  BLACK OR AFRICAN AMERICAN                                            0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               92
                                           clus
vv                                          DEL PEAK 39(18Q21.2) WILD-TYPE
  ASIAN                                                                 42
  BLACK OR AFRICAN AMERICAN                                              3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                116
[1] 4 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 40(19P13.3) MUTATION ANALYSIS
D73V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 40(19P13.3) MUTATED    74  29
  DEL PEAK 40(19P13.3) WILD-TYPE 148  64
  DEL PEAK 40(19P13.3) MUTATED DEL PEAK 40(19P13.3) WILD-TYPE 
                           103                            212 
  DEL PEAK 40(19P13.3) MUTATED DEL PEAK 40(19P13.3) WILD-TYPE 
                            29                             64 
$`DEL PEAK 40(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         2.27         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         0.07         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        13.35 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8573 
       10.26        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-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 
        5.19         1.41         6.87         5.56         1.81         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N6 
        5.56        60.56         8.61         4.67        37.91         8.94 
TCGA-SW-A7EB 
        5.79 

$`DEL PEAK 40(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-RD-A7BS 
        5.36        13.08         6.44         3.72         4.50        11.05 
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-ZA-A8F6 
       57.44         4.21 

  DEL PEAK 40(19P13.3) MUTATED DEL PEAK 40(19P13.3) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 40(19P13.3) MUTATED DEL PEAK 40(19P13.3) WILD-TYPE 
                         72.23                         122.30 
  DEL PEAK 40(19P13.3) MUTATED DEL PEAK 40(19P13.3) WILD-TYPE 
                         8.940                         11.885 
[1] "0.1 - 72.2 (8.9)"   "0.1 - 122.3 (11.9)"
[1] "hr=" "1.1"
D73V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 40(19P13.3) MUTATED         0        6       12       13        10
  DEL PEAK 40(19P13.3) WILD-TYPE       2        6       26       14        22
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 40(19P13.3) MUTATED          20         0         21          9
  DEL PEAK 40(19P13.3) WILD-TYPE        27         3         40         36
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 40(19P13.3) MUTATED            7       11
  DEL PEAK 40(19P13.3) WILD-TYPE         25       20
D73V3, multiclass
            clus
vv           DEL PEAK 40(19P13.3) MUTATED DEL PEAK 40(19P13.3) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              6                              6
  STAGE IB                             12                             26
  STAGE II                             13                             14
  STAGE IIA                            10                             22
  STAGE IIB                            20                             27
  STAGE III                             0                              3
  STAGE IIIA                           21                             40
  STAGE IIIB                            9                             36
  STAGE IIIC                            7                             25
  STAGE IV                             11                             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 40(19P13.3) MUTATED    7 32 52 19
  DEL PEAK 40(19P13.3) WILD-TYPE 13 53 94 66
D73V4, multiclass
    clus
vv   DEL PEAK 40(19P13.3) MUTATED DEL PEAK 40(19P13.3) WILD-TYPE
  T1                            7                             13
  T2                           32                             53
  T3                           52                             94
  T4                           19                             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 40(19P13.3) MUTATED   39 34 18 19
  DEL PEAK 40(19P13.3) WILD-TYPE 70 58 48 48
D73V5, multiclass
    clus
vv   DEL PEAK 40(19P13.3) MUTATED DEL PEAK 40(19P13.3) WILD-TYPE
  N0                           39                             70
  N1                           34                             58
  N2                           18                             48
  N3                           19                             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 40(19P13.3) MUTATED   101   6   7
  DEL PEAK 40(19P13.3) WILD-TYPE 207  15  10
D73V6, multiclass
    clus
vv   DEL PEAK 40(19P13.3) MUTATED DEL PEAK 40(19P13.3) WILD-TYPE
  M0                          101                            207
  M1                            6                             15
  MX                            7                             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"
D73V7, binary
                                cls
clus                               0   1
  DEL PEAK 40(19P13.3) MUTATED    39  75
  DEL PEAK 40(19P13.3) WILD-TYPE  98 134
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(19P13.3) MUTATED     39   75
  DEL PEAK 40(19P13.3) WILD-TYPE   98  134
        clus
vv       DEL PEAK 40(19P13.3) MUTATED DEL PEAK 40(19P13.3) WILD-TYPE
  FEMALE                           39                             98
  MALE                             75                            134
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 40(19P13.3) MUTATED                                      14
  DEL PEAK 40(19P13.3) WILD-TYPE                                    48
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 40(19P13.3) MUTATED                                                       51
  DEL PEAK 40(19P13.3) WILD-TYPE                                                    103
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 40(19P13.3) MUTATED                                                                  26
  DEL PEAK 40(19P13.3) WILD-TYPE                                                                28
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 40(19P13.3) MUTATED                                                 13
  DEL PEAK 40(19P13.3) WILD-TYPE                                               32
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 40(19P13.3) MUTATED                                                           1
  DEL PEAK 40(19P13.3) WILD-TYPE                                                         0
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 40(19P13.3) MUTATED                                                          5
  DEL PEAK 40(19P13.3) WILD-TYPE                                                       14
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 40(19P13.3) MUTATED                                                           3
  DEL PEAK 40(19P13.3) WILD-TYPE                                                         2
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 40(19P13.3) MUTATED                                          0
  DEL PEAK 40(19P13.3) WILD-TYPE                                        4
D73V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 40(19P13.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       14
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      51
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           26
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            13
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     0
                                                                   clus
vv                                                                  DEL PEAK 40(19P13.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       103
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             28
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              32
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       4
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V9, binary
                                cls
clus                               0   1
  DEL PEAK 40(19P13.3) MUTATED     6 108
  DEL PEAK 40(19P13.3) WILD-TYPE   1 231
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(19P13.3) MUTATED      6  108
  DEL PEAK 40(19P13.3) WILD-TYPE    1  231
     clus
vv    DEL PEAK 40(19P13.3) MUTATED DEL PEAK 40(19P13.3) WILD-TYPE
  NO                             6                              1
  YES                          108                            231
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 40(19P13.3) MUTATED    91   2   5   6
  DEL PEAK 40(19P13.3) WILD-TYPE 186  11   8  19
D73V10, multiclass
    clus
vv   DEL PEAK 40(19P13.3) MUTATED DEL PEAK 40(19P13.3) WILD-TYPE
  R0                           91                            186
  R1                            2                             11
  R2                            5                              8
  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 40(19P13.3) MUTATED      34                         1
  DEL PEAK 40(19P13.3) WILD-TYPE    50                         2
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 40(19P13.3) MUTATED                                           1
  DEL PEAK 40(19P13.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 40(19P13.3) MUTATED      58
  DEL PEAK 40(19P13.3) WILD-TYPE   150
D73V12, multiclass
                                           clus
vv                                          DEL PEAK 40(19P13.3) MUTATED
  ASIAN                                                               34
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               58
                                           clus
vv                                          DEL PEAK 40(19P13.3) WILD-TYPE
  ASIAN                                                                 50
  BLACK OR AFRICAN AMERICAN                                              2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  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(74) Variable = DEL PEAK 41(19Q13.11) MUTATION ANALYSIS
D74V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 41(19Q13.11) MUTATED    36  13
  DEL PEAK 41(19Q13.11) WILD-TYPE 186  80
  DEL PEAK 41(19Q13.11) MUTATED DEL PEAK 41(19Q13.11) WILD-TYPE 
                             49                             266 
  DEL PEAK 41(19Q13.11) MUTATED DEL PEAK 41(19Q13.11) WILD-TYPE 
                             13                              80 
$`DEL PEAK 41(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 
        0.07         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        10.26        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-RD-A8MW 
       37.91 

$`DEL PEAK 41(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 
        2.27        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        13.35        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-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-A5UJ TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        4.50        11.05         8.61         4.67        16.67       122.30 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-SW-A7EB TCGA-ZA-A8F6 
        5.79         4.21 

  DEL PEAK 41(19Q13.11) MUTATED DEL PEAK 41(19Q13.11) WILD-TYPE 
                           0.07                            0.07 
  DEL PEAK 41(19Q13.11) MUTATED DEL PEAK 41(19Q13.11) WILD-TYPE 
                          37.91                          122.30 
  DEL PEAK 41(19Q13.11) MUTATED DEL PEAK 41(19Q13.11) WILD-TYPE 
                         10.260                          11.145 
[1] "0.1 - 37.9 (10.3)"  "0.1 - 122.3 (11.1)"
[1] "hr=" "1"  
D74V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 41(19Q13.11) MUTATED         0        2        6        7         6
  DEL PEAK 41(19Q13.11) WILD-TYPE       2       10       32       20        26
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 41(19Q13.11) MUTATED           5         0          6          9
  DEL PEAK 41(19Q13.11) WILD-TYPE        42         3         55         36
                                 vv
clus                              STAGE IIIC STAGE IV
  DEL PEAK 41(19Q13.11) MUTATED            4        5
  DEL PEAK 41(19Q13.11) WILD-TYPE         28       26
D74V3, multiclass
            clus
vv           DEL PEAK 41(19Q13.11) MUTATED DEL PEAK 41(19Q13.11) WILD-TYPE
  STAGE I                                0                               2
  STAGE IA                               2                              10
  STAGE IB                               6                              32
  STAGE II                               7                              20
  STAGE IIA                              6                              26
  STAGE IIB                              5                              42
  STAGE III                              0                               3
  STAGE IIIA                             6                              55
  STAGE IIIB                             9                              36
  STAGE IIIC                             4                              28
  STAGE IV                               5                              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 41(19Q13.11) MUTATED     3  13  26   8
  DEL PEAK 41(19Q13.11) WILD-TYPE  17  72 120  77
D74V4, multiclass
    clus
vv   DEL PEAK 41(19Q13.11) MUTATED DEL PEAK 41(19Q13.11) WILD-TYPE
  T1                             3                              17
  T2                            13                              72
  T3                            26                             120
  T4                             8                              77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2 N3
  DEL PEAK 41(19Q13.11) MUTATED   18 10  9 13
  DEL PEAK 41(19Q13.11) WILD-TYPE 91 82 57 54
D74V5, multiclass
    clus
vv   DEL PEAK 41(19Q13.11) MUTATED DEL PEAK 41(19Q13.11) WILD-TYPE
  N0                            18                              91
  N1                            10                              82
  N2                             9                              57
  N3                            13                              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
  DEL PEAK 41(19Q13.11) MUTATED    45   5   2
  DEL PEAK 41(19Q13.11) WILD-TYPE 263  16  15
D74V6, multiclass
    clus
vv   DEL PEAK 41(19Q13.11) MUTATED DEL PEAK 41(19Q13.11) WILD-TYPE
  M0                            45                             263
  M1                             5                              16
  MX                             2                              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"
D74V7, binary
                                 cls
clus                                0   1
  DEL PEAK 41(19Q13.11) MUTATED    19  33
  DEL PEAK 41(19Q13.11) WILD-TYPE 118 176
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 41(19Q13.11) MUTATED     19   33
  DEL PEAK 41(19Q13.11) WILD-TYPE  118  176
        clus
vv       DEL PEAK 41(19Q13.11) MUTATED DEL PEAK 41(19Q13.11) WILD-TYPE
  FEMALE                            19                             118
  MALE                              33                             176
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 41(19Q13.11) MUTATED                                       5
  DEL PEAK 41(19Q13.11) WILD-TYPE                                    57
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 41(19Q13.11) MUTATED                                                       23
  DEL PEAK 41(19Q13.11) WILD-TYPE                                                    131
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 41(19Q13.11) MUTATED                                                                  10
  DEL PEAK 41(19Q13.11) WILD-TYPE                                                                44
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 41(19Q13.11) MUTATED                                                 11
  DEL PEAK 41(19Q13.11) WILD-TYPE                                               34
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 41(19Q13.11) MUTATED                                                           1
  DEL PEAK 41(19Q13.11) WILD-TYPE                                                         0
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 41(19Q13.11) MUTATED                                                          1
  DEL PEAK 41(19Q13.11) WILD-TYPE                                                       18
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 41(19Q13.11) MUTATED                                                           1
  DEL PEAK 41(19Q13.11) WILD-TYPE                                                         4
                                 vv
clus                              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 41(19Q13.11) MUTATED                                          0
  DEL PEAK 41(19Q13.11) WILD-TYPE                                        4
D74V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 41(19Q13.11) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       23
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            10
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             11
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      0
                                                                   clus
vv                                                                  DEL PEAK 41(19Q13.11) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          57
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              44
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               34
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                        4
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V9, binary
                                 cls
clus                                0   1
  DEL PEAK 41(19Q13.11) MUTATED     2  50
  DEL PEAK 41(19Q13.11) WILD-TYPE   5 289
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 41(19Q13.11) MUTATED      2   50
  DEL PEAK 41(19Q13.11) WILD-TYPE    5  289
     clus
vv    DEL PEAK 41(19Q13.11) MUTATED DEL PEAK 41(19Q13.11) WILD-TYPE
  NO                              2                               5
  YES                            50                             289
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 41(19Q13.11) MUTATED    43   0   3   3
  DEL PEAK 41(19Q13.11) WILD-TYPE 234  13  10  22
D74V10, multiclass
    clus
vv   DEL PEAK 41(19Q13.11) MUTATED DEL PEAK 41(19Q13.11) WILD-TYPE
  R0                            43                             234
  R1                             0                              13
  R2                             3                              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"
D74V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 41(19Q13.11) MUTATED      14                         0
  DEL PEAK 41(19Q13.11) WILD-TYPE    70                         3
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 41(19Q13.11) MUTATED                                           0
  DEL PEAK 41(19Q13.11) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 41(19Q13.11) MUTATED      33
  DEL PEAK 41(19Q13.11) WILD-TYPE   175
D74V12, multiclass
                                           clus
vv                                          DEL PEAK 41(19Q13.11) MUTATED
  ASIAN                                                                14
  BLACK OR AFRICAN AMERICAN                                             0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                33
                                           clus
vv                                          DEL PEAK 41(19Q13.11) WILD-TYPE
  ASIAN                                                                  70
  BLACK OR AFRICAN AMERICAN                                               3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 175
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(75) Variable = DEL PEAK 42(20P12.1) MUTATION ANALYSIS
D75V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 42(20P12.1) MUTATED    13  13
  DEL PEAK 42(20P12.1) WILD-TYPE 209  80
  DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE 
                            26                            289 
  DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE 
                            13                             80 
$`DEL PEAK 42(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        10.26         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 
        2.53        37.91 

$`DEL PEAK 42(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 
        2.27         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         0.07         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 
       13.35        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-A6RS 
        3.39        18.38         5.19        13.08         6.44         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         4.50 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 
       11.05         8.61         4.67        16.67       122.30        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-SW-A7EB 
      115.69       116.38        71.38        57.44         8.94         5.79 
TCGA-ZA-A8F6 
        4.21 

  DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE 
                         37.91                         122.30 
  DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE 
                          8.55                          11.31 
[1] "0.1 - 37.9 (8.6)"   "0.1 - 122.3 (11.3)"
[1] "hr=" "2.1"
D75V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 42(20P12.1) MUTATED         0        1        4        2         2
  DEL PEAK 42(20P12.1) WILD-TYPE       2       11       34       25        30
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 42(20P12.1) MUTATED           4         0          4          7
  DEL PEAK 42(20P12.1) WILD-TYPE        43         3         57         38
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 42(20P12.1) MUTATED            0        4
  DEL PEAK 42(20P12.1) WILD-TYPE         32       27
D75V3, multiclass
            clus
vv           DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              1                             11
  STAGE IB                              4                             34
  STAGE II                              2                             25
  STAGE IIA                             2                             30
  STAGE IIB                             4                             43
  STAGE III                             0                              3
  STAGE IIIA                            4                             57
  STAGE IIIB                            7                             38
  STAGE IIIC                            0                             32
  STAGE IV                              4                             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 42(20P12.1) MUTATED     2   7  13   6
  DEL PEAK 42(20P12.1) WILD-TYPE  18  78 133  79
D75V4, multiclass
    clus
vv   DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE
  T1                            2                             18
  T2                            7                             78
  T3                           13                            133
  T4                            6                             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 42(20P12.1) MUTATED     9   8   6   5
  DEL PEAK 42(20P12.1) WILD-TYPE 100  84  60  62
D75V5, multiclass
    clus
vv   DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE
  N0                            9                            100
  N1                            8                             84
  N2                            6                             60
  N3                            5                             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 42(20P12.1) MUTATED    22   3   3
  DEL PEAK 42(20P12.1) WILD-TYPE 286  18  14
D75V6, multiclass
    clus
vv   DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE
  M0                           22                            286
  M1                            3                             18
  MX                            3                             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"
D75V7, binary
                                cls
clus                               0   1
  DEL PEAK 42(20P12.1) MUTATED    13  15
  DEL PEAK 42(20P12.1) WILD-TYPE 124 194
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(20P12.1) MUTATED     13   15
  DEL PEAK 42(20P12.1) WILD-TYPE  124  194
        clus
vv       DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE
  FEMALE                           13                            124
  MALE                             15                            194
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 42(20P12.1) MUTATED                                       2
  DEL PEAK 42(20P12.1) WILD-TYPE                                    60
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 42(20P12.1) MUTATED                                                       16
  DEL PEAK 42(20P12.1) WILD-TYPE                                                    138
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 42(20P12.1) MUTATED                                                                   2
  DEL PEAK 42(20P12.1) WILD-TYPE                                                                52
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 42(20P12.1) MUTATED                                                  5
  DEL PEAK 42(20P12.1) WILD-TYPE                                               40
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 42(20P12.1) MUTATED                                                           1
  DEL PEAK 42(20P12.1) WILD-TYPE                                                         0
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 42(20P12.1) MUTATED                                                          2
  DEL PEAK 42(20P12.1) WILD-TYPE                                                       17
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 42(20P12.1) MUTATED                                                           0
  DEL PEAK 42(20P12.1) WILD-TYPE                                                         5
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 42(20P12.1) MUTATED                                          0
  DEL PEAK 42(20P12.1) WILD-TYPE                                        4
D75V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 42(20P12.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      16
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             5
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     0
                                                                   clus
vv                                                                  DEL PEAK 42(20P12.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         60
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       138
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             52
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              40
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       4
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V9, binary
                                cls
clus                               0   1
  DEL PEAK 42(20P12.1) MUTATED     3  25
  DEL PEAK 42(20P12.1) WILD-TYPE   4 314
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(20P12.1) MUTATED      3   25
  DEL PEAK 42(20P12.1) WILD-TYPE    4  314
     clus
vv    DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE
  NO                             3                              4
  YES                           25                            314
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 42(20P12.1) MUTATED    23   1   2   1
  DEL PEAK 42(20P12.1) WILD-TYPE 254  12  11  24
D75V10, multiclass
    clus
vv   DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE
  R0                           23                            254
  R1                            1                             12
  R2                            2                             11
  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"
D75V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 42(20P12.1) MUTATED       6                         0
  DEL PEAK 42(20P12.1) WILD-TYPE    78                         3
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 42(20P12.1) MUTATED                                           0
  DEL PEAK 42(20P12.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 42(20P12.1) MUTATED      17
  DEL PEAK 42(20P12.1) WILD-TYPE   191
D75V12, multiclass
                                           clus
vv                                          DEL PEAK 42(20P12.1) MUTATED
  ASIAN                                                                6
  BLACK OR AFRICAN AMERICAN                                            0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               17
                                           clus
vv                                          DEL PEAK 42(20P12.1) WILD-TYPE
  ASIAN                                                                 78
  BLACK OR AFRICAN AMERICAN                                              3
  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(76) Variable = DEL PEAK 43(21Q11.2) MUTATION ANALYSIS
D76V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 43(21Q11.2) MUTATED    85  31
  DEL PEAK 43(21Q11.2) WILD-TYPE 137  62
  DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE 
                           116                            199 
  DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE 
                            31                             62 
$`DEL PEAK 43(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-8361 
        1.32        12.26         0.49         0.72        16.31        19.50 
TCGA-BR-8365 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8484 
        2.96         4.31        14.04        14.79         5.39         0.72 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        9.21        20.22        11.54         0.59        15.68         0.62 
TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J8 
       10.68         0.66         2.27         0.92         0.72        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-8524 
        0.46        20.65        20.42         1.15        13.64         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 
        0.07         0.07         0.16         0.13         0.13         0.13 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-4440 
        0.13         0.13         0.10        20.02        54.08         4.01 
TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
       47.05        12.03        18.97        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5728 TCGA-CG-5730 TCGA-D7-5579 
        1.02         1.02        12.03        65.10         4.01        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 
       19.13        20.55        13.35        17.19        15.98        12.79 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EX 
       11.31        12.33         6.97        21.14        16.44        11.31 
TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7829 
       15.65         0.62         7.79        72.23         8.12        19.53 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8604 
        1.55         0.23        26.47         1.51        14.17        12.10 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GP TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H5 
       11.84         3.25         8.98         0.26        19.36        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-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-A6F5 TCGA-KB-A6F7 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 
        5.56        60.56       122.30        37.91       115.69        57.44 
TCGA-RD-A8N6 TCGA-SW-A7EB 
        8.94         5.79 

$`DEL PEAK 43(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-8296 
       20.55         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-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 
       13.74         3.32         0.36        19.17         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-8680 TCGA-BR-8682 
       13.45         0.20         7.53         0.49        15.81        16.44 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-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-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-8528 TCGA-CD-8529 TCGA-CD-8531 
        0.30         0.07         0.07         0.10         0.13         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A4MG TCGA-CD-A4MI 
        0.10         0.13         0.10         0.07         0.07         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-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4465 
        8.05        14.01        29.98        19.07        21.99         9.01 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        7.07        12.00         0.99         6.02         0.99       105.07 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        28.96        79.07        55.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       12.36        12.66        18.84        18.54        18.61        17.85 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.26        15.22        10.55        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX 
       17.19         0.23        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-A74A TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6177 
        2.96         4.34         7.40         7.13        16.24         6.58 
TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       14.47        21.27         0.39         3.02        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-A5NB TCGA-HU-8243 
       59.54         5.03        13.58         0.56        18.08         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-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
        5.59        12.30        24.20        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-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 
        2.10        12.95        17.69         8.88         8.81         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         4.50        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
        8.61         4.67        16.67        40.64       116.38        71.38 
TCGA-ZA-A8F6 
        4.21 

  DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE 
                        122.30                         116.38 
  DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE 
                         11.31                          10.62 
[1] "0.1 - 122.3 (11.3)" "0.1 - 116.4 (10.6)"
[1] "hr=" "1.2"
D76V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 43(21Q11.2) MUTATED         0        3       17        7        12
  DEL PEAK 43(21Q11.2) WILD-TYPE       2        9       21       20        20
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 43(21Q11.2) MUTATED          18         0         31         17
  DEL PEAK 43(21Q11.2) WILD-TYPE        29         3         30         28
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 43(21Q11.2) MUTATED           10        8
  DEL PEAK 43(21Q11.2) WILD-TYPE         22       23
D76V3, multiclass
            clus
vv           DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              3                              9
  STAGE IB                             17                             21
  STAGE II                              7                             20
  STAGE IIA                            12                             20
  STAGE IIB                            18                             29
  STAGE III                             0                              3
  STAGE IIIA                           31                             30
  STAGE IIIB                           17                             28
  STAGE IIIC                           10                             22
  STAGE IV                              8                             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(21Q11.2) MUTATED    5 34 59 26
  DEL PEAK 43(21Q11.2) WILD-TYPE 15 51 87 59
D76V4, multiclass
    clus
vv   DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE
  T1                            5                             15
  T2                           34                             51
  T3                           59                             87
  T4                           26                             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                             N0 N1 N2 N3
  DEL PEAK 43(21Q11.2) MUTATED   37 38 29 20
  DEL PEAK 43(21Q11.2) WILD-TYPE 72 54 37 47
D76V5, multiclass
    clus
vv   DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE
  N0                           37                             72
  N1                           38                             54
  N2                           29                             37
  N3                           20                             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 43(21Q11.2) MUTATED   115   5   7
  DEL PEAK 43(21Q11.2) WILD-TYPE 193  16  10
D76V6, multiclass
    clus
vv   DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE
  M0                          115                            193
  M1                            5                             16
  MX                            7                             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"
D76V7, binary
                                cls
clus                               0   1
  DEL PEAK 43(21Q11.2) MUTATED    57  70
  DEL PEAK 43(21Q11.2) WILD-TYPE  80 139
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(21Q11.2) MUTATED     57   70
  DEL PEAK 43(21Q11.2) WILD-TYPE   80  139
        clus
vv       DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE
  FEMALE                           57                             80
  MALE                             70                            139
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 43(21Q11.2) MUTATED                                      20
  DEL PEAK 43(21Q11.2) WILD-TYPE                                    42
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 43(21Q11.2) MUTATED                                                       56
  DEL PEAK 43(21Q11.2) WILD-TYPE                                                     98
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 43(21Q11.2) MUTATED                                                                  22
  DEL PEAK 43(21Q11.2) WILD-TYPE                                                                32
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 43(21Q11.2) MUTATED                                                 16
  DEL PEAK 43(21Q11.2) WILD-TYPE                                               29
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 43(21Q11.2) MUTATED                                                           0
  DEL PEAK 43(21Q11.2) WILD-TYPE                                                         1
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 43(21Q11.2) MUTATED                                                          8
  DEL PEAK 43(21Q11.2) WILD-TYPE                                                       11
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 43(21Q11.2) MUTATED                                                           1
  DEL PEAK 43(21Q11.2) WILD-TYPE                                                         4
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 43(21Q11.2) MUTATED                                          3
  DEL PEAK 43(21Q11.2) WILD-TYPE                                        1
D76V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 43(21Q11.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       20
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      56
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           22
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            16
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     3
                                                                   clus
vv                                                                  DEL PEAK 43(21Q11.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         42
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        98
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             32
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              29
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V9, binary
                                cls
clus                               0   1
  DEL PEAK 43(21Q11.2) MUTATED     4 123
  DEL PEAK 43(21Q11.2) WILD-TYPE   3 216
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(21Q11.2) MUTATED      4  123
  DEL PEAK 43(21Q11.2) WILD-TYPE    3  216
     clus
vv    DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE
  NO                             4                              3
  YES                          123                            216
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 43(21Q11.2) MUTATED   103   7   4   6
  DEL PEAK 43(21Q11.2) WILD-TYPE 174   6   9  19
D76V10, multiclass
    clus
vv   DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE
  R0                          103                            174
  R1                            7                              6
  R2                            4                              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"
D76V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 43(21Q11.2) MUTATED      28                         1
  DEL PEAK 43(21Q11.2) WILD-TYPE    56                         2
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 43(21Q11.2) MUTATED                                           0
  DEL PEAK 43(21Q11.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 43(21Q11.2) MUTATED      78
  DEL PEAK 43(21Q11.2) WILD-TYPE   130
D76V12, multiclass
                                           clus
vv                                          DEL PEAK 43(21Q11.2) MUTATED
  ASIAN                                                               28
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               78
                                           clus
vv                                          DEL PEAK 43(21Q11.2) WILD-TYPE
  ASIAN                                                                 56
  BLACK OR AFRICAN AMERICAN                                              2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                130
[1] 4 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 44(21Q22.13) MUTATION ANALYSIS
D77V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 44(21Q22.13) MUTATED    92  33
  DEL PEAK 44(21Q22.13) WILD-TYPE 130  60
  DEL PEAK 44(21Q22.13) MUTATED DEL PEAK 44(21Q22.13) WILD-TYPE 
                            125                             190 
  DEL PEAK 44(21Q22.13) MUTATED DEL PEAK 44(21Q22.13) WILD-TYPE 
                             33                              60 
$`DEL PEAK 44(21Q22.13) 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-7723 
        0.62        31.20        35.24        15.42        28.01        18.54 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8291 
       18.71         0.82         1.32         0.49         0.72        16.31 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8365 TCGA-BR-8368 TCGA-BR-8369 
        1.48         7.40        19.50         2.96         4.31        14.04 
TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8682 
       14.79         5.39         0.72         9.21        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
        0.59        15.68        10.68         0.66         2.27         0.92 
TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
       12.89         0.72        13.51         0.46        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        1.15        13.64         0.07         0.07         0.07         0.10 
TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        0.16         0.13         0.13         0.13         0.13         0.10 
TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
       20.02        54.08         4.01        47.05        19.07        12.03 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 
       18.97         7.07        22.98        30.97         6.97         1.02 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5579 
       12.03        15.02        65.10         4.01        55.04        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 
       19.13        20.55        13.35        17.19        15.98        12.79 
TCGA-D7-6820 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 
       11.31        21.14        14.27        16.44        11.31        15.65 
TCGA-D7-A74A TCGA-EQ-5647 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-8099 
        7.40         0.62        72.23         8.12        19.53        17.06 
TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G8 
        0.23        26.47         1.51        14.17        12.10        11.84 
TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H2 
        3.25        11.77         8.98         6.25         0.26        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-8462 
       19.36        17.69        12.30         9.67        21.21        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A7NT 
        3.39        18.38         5.36         5.19         1.41         5.56 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-RD-A7C1 TCGA-RD-A8MV 
        1.81         2.53         5.56        60.56        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-SW-A7EB 
       37.91       115.69        57.44         8.94         5.79 

$`DEL PEAK 44(21Q22.13) 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-7851 TCGA-BR-7901 
       24.76        23.93         0.69         0.16        12.43         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 
        0.69        12.76        17.49         0.69        12.26        20.55 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8362 
        0.26        12.95         0.26         1.55         6.18         0.36 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8370 TCGA-BR-8371 
        0.26        22.19         0.95        13.74         3.32         0.36 
TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8486 
       19.17         0.69         0.26        15.85         3.72        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         2.14        13.45         0.20 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U 
        7.53         0.49        15.81         0.62        12.56         1.15 
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-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       12.82         0.66        19.36        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 
        3.25        13.15        13.18         0.30         0.07         0.07 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 
        0.13         0.10         0.10         0.13         0.10         0.07 
TCGA-CD-A487 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-4441 TCGA-CG-4443 
       15.95         1.02         7.99         8.05        14.01        29.98 
TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 
       21.99         9.01        12.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5733 TCGA-CG-5734 
        0.99       105.07        28.96        79.07        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       12.36        12.66        18.84        18.54        18.61        17.85 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       10.26        15.22        10.55        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YV 
       19.50        17.19         0.23         6.97        20.91         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
       15.16        13.78        14.76        13.71        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO 
        9.76         2.96         4.34         7.13         7.79        16.24 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
        6.58        14.47        21.27         0.39         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-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
        5.92        14.27        12.59        11.41        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF 
       24.30         5.59        12.30        24.20        22.75        25.81 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H0 
       21.37        29.98         0.10         6.51        10.19         2.10 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RN TCGA-IN-A6RP 
        8.88         8.81        27.42         3.45        13.08         6.44 
TCGA-IN-A6RS TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.87         3.72         4.50        11.05         8.61         4.67 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-ZA-A8F6 
       40.64       116.38        71.38         4.21 

  DEL PEAK 44(21Q22.13) MUTATED DEL PEAK 44(21Q22.13) WILD-TYPE 
                           0.07                            0.07 
  DEL PEAK 44(21Q22.13) MUTATED DEL PEAK 44(21Q22.13) WILD-TYPE 
                         122.30                          116.38 
  DEL PEAK 44(21Q22.13) MUTATED DEL PEAK 44(21Q22.13) WILD-TYPE 
                          11.77                           10.16 
[1] "0.1 - 122.3 (11.8)" "0.1 - 116.4 (10.2)"
[1] "hr=" "1.3"
D77V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 44(21Q22.13) MUTATED         0        3       17        7        14
  DEL PEAK 44(21Q22.13) WILD-TYPE       2        9       21       20        18
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 44(21Q22.13) MUTATED          19         1         31         17
  DEL PEAK 44(21Q22.13) WILD-TYPE        28         2         30         28
                                 vv
clus                              STAGE IIIC STAGE IV
  DEL PEAK 44(21Q22.13) MUTATED           11       10
  DEL PEAK 44(21Q22.13) WILD-TYPE         21       21
D77V3, multiclass
            clus
vv           DEL PEAK 44(21Q22.13) MUTATED DEL PEAK 44(21Q22.13) WILD-TYPE
  STAGE I                                0                               2
  STAGE IA                               3                               9
  STAGE IB                              17                              21
  STAGE II                               7                              20
  STAGE IIA                             14                              18
  STAGE IIB                             19                              28
  STAGE III                              1                               2
  STAGE IIIA                            31                              30
  STAGE IIIB                            17                              28
  STAGE IIIC                            11                              21
  STAGE IV                              10                              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(21Q22.13) MUTATED    5 37 59 30
  DEL PEAK 44(21Q22.13) WILD-TYPE 15 48 87 55
D77V4, multiclass
    clus
vv   DEL PEAK 44(21Q22.13) MUTATED DEL PEAK 44(21Q22.13) WILD-TYPE
  T1                             5                              15
  T2                            37                              48
  T3                            59                              87
  T4                            30                              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
  DEL PEAK 44(21Q22.13) MUTATED   41 38 29 24
  DEL PEAK 44(21Q22.13) WILD-TYPE 68 54 37 43
D77V5, multiclass
    clus
vv   DEL PEAK 44(21Q22.13) MUTATED DEL PEAK 44(21Q22.13) WILD-TYPE
  N0                            41                              68
  N1                            38                              54
  N2                            29                              37
  N3                            24                              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 44(21Q22.13) MUTATED   125   5   6
  DEL PEAK 44(21Q22.13) WILD-TYPE 183  16  11
D77V6, multiclass
    clus
vv   DEL PEAK 44(21Q22.13) MUTATED DEL PEAK 44(21Q22.13) WILD-TYPE
  M0                           125                             183
  M1                             5                              16
  MX                             6                              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"
D77V7, binary
                                 cls
clus                                0   1
  DEL PEAK 44(21Q22.13) MUTATED    56  80
  DEL PEAK 44(21Q22.13) WILD-TYPE  81 129
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(21Q22.13) MUTATED     56   80
  DEL PEAK 44(21Q22.13) WILD-TYPE   81  129
        clus
vv       DEL PEAK 44(21Q22.13) MUTATED DEL PEAK 44(21Q22.13) WILD-TYPE
  FEMALE                            56                              81
  MALE                              80                             129
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 44(21Q22.13) MUTATED                                      22
  DEL PEAK 44(21Q22.13) WILD-TYPE                                    40
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 44(21Q22.13) MUTATED                                                       58
  DEL PEAK 44(21Q22.13) WILD-TYPE                                                     96
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 44(21Q22.13) MUTATED                                                                  24
  DEL PEAK 44(21Q22.13) WILD-TYPE                                                                30
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 44(21Q22.13) MUTATED                                                 18
  DEL PEAK 44(21Q22.13) WILD-TYPE                                               27
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 44(21Q22.13) MUTATED                                                           0
  DEL PEAK 44(21Q22.13) WILD-TYPE                                                         1
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 44(21Q22.13) MUTATED                                                         10
  DEL PEAK 44(21Q22.13) WILD-TYPE                                                        9
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 44(21Q22.13) MUTATED                                                           1
  DEL PEAK 44(21Q22.13) WILD-TYPE                                                         4
                                 vv
clus                              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 44(21Q22.13) MUTATED                                          2
  DEL PEAK 44(21Q22.13) WILD-TYPE                                        2
D77V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 44(21Q22.13) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        22
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       58
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            24
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             18
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      2
                                                                   clus
vv                                                                  DEL PEAK 44(21Q22.13) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          40
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                         96
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              30
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               27
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                        9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                        2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V9, binary
                                 cls
clus                                0   1
  DEL PEAK 44(21Q22.13) MUTATED     3 133
  DEL PEAK 44(21Q22.13) WILD-TYPE   4 206
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(21Q22.13) MUTATED      3  133
  DEL PEAK 44(21Q22.13) WILD-TYPE    4  206
     clus
vv    DEL PEAK 44(21Q22.13) MUTATED DEL PEAK 44(21Q22.13) WILD-TYPE
  NO                              3                               4
  YES                           133                             206
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 44(21Q22.13) MUTATED   113   6   4   8
  DEL PEAK 44(21Q22.13) WILD-TYPE 164   7   9  17
D77V10, multiclass
    clus
vv   DEL PEAK 44(21Q22.13) MUTATED DEL PEAK 44(21Q22.13) WILD-TYPE
  R0                           113                             164
  R1                             6                               7
  R2                             4                               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"
D77V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 44(21Q22.13) MUTATED      32                         1
  DEL PEAK 44(21Q22.13) WILD-TYPE    52                         2
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 44(21Q22.13) MUTATED                                           0
  DEL PEAK 44(21Q22.13) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 44(21Q22.13) MUTATED      81
  DEL PEAK 44(21Q22.13) WILD-TYPE   127
D77V12, multiclass
                                           clus
vv                                          DEL PEAK 44(21Q22.13) MUTATED
  ASIAN                                                                32
  BLACK OR AFRICAN AMERICAN                                             1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                81
                                           clus
vv                                          DEL PEAK 44(21Q22.13) WILD-TYPE
  ASIAN                                                                  52
  BLACK OR AFRICAN AMERICAN                                               2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  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(78) Variable = DEL PEAK 45(22Q13.31) MUTATION ANALYSIS
D78V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 45(22Q13.31) MUTATED    76  30
  DEL PEAK 45(22Q13.31) WILD-TYPE 146  63
  DEL PEAK 45(22Q13.31) MUTATED DEL PEAK 45(22Q13.31) WILD-TYPE 
                            106                             209 
  DEL PEAK 45(22Q13.31) MUTATED DEL PEAK 45(22Q13.31) WILD-TYPE 
                             30                              63 
$`DEL PEAK 45(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         2.27        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         0.07         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        13.35        17.19        10.26        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-A7NU TCGA-IP-7968 TCGA-KB-A6F5 
        5.19        13.08         6.44         1.81         2.53         5.56 
TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-SW-A7EB 
        8.61        16.67       115.69         5.79 

$`DEL PEAK 45(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-MX-A5UG 
       18.81         1.41         6.87         5.56        60.56         3.72 
TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        4.50        11.05         4.67       122.30        37.91        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-ZA-A8F6 
      116.38        71.38        57.44         8.94         4.21 

  DEL PEAK 45(22Q13.31) MUTATED DEL PEAK 45(22Q13.31) WILD-TYPE 
                           0.07                            0.07 
  DEL PEAK 45(22Q13.31) MUTATED DEL PEAK 45(22Q13.31) WILD-TYPE 
                         115.69                          122.30 
  DEL PEAK 45(22Q13.31) MUTATED DEL PEAK 45(22Q13.31) WILD-TYPE 
                           9.44                           11.57 
[1] "0.1 - 115.7 (9.4)"  "0.1 - 122.3 (11.6)"
[1] "hr=" "1.1"
D78V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 45(22Q13.31) MUTATED         0        0       14       10        10
  DEL PEAK 45(22Q13.31) WILD-TYPE       2       12       24       17        22
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 45(22Q13.31) MUTATED          18         1         24         16
  DEL PEAK 45(22Q13.31) WILD-TYPE        29         2         37         29
                                 vv
clus                              STAGE IIIC STAGE IV
  DEL PEAK 45(22Q13.31) MUTATED           10        9
  DEL PEAK 45(22Q13.31) WILD-TYPE         22       22
D78V3, multiclass
            clus
vv           DEL PEAK 45(22Q13.31) MUTATED DEL PEAK 45(22Q13.31) WILD-TYPE
  STAGE I                                0                               2
  STAGE IA                               0                              12
  STAGE IB                              14                              24
  STAGE II                              10                              17
  STAGE IIA                             10                              22
  STAGE IIB                             18                              29
  STAGE III                              1                               2
  STAGE IIIA                            24                              37
  STAGE IIIB                            16                              29
  STAGE IIIC                            10                              22
  STAGE IV                               9                              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(22Q13.31) MUTATED    4 30 52 27
  DEL PEAK 45(22Q13.31) WILD-TYPE 16 55 94 58
D78V4, multiclass
    clus
vv   DEL PEAK 45(22Q13.31) MUTATED DEL PEAK 45(22Q13.31) WILD-TYPE
  T1                             4                              16
  T2                            30                              55
  T3                            52                              94
  T4                            27                              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
  DEL PEAK 45(22Q13.31) MUTATED   34 29 28 22
  DEL PEAK 45(22Q13.31) WILD-TYPE 75 63 38 45
D78V5, multiclass
    clus
vv   DEL PEAK 45(22Q13.31) MUTATED DEL PEAK 45(22Q13.31) WILD-TYPE
  N0                            34                              75
  N1                            29                              63
  N2                            28                              38
  N3                            22                              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 45(22Q13.31) MUTATED   107   5   5
  DEL PEAK 45(22Q13.31) WILD-TYPE 201  16  12
D78V6, multiclass
    clus
vv   DEL PEAK 45(22Q13.31) MUTATED DEL PEAK 45(22Q13.31) WILD-TYPE
  M0                           107                             201
  M1                             5                              16
  MX                             5                              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"
D78V7, binary
                                 cls
clus                                0   1
  DEL PEAK 45(22Q13.31) MUTATED    45  72
  DEL PEAK 45(22Q13.31) WILD-TYPE  92 137
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 45(22Q13.31) MUTATED     45   72
  DEL PEAK 45(22Q13.31) WILD-TYPE   92  137
        clus
vv       DEL PEAK 45(22Q13.31) MUTATED DEL PEAK 45(22Q13.31) WILD-TYPE
  FEMALE                            45                              92
  MALE                              72                             137
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 45(22Q13.31) MUTATED                                      16
  DEL PEAK 45(22Q13.31) WILD-TYPE                                    46
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 45(22Q13.31) MUTATED                                                       52
  DEL PEAK 45(22Q13.31) WILD-TYPE                                                    102
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 45(22Q13.31) MUTATED                                                                  17
  DEL PEAK 45(22Q13.31) WILD-TYPE                                                                37
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 45(22Q13.31) MUTATED                                                 21
  DEL PEAK 45(22Q13.31) WILD-TYPE                                               24
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 45(22Q13.31) MUTATED                                                           1
  DEL PEAK 45(22Q13.31) WILD-TYPE                                                         0
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 45(22Q13.31) MUTATED                                                          8
  DEL PEAK 45(22Q13.31) WILD-TYPE                                                       11
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 45(22Q13.31) MUTATED                                                           1
  DEL PEAK 45(22Q13.31) WILD-TYPE                                                         4
                                 vv
clus                              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 45(22Q13.31) MUTATED                                          1
  DEL PEAK 45(22Q13.31) WILD-TYPE                                        3
D78V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 45(22Q13.31) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        16
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       52
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             21
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      1
                                                                   clus
vv                                                                  DEL PEAK 45(22Q13.31) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        102
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               24
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                        3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V9, binary
                                 cls
clus                                0   1
  DEL PEAK 45(22Q13.31) MUTATED     5 112
  DEL PEAK 45(22Q13.31) WILD-TYPE   2 227
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 45(22Q13.31) MUTATED      5  112
  DEL PEAK 45(22Q13.31) WILD-TYPE    2  227
     clus
vv    DEL PEAK 45(22Q13.31) MUTATED DEL PEAK 45(22Q13.31) WILD-TYPE
  NO                              5                               2
  YES                           112                             227
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 45(22Q13.31) MUTATED    89   7   6   8
  DEL PEAK 45(22Q13.31) WILD-TYPE 188   6   7  17
D78V10, multiclass
    clus
vv   DEL PEAK 45(22Q13.31) MUTATED DEL PEAK 45(22Q13.31) WILD-TYPE
  R0                            89                             188
  R1                             7                               6
  R2                             6                               7
  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"
D78V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 45(22Q13.31) MUTATED      28                         0
  DEL PEAK 45(22Q13.31) WILD-TYPE    56                         3
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 45(22Q13.31) MUTATED                                           1
  DEL PEAK 45(22Q13.31) WILD-TYPE                                         0
                                 vv
clus                              WHITE
  DEL PEAK 45(22Q13.31) MUTATED      70
  DEL PEAK 45(22Q13.31) WILD-TYPE   138
D78V12, multiclass
                                           clus
vv                                          DEL PEAK 45(22Q13.31) MUTATED
  ASIAN                                                                28
  BLACK OR AFRICAN AMERICAN                                             0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                70
                                           clus
vv                                          DEL PEAK 45(22Q13.31) WILD-TYPE
  ASIAN                                                                  56
  BLACK OR AFRICAN AMERICAN                                               3
  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(79) Variable = DEL PEAK 46(XP22.2) MUTATION ANALYSIS
D79V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 46(XP22.2) MUTATED    43  19
  DEL PEAK 46(XP22.2) WILD-TYPE 179  74
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                           62                           253 
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                           19                            74 
$`DEL PEAK 46(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-A44U TCGA-BR-A4CQ TCGA-BR-A4J6 TCGA-BR-A4PD TCGA-BR-A4PF 
        0.59         1.15         2.27         0.66        20.65         1.15 
TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8531 TCGA-CD-8533 
       13.64         3.25         0.30         0.07         0.10         0.13 
TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MH TCGA-CG-4438 TCGA-CG-4441 
        0.13         0.13         0.13         0.10        54.08        14.01 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-5718 TCGA-CG-5725 TCGA-CG-5734 
       47.05        19.07        21.99         1.02        15.02         7.99 
TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       11.93        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A74A 
       12.33         0.23        11.31         9.76        15.65         7.40 
TCGA-EQ-5647 TCGA-FP-8211 TCGA-FP-A4BF TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GU 
        0.62        13.58         1.55        22.75        25.81         6.25 
TCGA-HU-A4H5 TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL 
       12.30        21.21         3.45         3.39        18.38         5.19 
TCGA-IN-A6RP TCGA-RD-A8N6 
        6.44         8.94 

$`DEL PEAK 46(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-8690 
        0.49        11.54        16.44        15.68         0.62        10.68 
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-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         0.79         0.72        14.17         0.53        12.82 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM 
       19.36        13.51         0.46        20.42        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 
        2.83        13.15        13.18         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8536 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.07         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-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 
        8.05         4.01        29.98        12.03         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 
        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-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-D7-5577 
       79.07        65.10         4.01        55.04        21.07        12.36 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.66        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 
       17.85        13.35        10.55        11.31        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-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-EQ-8122 
       11.24        11.44         2.96         4.34         7.13         7.79 
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-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-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        5.03         0.56         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-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       24.20         3.25        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       19.36        17.69         9.67         8.88         8.81        27.42 
TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NT 
       18.81         5.36        13.08         1.41         6.87         5.56 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ 
        1.81         2.53         5.56        60.56         3.72         4.50 
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-SW-A7EB 
       40.64       115.69       116.38        71.38        57.44         5.79 
TCGA-ZA-A8F6 
        4.21 

  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                        54.08                        122.30 
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                        8.465                        11.440 
[1] "0.1 - 54.1 (8.5)"   "0.1 - 122.3 (11.4)"
[1] "hr=" "1.3"
D79V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 46(XP22.2) MUTATED         0        1        6        8         6
  DEL PEAK 46(XP22.2) WILD-TYPE       2       11       32       19        26
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 46(XP22.2) MUTATED          10         2         15          5
  DEL PEAK 46(XP22.2) WILD-TYPE        37         1         46         40
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 46(XP22.2) MUTATED            5        5
  DEL PEAK 46(XP22.2) WILD-TYPE         27       26
D79V3, multiclass
            clus
vv           DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             1                            11
  STAGE IB                             6                            32
  STAGE II                             8                            19
  STAGE IIA                            6                            26
  STAGE IIB                           10                            37
  STAGE III                            2                             1
  STAGE IIIA                          15                            46
  STAGE IIIB                           5                            40
  STAGE IIIC                           5                            27
  STAGE IV                             5                            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 46(XP22.2) MUTATED     3  17  30  14
  DEL PEAK 46(XP22.2) WILD-TYPE  17  68 116  71
D79V4, multiclass
    clus
vv   DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  T1                           3                            17
  T2                          17                            68
  T3                          30                           116
  T4                          14                            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 46(XP22.2) MUTATED   18 19 17 10
  DEL PEAK 46(XP22.2) WILD-TYPE 91 73 49 57
D79V5, multiclass
    clus
vv   DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  N0                          18                            91
  N1                          19                            73
  N2                          17                            49
  N3                          10                            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 46(XP22.2) MUTATED    59   5   1
  DEL PEAK 46(XP22.2) WILD-TYPE 249  16  16
D79V6, multiclass
    clus
vv   DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  M0                          59                           249
  M1                           5                            16
  MX                           1                            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"
D79V7, binary
                               cls
clus                              0   1
  DEL PEAK 46(XP22.2) MUTATED    21  44
  DEL PEAK 46(XP22.2) WILD-TYPE 116 165
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 46(XP22.2) MUTATED     21   44
  DEL PEAK 46(XP22.2) WILD-TYPE  116  165
        clus
vv       DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  FEMALE                          21                           116
  MALE                            44                           165
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 46(XP22.2) MUTATED                                       9
  DEL PEAK 46(XP22.2) WILD-TYPE                                    53
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 46(XP22.2) MUTATED                                                       27
  DEL PEAK 46(XP22.2) WILD-TYPE                                                    127
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 46(XP22.2) MUTATED                                                                  11
  DEL PEAK 46(XP22.2) WILD-TYPE                                                                43
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 46(XP22.2) MUTATED                                                 13
  DEL PEAK 46(XP22.2) WILD-TYPE                                               32
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 46(XP22.2) MUTATED                                                           1
  DEL PEAK 46(XP22.2) WILD-TYPE                                                         0
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 46(XP22.2) MUTATED                                                          2
  DEL PEAK 46(XP22.2) WILD-TYPE                                                       17
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 46(XP22.2) MUTATED                                                           1
  DEL PEAK 46(XP22.2) WILD-TYPE                                                         4
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 46(XP22.2) MUTATED                                          1
  DEL PEAK 46(XP22.2) WILD-TYPE                                        3
D79V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 46(XP22.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     27
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           13
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    1
                                                                   clus
vv                                                                  DEL PEAK 46(XP22.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        53
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            43
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             32
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V9, binary
                               cls
clus                              0   1
  DEL PEAK 46(XP22.2) MUTATED     2  63
  DEL PEAK 46(XP22.2) WILD-TYPE   5 276
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 46(XP22.2) MUTATED      2   63
  DEL PEAK 46(XP22.2) WILD-TYPE    5  276
     clus
vv    DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  NO                            2                             5
  YES                          63                           276
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 46(XP22.2) MUTATED    52   3   2   2
  DEL PEAK 46(XP22.2) WILD-TYPE 225  10  11  23
D79V10, multiclass
    clus
vv   DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  R0                          52                           225
  R1                           3                            10
  R2                           2                            11
  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"
D79V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 46(XP22.2) MUTATED      16                         0
  DEL PEAK 46(XP22.2) WILD-TYPE    68                         3
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 46(XP22.2) MUTATED                                           0    41
  DEL PEAK 46(XP22.2) WILD-TYPE                                         1   167
D79V12, multiclass
                                           clus
vv                                          DEL PEAK 46(XP22.2) MUTATED
  ASIAN                                                              16
  BLACK OR AFRICAN AMERICAN                                           0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              41
                                           clus
vv                                          DEL PEAK 46(XP22.2) WILD-TYPE
  ASIAN                                                                68
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(80) Variable = DEL PEAK 47(XP21.1) MUTATION ANALYSIS
D80V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 47(XP21.1) MUTATED    38  20
  DEL PEAK 47(XP21.1) WILD-TYPE 184  73
  DEL PEAK 47(XP21.1) MUTATED DEL PEAK 47(XP21.1) WILD-TYPE 
                           58                           257 
  DEL PEAK 47(XP21.1) MUTATED DEL PEAK 47(XP21.1) WILD-TYPE 
                           20                            73 
$`DEL PEAK 47(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         2.27 
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-5724 TCGA-CG-5725 TCGA-CG-5734 
       19.07        21.99         7.07        12.03        15.02         7.99 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       11.93        19.13        13.35        15.22        15.98        12.79 
TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A74A 
       12.33         0.23        11.31         9.76        15.65         7.40 
TCGA-EQ-5647 TCGA-FP-8211 TCGA-FP-A4BF TCGA-HU-A4GD TCGA-HU-A4H5 TCGA-IN-7806 
        0.62        13.58         1.55        22.75        12.30        21.21 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP 
        3.45         3.39        18.38         5.36         5.19         6.44 
TCGA-IN-A6RS TCGA-KB-A6F7 TCGA-RD-A7BT TCGA-RD-A8N6 
        6.87        60.56         8.61         8.94 

$`DEL PEAK 47(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         0.07         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-5726 
        1.02         0.99         6.02         0.99       105.07        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-D7-5577 
       79.07        65.10         4.01        55.04        21.07        12.36 
TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       12.66        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 
       17.19        10.26        10.55        11.31        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-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-EQ-8122 
       11.24        11.44         2.96         4.34         7.13         7.79 
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-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-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        5.03         0.56         0.23        18.08        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        5.92        14.27        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        19.36        17.69         9.67         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A7NT 
        8.81        27.42        18.81        13.08         1.41         5.56 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS 
        1.81         2.53         5.56         3.72         4.50        11.05 
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-SW-A7EB TCGA-ZA-A8F6 
      116.38        71.38        57.44         5.79         4.21 

  DEL PEAK 47(XP21.1) MUTATED DEL PEAK 47(XP21.1) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 47(XP21.1) MUTATED DEL PEAK 47(XP21.1) WILD-TYPE 
                        60.56                        122.30 
  DEL PEAK 47(XP21.1) MUTATED DEL PEAK 47(XP21.1) WILD-TYPE 
                        8.775                        11.310 
[1] "0.1 - 60.6 (8.8)"   "0.1 - 122.3 (11.3)"
[1] "hr=" "1.3"
D80V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 47(XP21.1) MUTATED         0        2        8        5         5
  DEL PEAK 47(XP21.1) WILD-TYPE       2       10       30       22        27
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 47(XP21.1) MUTATED           8         2         15          4
  DEL PEAK 47(XP21.1) WILD-TYPE        39         1         46         41
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 47(XP21.1) MUTATED            3        7
  DEL PEAK 47(XP21.1) WILD-TYPE         29       24
D80V3, multiclass
            clus
vv           DEL PEAK 47(XP21.1) MUTATED DEL PEAK 47(XP21.1) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             2                            10
  STAGE IB                             8                            30
  STAGE II                             5                            22
  STAGE IIA                            5                            27
  STAGE IIB                            8                            39
  STAGE III                            2                             1
  STAGE IIIA                          15                            46
  STAGE IIIB                           4                            41
  STAGE IIIC                           3                            29
  STAGE IV                             7                            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 47(XP21.1) MUTATED     6  16  27  11
  DEL PEAK 47(XP21.1) WILD-TYPE  14  69 119  74
D80V4, multiclass
    clus
vv   DEL PEAK 47(XP21.1) MUTATED DEL PEAK 47(XP21.1) WILD-TYPE
  T1                           6                            14
  T2                          16                            69
  T3                          27                           119
  T4                          11                            74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 47(XP21.1) MUTATED   18 16 14 12
  DEL PEAK 47(XP21.1) WILD-TYPE 91 76 52 55
D80V5, multiclass
    clus
vv   DEL PEAK 47(XP21.1) MUTATED DEL PEAK 47(XP21.1) WILD-TYPE
  N0                          18                            91
  N1                          16                            76
  N2                          14                            52
  N3                          12                            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                             M0  M1  MX
  DEL PEAK 47(XP21.1) MUTATED    56   4   1
  DEL PEAK 47(XP21.1) WILD-TYPE 252  17  16
D80V6, multiclass
    clus
vv   DEL PEAK 47(XP21.1) MUTATED DEL PEAK 47(XP21.1) WILD-TYPE
  M0                          56                           252
  M1                           4                            17
  MX                           1                            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"
D80V7, binary
                               cls
clus                              0   1
  DEL PEAK 47(XP21.1) MUTATED    17  44
  DEL PEAK 47(XP21.1) WILD-TYPE 120 165
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 47(XP21.1) MUTATED     17   44
  DEL PEAK 47(XP21.1) WILD-TYPE  120  165
        clus
vv       DEL PEAK 47(XP21.1) MUTATED DEL PEAK 47(XP21.1) WILD-TYPE
  FEMALE                          17                           120
  MALE                            44                           165
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 47(XP21.1) MUTATED                                      10
  DEL PEAK 47(XP21.1) WILD-TYPE                                    52
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 47(XP21.1) MUTATED                                                       24
  DEL PEAK 47(XP21.1) WILD-TYPE                                                    130
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 47(XP21.1) MUTATED                                                                  12
  DEL PEAK 47(XP21.1) WILD-TYPE                                                                42
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 47(XP21.1) MUTATED                                                 11
  DEL PEAK 47(XP21.1) WILD-TYPE                                               34
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 47(XP21.1) MUTATED                                                           0
  DEL PEAK 47(XP21.1) WILD-TYPE                                                         1
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 47(XP21.1) MUTATED                                                          2
  DEL PEAK 47(XP21.1) WILD-TYPE                                                       17
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 47(XP21.1) MUTATED                                                           1
  DEL PEAK 47(XP21.1) WILD-TYPE                                                         4
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 47(XP21.1) MUTATED                                          1
  DEL PEAK 47(XP21.1) WILD-TYPE                                        3
D80V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 47(XP21.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      10
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     24
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          12
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           11
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                   0
  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(XP21.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        52
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            42
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             34
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V9, binary
                               cls
clus                              0   1
  DEL PEAK 47(XP21.1) MUTATED     2  59
  DEL PEAK 47(XP21.1) WILD-TYPE   5 280
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 47(XP21.1) MUTATED      2   59
  DEL PEAK 47(XP21.1) WILD-TYPE    5  280
     clus
vv    DEL PEAK 47(XP21.1) MUTATED DEL PEAK 47(XP21.1) WILD-TYPE
  NO                            2                             5
  YES                          59                           280
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 47(XP21.1) MUTATED    46   6   4   2
  DEL PEAK 47(XP21.1) WILD-TYPE 231   7   9  23
D80V10, multiclass
    clus
vv   DEL PEAK 47(XP21.1) MUTATED DEL PEAK 47(XP21.1) WILD-TYPE
  R0                          46                           231
  R1                           6                             7
  R2                           4                             9
  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"
D80V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 47(XP21.1) MUTATED       9                         0
  DEL PEAK 47(XP21.1) WILD-TYPE    75                         3
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 47(XP21.1) MUTATED                                           1    39
  DEL PEAK 47(XP21.1) WILD-TYPE                                         0   169
D80V12, multiclass
                                           clus
vv                                          DEL PEAK 47(XP21.1) MUTATED
  ASIAN                                                               9
  BLACK OR AFRICAN AMERICAN                                           0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              39
                                           clus
vv                                          DEL PEAK 47(XP21.1) WILD-TYPE
  ASIAN                                                                75
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               169
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(81) Variable = DEL PEAK 48(XQ21.33) MUTATION ANALYSIS
D81V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 48(XQ21.33) MUTATED    30   9
  DEL PEAK 48(XQ21.33) WILD-TYPE 192  84
  DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE 
                            39                            276 
  DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE 
                             9                             84 
$`DEL PEAK 48(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         2.27 
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 
       27.42        21.21        18.38 

$`DEL PEAK 48(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         0.07         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        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        10.26        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-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BT 
        5.56        60.56         3.72         4.50        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-SW-A7EB TCGA-ZA-A8F6 
      116.38        71.38        57.44         8.94         5.79         4.21 

  DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE 
                         47.05                         122.30 
  DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE 
                        12.300                         10.405 
[1] "0.1 - 47.0 (12.3)"  "0.1 - 122.3 (10.4)"
[1] "hr=" "1.4"
D81V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 48(XQ21.33) MUTATED         0        1        8        5         2
  DEL PEAK 48(XQ21.33) WILD-TYPE       2       11       30       22        30
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 48(XQ21.33) MUTATED           5         0          8          5
  DEL PEAK 48(XQ21.33) WILD-TYPE        42         3         53         40
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 48(XQ21.33) MUTATED            2        5
  DEL PEAK 48(XQ21.33) WILD-TYPE         30       26
D81V3, multiclass
            clus
vv           DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                              1                             11
  STAGE IB                              8                             30
  STAGE II                              5                             22
  STAGE IIA                             2                             30
  STAGE IIB                             5                             42
  STAGE III                             0                              3
  STAGE IIIA                            8                             53
  STAGE IIIB                            5                             40
  STAGE IIIC                            2                             30
  STAGE IV                              5                             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 48(XQ21.33) MUTATED     2  13  19   8
  DEL PEAK 48(XQ21.33) WILD-TYPE  18  72 127  77
D81V4, multiclass
    clus
vv   DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE
  T1                            2                             18
  T2                           13                             72
  T3                           19                            127
  T4                            8                             77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 48(XQ21.33) MUTATED   15 11 10  5
  DEL PEAK 48(XQ21.33) WILD-TYPE 94 81 56 62
D81V5, multiclass
    clus
vv   DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE
  N0                           15                             94
  N1                           11                             81
  N2                           10                             56
  N3                            5                             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 48(XQ21.33) MUTATED    37   3   2
  DEL PEAK 48(XQ21.33) WILD-TYPE 271  18  15
D81V6, multiclass
    clus
vv   DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE
  M0                           37                            271
  M1                            3                             18
  MX                            2                             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"
D81V7, binary
                                cls
clus                               0   1
  DEL PEAK 48(XQ21.33) MUTATED    14  28
  DEL PEAK 48(XQ21.33) WILD-TYPE 123 181
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(XQ21.33) MUTATED     14   28
  DEL PEAK 48(XQ21.33) WILD-TYPE  123  181
        clus
vv       DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE
  FEMALE                           14                            123
  MALE                             28                            181
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 48(XQ21.33) MUTATED                                       7
  DEL PEAK 48(XQ21.33) WILD-TYPE                                    55
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 48(XQ21.33) MUTATED                                                       16
  DEL PEAK 48(XQ21.33) WILD-TYPE                                                    138
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 48(XQ21.33) MUTATED                                                                   6
  DEL PEAK 48(XQ21.33) WILD-TYPE                                                                48
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 48(XQ21.33) MUTATED                                                  8
  DEL PEAK 48(XQ21.33) WILD-TYPE                                               37
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  DEL PEAK 48(XQ21.33) MUTATED                                                           0
  DEL PEAK 48(XQ21.33) WILD-TYPE                                                         1
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 48(XQ21.33) MUTATED                                                          3
  DEL PEAK 48(XQ21.33) WILD-TYPE                                                       16
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 48(XQ21.33) MUTATED                                                           2
  DEL PEAK 48(XQ21.33) WILD-TYPE                                                         3
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 48(XQ21.33) MUTATED                                          0
  DEL PEAK 48(XQ21.33) WILD-TYPE                                        4
D81V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 48(XQ21.33) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      16
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             8
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     0
                                                                   clus
vv                                                                  DEL PEAK 48(XQ21.33) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         55
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       138
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             48
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              37
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       4
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V9, binary
                                cls
clus                               0   1
  DEL PEAK 48(XQ21.33) MUTATED     1  41
  DEL PEAK 48(XQ21.33) WILD-TYPE   6 298
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(XQ21.33) MUTATED      1   41
  DEL PEAK 48(XQ21.33) WILD-TYPE    6  298
     clus
vv    DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE
  NO                             1                              6
  YES                           41                            298
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 48(XQ21.33) MUTATED    35   3   1   1
  DEL PEAK 48(XQ21.33) WILD-TYPE 242  10  12  24
D81V10, multiclass
    clus
vv   DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE
  R0                           35                            242
  R1                            3                             10
  R2                            1                             12
  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"
D81V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 48(XQ21.33) MUTATED       9                         0
  DEL PEAK 48(XQ21.33) WILD-TYPE    75                         3
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 48(XQ21.33) MUTATED                                           0
  DEL PEAK 48(XQ21.33) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 48(XQ21.33) MUTATED      24
  DEL PEAK 48(XQ21.33) WILD-TYPE   184
D81V12, multiclass
                                           clus
vv                                          DEL PEAK 48(XQ21.33) MUTATED
  ASIAN                                                                9
  BLACK OR AFRICAN AMERICAN                                            0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               24
                                           clus
vv                                          DEL PEAK 48(XQ21.33) WILD-TYPE
  ASIAN                                                                 75
  BLACK OR AFRICAN AMERICAN                                              3
  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"
